Genomics Analysis and Degradation Characteristics of Lignin by Streptomyces Thermocarboxydus Strain DF3-3

Genomics Analysis and Degradation Characteristics of Lignin by Streptomyces Thermocarboxydus Strain DF3-3 | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Genomics Analysis and Degradation Characteristics of Lignin by Streptomyces Thermocarboxydus Strain DF3-3 Fangyun Tan, Jun Cheng, Yu Zhang, Xingfu Jiang, Yueqiu Liu This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-996090/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 8 You are reading this latest preprint version Abstract Background: Lignocellulose is an important raw material for biomass-to-energy conversion, and it exhibits a complex but inefficient degradation mechanism. Microbial degradation is promising due to its environmental adaptability and biochemical versatility, but the pathways used by microbes for lignin degradation have not been fully studied. Degradation intermediates and complex metabolic pathways require more study. Results: A novel actinomycete DF3-3, with the potential for lignin degradation, was screened and isolated. After morphological and molecular identification, DF3-3 was determined to be Streptomyces thermocarboxydus . The degradation of alkali lignin reached 31% within 15 days. Manganese peroxidase and laccase demonstrated their greatest activity levels, 1821.66 UL -1 and 1265.58 UL -1 , respectively, on the sixth day. The highest lignin peroxidase activity was 480.33 UL -1 on the fourth day. A total of 19 lignin degradation intermediates were identified by gas chromatography-mass spectrometry (GC-MS), including 10 aromatic compounds. Genome sequencing and annotation identified 107 lignin-degrading enzyme-coding genes containing three core enzymatic systems for lignin depolymerization: laccases, peroxidases and manganese peroxidase. In total, 7 lignin metabolic pathways were predicted. Conclusions: Streptomyces thermocarboxydus strain DF3-3 has good lignin degradation ability. Degradation products and genomics analyses of DF3-3 show that it has a relatively complete lignin degradation pathway, including the β-ketoadipate pathway and peripheral reactions; gentisate pathway; anthranilate pathway; homogentisic pathway; and catabolic pathway for resorcinol. Two other pathways, the phenylacetate-CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway, are predicted based on genome data alone. This study provides the basis for future characterization of potential biotransformation enzyme systems for biomass energy conversion. Biotechnology and Bioengineering Applied Biochemistry Renewable Resources Streptomyces thermocarboxydus strain DF3-3 alkali lignin enzyme activity genomics metabolic pathways Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Background Lignocellulosic biomass is an easily available, low cost and renewable alternative to fossil fuels. Currently, the process for pretreatment of lignocellulosic biofuel requires removal or delocalization of lignin, which might generate aromatic compounds that inhibit enzymatic hydrolysis and fermentation [ 1 ]. Due to its rich aromatic content, lignin is a valuable waste from the biomass industry [ 2 ]. Researchers worldwide are focusing on lignin and its components for conversion into value-added products. Lignin is a complex aromatic heteropolymer derived from the condensation of hydroxyphenylpropane monomers and comprises various ether bonds and carbon-carbon bonds [ 3 ]. It is mainly composed of three basic monomers: guaiacyl (G) units, syringyl (S) units and p-hydroxyphenyl (H) units [ 4 , 5 ]. Microorganisms that degrade lignocellulose are widely distributed in nature, and known examples include bacteria, fungi and actinomycetes. Among them, fungi and some bacteria have mainly been studied, and white-rot fungi, and brown rot fungi in particular have obvious degradation effects on lignin [ 6 , 7 ], but the development of industrial applications has been difficult [ 8 ]. Some actinomycetes and bacteria also participate in lignin degradation. Several typical lignin-degrading bacteria, such as Rhodococcus , Pseudomonas, Sphingobium and Sphingomonas , have been identified [ 9 – 12 ]. Streptomyces are among the identified bacteria capable of degrading lignin [ 13 ]. Pasti et al. [ 14 ] isolated 11 strains of actinomycetes from the intestines of termites and analysed their ability to degrade lignocellulose, lignin and carbohydrates. Other researchers have also screened streptomyces from the soil that degrade lignin [ 15 – 17 ]. There are many kinds of enzymes involved in the degradation of lignin, including laccase (Lac), lignin peroxidase (LiP), manganese peroxidase (MnP), multifunctional peroxidase (VP), and dye decolouring peroxidase (DyPs) [ 18 ]. The specific mechanism for biological degradation of lignin needs to be studied further. Lignin is rich in high-value degradation intermediates, such as vanillin, guaiacol, catechin and protocatechin [ 19 ]. At the same time, the study of the metabolic mechanism of lignin and its transformation and utilization is an important part of the research needed for production of "second-generation biofuels" [ 20 ]. Hundreds of lignin derivatives have been identified in studies of bacterial degradation of lignin [ 21 ]. Because of the complex degradation mechanism, the interpretation of metabolic pathways and intermediate products is an important part of understanding the degradation of lignin. With the development of sequencing technology and bioinformatics, genomics research has become an important method for studying degradation mechanisms. Researchers are paying increasing attention to analysing metabolism of intermediate products through annotations of related degradation genes. Pseudomonas putida is a lignin-degrading bacterium that has been studied earlier. Lin et al. [ 22 ] identified several lignin-degrading enzymes, including haem peroxidase, from its genome and constructed five lignin metabolic pathways. Masai et al. [ 23 ] conducted a series of studies on lignin degradation and related genes in Sphingomonas paucimobilis SYK-6 and established a relatively complete lignin degradation metabolic pathway. Niewerth et al. [ 24 ] determined and analysed the whole genome sequence of Arthrobacter sp. Rue61a in soil, and the results showed that it has an aromatic degradation pathway that utilizes the characteristic products of lignin degradation, reflecting the saprophytic capabilities and nutritional diversity of organisms. Several Streptomyces strains, such as Streptomyces viridosporus T7A [ 25 ] and Streptomyces setonii 75Vi2 [ 26 ], have been reported to degrade lignin. However, the actual catabolic pathways of lignin derivatives and the responsible enzymes and genes have not been investigated by using molecular methods with Streptomyces . In our present study, a novel isolate, DF3-3, identified as Streptomyces thermocarboxydus , was found to degrade lignin. Alkali lignin is a model compound with a structure similar to that of lignocellulose and is often used as a raw material for lignin degradation studies [ 27 ]. This study used alkali lignin to investigate the characteristics of alkali lignin degradation by Streptomyces thermocarboxydus strain DF3-3. GC–MS combined with genomics was used to identify the genes responsible for lignin degradation and explore the metabolic pathway for lignin degradation by Streptomyces thermocarboxydus strain DF3-3. Results Morphological and physiological characteristics of DF3-3 A strain of actinomycete named DF3-3 was isolated from the greening litter of Beijing University of Agriculture. The scribing form of the plate shows a rough white surface, the upper and lower surfaces are inconsistent in colour, and the hyphae in the base are obvious on Gause's medium. (Figure 1 a). When DF3-3 was inoculated on Gause’s guaiacol medium, a clear colour reaction appeared. When inoculated on Gause’s-Azure B medium, a transparent fading circle appeared (Figure 1 b and c). This shows that DF3-3 has the ability to degrade lignin [ 28 ]. Microscopy was used to observe the morphology of DF3-3 (Figure 1 d). DF3-3 grew luxuriantly on the plate, hyphae were developed, and aerial hyphae were slender. The spore filaments were spiral-shaped with obvious characteristics of Streptomyces . Figure 1 d shows a scanning electron micrograph of DF3-3 grown on Gause's medium. Mature spore chains were moderately long, with 40 to 80 spores per chain. The single spores were oval or cylindrical with diameters of 0.5 to 0.7 µm and lengths of 1.1 to 1.3 µm and have rough surfaces. While keeping the conditions of the basal medium otherwise unchanged, different nitrogen sources and carbon sources were added to observe the growth of DF3-3 with different nitrogen sources. The results are shown in Table 1 . Table 1 Utilization characteristics of the nitrogen source and carbon source of DF3-3. Trait Result Trait Result Trait Result Nitrogen source NH 4 Cl + (NH 4 ) 2 SO 4 + Acrylamide + Potassium nitrate + Ammonium tartrate + Peptone + Carbon source Glucose + Alpha-D-methylglucoside + Sodium lactate - Mannose + trehalose + Sodium acetate - Melibiose + Cellobiose + Sodium formate - L-arabinose - Xylose + Sodium malate + Starch + Ribose - Sodium succinate + Melezitose - Inulin - Sodium malonate + Erythritol - Salicin + Sodium tartrate - Maltose + Glycerin + Sodium tyrosine + Sucrose - Sodium butyrate - Amylase + Molecular identification Genome de novo sequencing was performed on DF3-3 cells using second- and third-generation sequencing methods, namely, Illumina HiSeq+PacBio, and the gene location and sequence information of the samples were obtained through de novo assembly and gene prediction. According to the whole genome sequencing results (Table 2 ), strain DF3-3 has a chromosome with a total genome length of 7311713 bp. GeneMarkS predicted and annotated a total of 6929 coding sequences (CDSs), with a G+C content of 72.24%. Table 2 Genome-wide characteristics of DF3-3. value Genome Size (bp) 7311713 Chrom No. 1 GC Content (%) 72.24 Gene No. 6929 GC Content in Gene Region (%) 72.52 Gene Average Len(bp) 927.29 Gene/Genome (%) 87.88 GC Content in Intergenetic Region (%) 70.17 tRNA No. 66 rRNA No. 18 At present, 95% of the average nucleotide identity (ANI) is often used as the standard for species classification and species clustering [ 29 ]. The whole genomes of eight strains with high homology to strain DF3-3 were selected and compared and analysed with DF3-3 using ANI. The results are shown in Figure 2 . The similarity between DF3-3 and Streptomyces thermocarboxydus reached 98.96%, and it can now be identified as Streptomyces thermocarboxydus . Biodegradation of alkali lignin by DF3-3 To investigate lignin degradation by strain DF3-3, cells were incubated at 30°C in medium with alkali lignin as the carbon source. The growth curve and degradation rate of alkali lignin are shown in Figure 3 . The degree of degradation of alkaline lignin by DF3-3 shows that the degradation rate increased significantly in days 1–4, and the increase was the largest on the fourth day. After 4–7 days, degradation continued, but the rate slowed down, and the efficiency for degradation of alkali lignin reached 31% on day 15. The degradation of lignin by microorganisms requires a relatively slow process to reach a significant level. The white-rot fungus Phanerochaete chrysosporium was used for degradation of lignin, and the efficiency reached approximately 20% on day 15 [ 30 ], so DF3-3 exhibited a better performance. This result is also similar to the degradation results seen with some Streptomyces strains, such as S. viridosporus T7A (lignin loss 30.9%) and S. setonii 75Vi2 (lignin loss 34.1%) [ 26 , 31 ]. Analysis of lignin-degrading enzymes Lignin molecules are not easily taken passively into the cell; therefore, Streptomyces thermocarboxydus DF3-3 might produce extracellular enzymes for synergistic degradation. Three major types of enzymes responsible for the degradation of lignin are lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac) [ 32 ]. MnPs oxidize Mn(II) to Mn(III), and Mn(III) oxidizes phenolic compounds and generates phenoxy radicals that in turn undergo a variety of reactions, resulting in depolymerization. In the presence of Mn(II), MnP oxidizes nonphenolic lignin model compounds via peroxidation of unsaturated lipids. LiP is the most effective peroxidase and can oxidize phenolic and nonphenolic compounds, amines, aromatic ethers, and polycyclic aromatics [ 33 ]. Lac is a copper oxidoreductase [ 34 ] that can degrade refractory polyphenols and nonphenolics in lignin, and the expression of its coding genes in bacteria has also been reported [ 35 ]. The activities of these three enzymes from DF3-3 are shown in Figure 4 . MnP and Lac activity increased constantly during the initial 6 days, with maxima of 1821.66 U/L and 1265.58 U/L seen at day 6, followed by slight decreases from day 7. Lip activity was maintained at a low level, with a maximum of 480.33 U/L on day 4. These results indicated that MnP and Lac play crucial roles during the entire process of alkaline lignin degradation by DF3-3. Aromatic intermediates identified by GC-MS analysis Using ethyl acetate as the solvent for GC-MS determination [ 36 ], the degradation products of alkali lignin produced in incubation with Streptomyces thermocarboxydus strain DF3-3 were analysed from the first day to the 15th day. In total, 19 degradation intermediate products were identified by GC-MS, including seven different types of compounds, including eight organic acids (butanoic acid ( 4 ), lactic acid ( 8 ), 2-hydroxypropanoic acid ( 9 ), pyrrole-2-carboxylic acid ( 10 ), 3-phenylpyruvic acid ( 12 ), 4-hydroxybenzoic acid ( 13 ), 4-hydroxyphenylpyruvate (14), palmitic acid ( 16 ), stearic acid ( 17 )), three esters (acetic acid butyl ester ( 1 ), dibutyl phthalate ( 15 ), bis(2-ethylhexyl) phthalate ( 19 )), two ethers (1-(1-ethoxy)propane ( 2 ) and 1-(1-propoxyethoxy)propane ( 6 )), two alcohols (2-ethoxyethanol ( 5 ) and ethylene glycol ( 7 )), one alkane (m-xylene ( 2 )), and 1-(1-propylene (6-di-butylphenol phenol (2,2 -ethylethylenes(11-methyl ). These 19 low molecular weight products are related to lignin metabolism, and their serial numbers, name, and retention times are shown in Table 3 . Table 3 Compounds identified from degradation of alkali lignin by DF3-3. Retention time Compounds Molecular formula Control group 1 4.530 Acetic acid, butyl ester C 6 H 12 O 2 + 2 4.651 1-(1-Ethoxyethoxy) propane C 7 H 16 O 2 + 3 5.690 M-Xylene C 8 H 10 + 4 6.055 Butyric acid C 4 H 8 O 2 * + 5 6.251 2-Ethoxyethanol C 4 H 10 O 2 * + 6 6.642 1-(1-Propoxyethoxy) propane C 8 H 18 O 2 + 7 8.793 Ethylene glycol C 2 H 6 O 2 * + 8 11.058 Lactic acid C 3 H 6 O 3 * + 9 13.038 2-Hydroxybutyric acid C 4 H 8 O 3 * - 10 19.375 Pyrrole-2-carboxylic acid C 5 H 5 NO 2 - 11 23.225 2,4-Di-tert-butylphenol C 14 H 22 O - 12 25.121 3-Phenylpyruvic acid C 9 H 8 O 3 * - 13 25.996 4-Hydroxybenzoic acid C 7 H 6 O 3 * - 14 32.028 4-Hydroxyphenylpyruvate C 9 H 8 O 4 * - 15 32.970 Dibutyl phthalate C 16 H 22 O 4 + 16 34.543 Palmitic acid C 16 H 32 O 2 * + 17 38.084 Stearic acid C 18 H 36 O 2 * + 18 41.008 2,2'-Methylenebis(6-tert-butyl-4-methyl-phenol) C 23 H 32 O 2 - 19 43.033 Bis(2-ethylhexyl) phthalate C 24 H 38 O 4 - “+” indicates that the product was detected in the uninoculated control group, “-“ indicates that the product was not detected in the uninoculated control group. The variations in the peak areas for products 3 , 8 , 10 , 11 , 12 , 13 , 14 , 15 , 18 , and 19 were plotted using the peak areas and culture times (days) as the ordinate and abscissa, respectively, and the result is shown in Figure 5 . The peak areas for products 12 , 15 , and 18 varied greatly; in comparison, the peak areas for products 3 , 8 , 10 , 11 , 13 , 14 , and 19 exhibited small changes. The content of product 12 gradually increased within 1–4 days after culture, reached a maximum on the 4th day, and then decreased to a minimum on the 6th day. The content of product 15 quickly increased to a high value on the first day of culture and then gradually decreased to the lowest value until the 7th day. The content of product 18 increased to the first high value on the 1st day after culture, dropped to the lowest point on the 3rd day, then rose to another highest point on the 4th day, and finally decreased to the lowest value. These data indicate that the contents of 12 , 15 , and 18 underwent two cycles in the first 8 days of culture. The process of lignin degradation can be divided into two main parts. First, through the rupture of aromatic ether bonds and carbon-carbon bonds, lignin polymers are depolymerized to form various oligomers. Then, these depolymerized aromatic organic compounds form other small molecular benzene compounds [ 37 ]. Here, m-xylene ( 3 ), 2,4-di-tert-butylphenol ( 11 ), 3-phenylpyruvic acid ( 12 ), 4-hydroxybenzoic acid ( 13 ), 4-hydroxyphenylpyruvate ( 14 ), dibutyl phthalate ( 15 ), 2,2’-methylenebis(4-methyl-6-tert-butylphenol), and bis(2-ethylhexyl) phthalate ( 19 ) were detected among the products produced by DF3-3 in degradation of alkaline lignin. Dibutyl phthalate ( 15 ) is a common lignin degradation intermediate [ 38 – 40 ] that can be metabolized to produce phthalic acid, which is further converted into syringyl, protocatechin and other phenolic compounds and then degraded [ 41 ]. According to the metabolic pathway for formation of dibutyl phthalate ( 15 ) and diisooctyl phthalate ( 19 ), product 19 is thought to have a similar degradation process. Both 4-hydroxyphenylpyruvate ( 14 ) and 3-phenylpyruvic acid ( 12 ) were detected among the products of the experimental group, and their aromatic structures were related to alkali lignin. 4-Hydroxybenzoic acid is an important intermediate in many lignin metabolic pathways, including the coumaric acid pathway, gentisic acid pathway, and cinnamic acid pathway [ 42 ]. This indicated that DF3-3 uses the β-ketoadipate metabolic pathway or other similar degradation pathways. In addition, small molecular compounds such as ethylene glycol ( 7 ) and 2-ethoxyethanol ( 5 ) were detected in the experiment, indicating that DF3-3 degradation of lignin has great potential for energy conversion. Analyses of the lignin metabolism pathways based on whole genome sequencing and annotation Initial degradation of lignin into low molecular weight compounds by extracellular phenoloxidases To identify the genes related to lignin degradation by DF3-3, the genes encoding known lignin enzymes of other bacterial species were selected as query sequences, and a BLASTp search of the DF3-3 genome was carried out. The results showed that DF3-3 has abundant genes encoding lignin-degrading enzymes, and a total of 107 different genes involved in the degradation process have been annotated (Tables 4 - 11 ). Table 4 Genes responsible for lignin depolymerization. Gene ID Size (aa) Gene Name Encode protein Species of reference gene Accession no. (NCBI) BLAST identity (%) gene 2915 2288 copA carbonate dehydratase Actinospica acidiphila WP_058917537.1 96.19 gene 5998 2267 copA carbonate dehydratase Streptomyces sp. UNC401CLCol WP_028959238.1 99.74 gene 3898 2225 katG catalase-peroxidase Streptomyces sp. Akac8 WP_136237873.1 99.87 gene 3899 380 fur transcriptional repressor Streptomyces sp. UNC401CLCol WP_028958816.1 99.21 gene 0904 1400 YhjG pentachlorophenol monooxygenase Streptomyces sp. 4F ALV51870.1 95.49 gene 1050 533 ahpD alkyl hydroperoxide reductase Actinospica acidiphila WP_163089316.1 99.44 gene 6181 1415 glcD FAD-linked oxidase Actinospica acidiphila NEC50278.1 98.73 gene 5348 716 yfiH laccase Streptomyces griseorubens GGQ64023.1 96.64 gene 4491 197 - multicopper oxidase domain-containing protein unclassified Streptomyces WP_106959434.1 98.46 gene 2609 989 - multicopper oxidase domain-containing protein Streptomyces sp. XHT-2 WP_161108161.1 99.39 gene 2857 983 - Phenoxybenzoate dioxygenase Streptomyces tuirus WP_190903372.1 88.07 gene 5116 1529 aldH aldehyde dehydrogenase Streptomyces sp. XHT-2 MXQ60577.1 99.61 gene 1234 1451 katE catalase Streptomyces sp. UNC401CLCol WP_028959332.1 99.79 gene 3983 1655 katE catalase Streptomyces sp. GESEQ-13 WP_210638384.1 99.09 gene 3220 2276 katE catalase HPII Streptomyces sp. XHT-2 WP_161108660.1 99.74 gene 3744 959 - Pimeloyl-ACP methyl ester carboxylesterase Streptomyces sp. di188 SCD58877.1 88.43 gene 6937 1277 - Dye-decolorizing peroxidase Streptomyces pharetrae CZA14 OSZ61955.1 83.61 Table 5 Genes responsible for the β-ketoadipate pathway and peripheral reactions. Gene ID Size (aa) Gene Name Encode protein Species of reference gene Accession no. (NCBI) BLAST identity (%) gene 3935 1001 - Vanillate O-demethylase oxygenase subuni Streptomyces sp. SID4956 WP_161232727.1 99.40 gene 2826 773 hpaI 4-hydroxy-2-oxovalerate aldolase Streptomyces sp. XHT-2 MXQ61669.1 99.61 gene 0228 335 - phenylpropionate dioxygenase-like ring-hydroxylating dioxygenase Streptomyces paradoxus MBB6077390.1 94.59 gene 0557 599 ubiX aromatic acid decarboxylase Streptomyces sp. 4F ALV54514.1 97.99 gene 0021 377 pcaC 4-carboxymuconolactone decarboxylase Streptomyces sp. ok210 WP_093930409.1 98.40 gene 0859 506 - carboxymuconolactone decarboxylase family protein Streptomyces sp. GESEQ-13 WP_210634556.1 99.40 gene 2323 1199 pcaL 4-carboxymuconolactone decarboxylase Streptomyces sp. Akac8 WP_136239018.1 99.75 gene 2838 1121 pcaL 3-oxoadipate enol-lactonase Streptomyces sp. SID4956 WP_161232455.1 99.73 gene 2839 1331 pcaB 3-carboxy-cis, cis-muconate cycloisomerase Streptomyces sp. UNC401CLCol WP_028959090.1 99.55 gene 2840 605 pcaG protocatechuate 3,4-dioxygenase subunit alpha Streptomyces sp. GESEQ-13 WP_210638048.1 99.50 gene 2841 773 pcaH protocatechuate 3,4-dioxygenase subunit beta Streptomyces sp. GESEQ-13 WP_210638047.1 99.22 gene 2842 1208 - β-ketoadipyl CoA thiolase Streptomyces sp. B9173 OQR62711.1 88.25 gene 2831 1364 pcaK 4-hydroxybenzoate transporter PcaK Streptomyces sp. GESEQ-13 WP_210638055.1 98.02 gene 2847 1439 pcaK 4-hydroxybenzoate transporter PcaK Streptomyces sp. Akac8 WP_136238348.1 99.79 gene 2852 734 pcaR Pca regulon regulatory protein Streptomyces cellulosae GHE61509.1 97.13 gene 2848 1013 hcaD Terephthalate 1,2-dioxygenase Streptomyces cellulosae GHE61489.1 97.63 gene 4139 1148 hcaD hypothetical protein Streptomyces sp. GESEQ-13 WP_210637914.1 98.43 gene 5175 317 hcaC 3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin subunit Streptomyces sp. di50b SCD40618.1 97.14 gene 5716 1265 hcaD pyridine nucleotide-disulfide oxidoreductase Streptomyces sp. 4F ALV50055.1 96.67 gene 5542 1025 - Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase Streptomyces afghaniensis 772 EPJ42281.1 82.27 gene 4140 923 - 4,5-dihydroxyphthalate decarboxylase Streptomyces sp. 3212.3 REE57871.1 84.69 gene 4458 1220 pobA 4-hydroxybenzoate 3-monooxygenase Streptomyces sp. XHT-2 WP_161108189.1 99.01 gene 6344 1175 pobA 4-hydroxybenzoate 3-monooxygenase Streptomyces sp. XHT-2 WP_161107724.1 99.49 gene 6436 1517 - cyclohexanone monooxygenase Streptomyces sp. 4F ALV51359.1 97.03 gene 6471 518 pat phosphinothricin N-acetyltransferase Streptomyces werraensis GHE99025.1 94.19 gene 4600 1322 - 4-methylmuconolactone transporter Streptomyces afghaniensis 772 EPJ35848.1 87.02 Table 6 Genes responsible for gentisate pathways. Gene ID Size (aa) Gene Name Encode protein Species of reference gene Accession no. (NCBI) BLAST identity (%) gene 1961 2366 - bifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase Streptomyces sp. 4F ALV52714.1 97.07 gene 0811 1613 gabD succinate-semialdehyde dehydrogenase Streptomyces sp. UNC401CLCol WP_028960221.1 99.81 gene 4361 1388 gabD NADP-dependent succinic semialdehyde dehydrogenase Streptomyces cellulosae GHE69900.1 98.70 gene 3797 1187 - fumarylacetoacetate hydrolase Streptomyces sp. SID8376 WP_205526335.1 99.75 gene 2855 1286 - aromatic ring-hydroxylating dioxygenase subunit alpha Streptomyces sp. GESEQ-13 WP_137208924.1 99.53 gene 4131 1280 - Phthalate 4,5-dioxygenase oxygenase subunit Streptomyces sp. MBT84 MBW8706675.1 70.79 gene 4137 620 - gentisate 1,2-dioxygenase Robiginitomaculum sp. PHR56577.1 81.03 gene 4928 1085 frmA alcohol dehydrogenase Streptomyces cellulosae GHE58756.1 97.23 gene 5219 689 - maleylpyruvate isomerase Streptomyces sp. XHT-2 WP_161107348.1 99.13 Table 7 Genes responsible for pathways for anthranilate. Gene ID Size (aa) Gene Name Encode protein Species of reference gene Accession no. (NCBI) BLAST identity (%) gene 1963 1610 abmG 2-aminobenzoate-CoA ligase Streptomyces sp. 4F ALV52716.1 94.03 gene 1964 1128 - acyl-CoA dehydrogenase Streptomyces sp. XHT-2 WP_161107119.1 99.47 gene 0037 638 pabA aminodeoxychorismate/anthranilate synthase component II Streptomyces sp. GESEQ-13 WP_210635465.1 99.53 gene 5387 1880 phzE anthranilate synthase Streptomyces sp. UNC401CLCol WP_028960786.1 99.52 gene 0262 1202 kynU L-kynurenine hydrolase Streptomyces sp. UNC401CLCol WP_028959521.1 99.25 gene 0261 830 TDO2 tryptophan 2,3-dioxygenase Streptomyces sp. GESEQ-13 WP_210635572.1 99.28 gene 4644 1697 - Tryptophan 2-monooxygenase Streptomyces sp. di50b SCD87347.1 97.35 gene 0499 1217 - Aromatic-amino-acid aminotransferase 1 Streptomyces sp. UNC401CLCol WP_064743320.1 99.49 gene 2090 873 - indole-3-glycerol phosphate synthase Streptomyces sp. I4 (2020) WP_199204736.1 96.82 gene 5302 806 trpC indole-3-glycerol phosphate synthase Streptomyces sp. I4 (2020) WP_199207289.1 99.63 gene 5306 1493 trpE anthranilate synthase component I Streptomyces sp. XHT-2 WP_161107330.1 99.8 Table 8 Genes responsible for pathways for resorcinol. Gene ID Size (aa) Gene Name Encode protein Species of reference gene Accession no. (NCBI) BLAST identity (%) gene 0128 971 - LysR family transcriptional regulator Streptomyces sp. UNC401CLCol WP_078611393.1 99.69 gene 2842 1208 - β-ketoadipyl CoA thiolase Streptomyces sp. B9173 OQR62711.1 88.25 gene 1964 1128 - acyl-CoA dehydrogenase Streptomyces sp. XHT-2 WP_161107119.1 99.47 gene 2768 1091 - aryl-alcohol dehydrogenase Streptomyces sp. di50b SCD35921.1 93.66 gene 2849 962 pdxA Terephthalate dihydrodiol dehydrogenase Streptomyces sp. McG7 WP_215047915.1 98.75 gene 2850 470 andAd terephthalate 1,2-dioxygenase Streptomyces sp. XHT-2 MXQ61646.1 100.00 gene 2851 1283 andAc Terephthalate 1,2-dioxygenase Rhodococcus pyridinivorans AK37 EHK83592.1 83.05 gene 3600 1502 - 2-polyprenyl-6-methoxyphenol hydroxylase Streptomyces sp. di50b SCD47389.1 85.06 gene 5989 1268 - dimethylaniline monooxygenase Streptomyces sp. 4F ALV54407.1 96.91 gene 3045 383 - extradiol dioxygenase Streptomyces sp. 4F ALV53653.1 93.70 gene 4526 476 - putative dehydrochlorinase Streptomyces sp. AUR34009.1 81.65 gene 5542 1025 - Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase Streptomyces afghaniensis 772 EPJ42281.1 82.27 gene 6472 785 - extradiol ring-cleavage dioxygenase Streptomyces griseorubens KEG41654.1 98.85 Table 9 Genes responsible for catabolic pathways for homogentisic. Gene ID Size (aa) Gene Name Encode protein Species of reference gene Accession no. (NCBI) BLAST identity (%) gene 4937 1361 hmgA homogentisate 1,2-dioxygenase Streptomyces sp. XHT-2 WP_161108369.1 99.78 gene 1961 2366 - bifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase Streptomyces sp. 4F ALV52714.1 97.07 gene 0499 1217 - Aromatic-amino-acid aminotransferase 1 Streptomyces sp. UNC401CLCol WP_064743320.1 99.49 gene 6956 1079 hisC Putative phenylalanine aminotransferase Streptomyces werraensis GHF12148.1 96.93 gene 0811 1613 gabD succinate-semialdehyde dehydrogenase Streptomyces sp. UNC401CLCol WP_028960221.1 99.81 gene 4361 1388 gabD NADP-dependent succinic semialdehyde dehydrogenase Streptomyces cellulosae GHE69900.1 98.70 gene 0636 1214 fahA Fumarylacetoacetate hydrolase Streptomyces sp. SID4956 WP_161232839.1 99.01 gene 3797 1187 - fumarylacetoacetate hydrolase Streptomyces sp. SID8376 WP_205526335.1 99.75 gene 2443 305 phhB 4a-hydroxytetrahydrobiopterin dehydratase Streptomyces griseorubens WP_033273716.1 98.02 gene 4811 2576 pheT phenylalanine--tRNA ligase subunit beta Streptomyces sp. GESEQ-13 WP_210636334.1 99.77 gene 4812 1121 pheS phenylalanine--tRNA ligase subunit alpha Streptomyces cellulosae GHE73990.1 100 gene 3632 1814 hppD 4-hydroxyphenylpyruvate dioxygenase Streptomyces cellulosae GHE74791.1 97.35 gene 3633 876 aroE shikimate dehydrogenase Streptomyces sp. FxanaD5 WP_019522987.1 99.66 gene 6183 1145 hppD 4-hydroxyphenylpyruvate dioxygenase Actinospica acidiphila WP_163089359.1 98.69 gene 4928 1085 frmA alcohol dehydrogenase Streptomyces cellulosae GHE58756.1 97.23 gene 5219 689 - maleylpyruvate isomerase Streptomyces sp. XHT-2 WP_161107348.1 99.13 Table 10 Genes responsible for pathways for phenylacetate-CoA. Gene ID Size (aa) Gene Name Encode protein Species of reference gene Accession no. (NCBI) BLAST identity (%) gene 0050 1061 paaE phenylacetic acid degradation protein Streptomyces cellulosae GHE31167.1 99.15 gene 0051 539 paaD phenylacetate-CoA oxygenase subunit Streptomyces cellulosae GHE31162.1 97.77 gene 0052 737 paaC phenylacetate-CoA oxygenase subunit Streptomyces sp. GESEQ-13 WP_210635474.1 98.78 gene 0053 287 paaB phenylacetate-CoA oxygenase subunit PaaB Streptomyces griseoruber WP_055636201.1 98.95 gene 0054 1016 paaA phenylacetate-CoA oxygenase subunit PaaA Streptomyces sp. SID4956 WP_161232185.1 99.41 gene 0058 1691 PaaN phenylacetic acid degradation protein Streptomyces sp. Akac8 WP_136238706.1 99.82 gene 0059 1514 paaH 3-hydroxyacyl-CoA dehydrogenase Streptomyces sp. SID4956 WP_161233084.1 100.00 gene 1159 803 paaG 1,2-epoxyphenylacetyl-CoA isomerase Streptomyces cellulosae GHE51256.1 98.13 gene 1381 848 paaH 3-hydroxybutyryl-CoA dehydrogenase Streptomyces sp. F-7 WP_093768152.1 99.65 gene 2386 1805 paaH 3-hydroxybutyryl-CoA dehydrogenase Streptomyces sp. SMS_SU21 WP_102640749.1 97.17 gene 2736 764 paaF 3-hydroxypropionyl-CoA dehydratase Streptomyces sp. GESEQ-13 WP_210638121.1 99.61 gene 4099 1523 paaK phenylacetate-CoA ligase Streptomyces sp. GESEQ-13 WP_210637941.1 99.77 gene 4804 860 paaH 3-hydroxybutyryl-CoA dehydrogenase Streptomyces sp. I4 (2020) WP_199207038.1 99.30 gene 6544 734 paaF enoyl-CoA hydratase Streptomyces cellulosae GHE27114.1 98.77 gene 4828 1376 Pad Phenylacetaldehyde dehydrogenase Streptomyces sp. DI166 SBT93309.1 87.53 gene 1454 767 - enoyl-CoA hydratase Streptomyces sp. Akac8 WP_136239245.1 99.61 gene 1960 827 - enoyl-CoA hydratase Streptomyces griseorubens WP_033274100.1 97.82 gene 1962 846 PaaX phenylacetic acid degradation operon negative regulatory protein Streptomyces aureorectus MBA8975440.1 90.71 Table 11 Genes responsible for catabolic pathways for 2,3-dihydroxyphenylpropionate. Gene ID Size (aa) Gene Name Encode protein Species of reference gene Accession no. (NCBI) BLAST identity (%) gene 3746 1028 - 3-hydroxycinnamic acid hydroxylase Streptomyces albogriseolus GHB97425.1 91.81 gene 1753 1640 mhpA 3-(3-hydroxy-phenyl) propionate acid hydroxylase Streptomyces sp. di50b SCE12787.1 96.15 gene 2825 1613 mhpA 3-(3-hydroxy-phenyl) propionate hydroxylase Streptomyces griseorubens GGQ79721.1 97.77 gene 2828 794 mhpD fumarylacetoacetate hydrolase Streptomyces sp. GESEQ-13 WP_210638174.1 99.62 gene 2830 935 mhpB 3-carboxyethylcatechol 2,3-dioxygenase Streptomyces sp. GESEQ-13 WP_210638056.1 99.04 gene 2826 773 hpaI 4-hydroxy-2-oxovalerate aldolase Streptomyces sp. XHT-2 MXQ61669.1 99.61 gene 5487 359 hpaF isomerase Streptomyces cellulosae GHE29375.1 97.48 gene 0171 431 - aldehyde dehydrogenase Streptomyces werraensis GHF03416.1 88.46 gene 0388 1460 - aldehyde dehydrogenase Streptomyces sp. GESEQ-13 WP_210635659.1 99.18 In the initial stages of lignin degradation, extracellular enzymes are responsible for depolymerization of lignin. Degradation enzyme systems involved in lignin degradation include the lignin oxidase system, hydrogen peroxide production enzyme system and other enzyme systems. In this study, multipl lignin depolymerization-related genes were found in the genome of DF3-3 (Table 4), including genes encoding multicopper oxidase (gene 5348, gene 4491, gene 2609), alcohol dehydrogenase (gene 2768), alcohol dioxygenase (gene 3045), aldehyde dehydrogenase (aldH), pentachlorophenol monooxygenase (gene 0904) and terephthalate dihydrodiol dehydrogenase (pdxA). Catabolism pathways for lignin components Many low molecular weight compounds are produced by initial depolymerization of lignin. Based on GC-MS and genome analysis, 5 metabolic pathways of lignin-based derivatives were predicted: β-ketoadipate pathway and peripheral reactions; gentisate pathway; anthranilate pathway; homogentisic pathway; and catabolic pathway for resorcinol (shown in Figure 7). Based on genome data alone, we predicted two other pathways: the phenylacetate-CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway ( Figure 8). β-ketoadipate pathway and peripheral reactions The β-ketoadipate pathway is an important aromatic metabolic pathway for many microorganisms. There are 26 genes involved in the degradation process of lignin in DF3-3 (Table 5), and they are scattered throughout the genome of DF3-3 (Figure 9). The key genes of the protocatechuic acid 3,4-dioxygenase (pcaG, pcaH) gene appear in the whole genome of DF3-3 and can be imagined to metabolize lignin intermediates through the β-ketoadipate pathway branched by protocatechin. There are two 4-hydroxycinnamic acid dioxygenases (hcaC, hcaD) in DF3-3, and 4-hydroxycinnamic acid can initially be degraded to generate 4-hydroxycinnamic acid coenzyme A and further converted into p-hydroxybenzoic acid, which was found among the degradation products of alkaline lignin produced by DF3-3. 3-Phenylpyruvic acid and 4-hydroxyphenylpyruvate were also detected as metabolites of DF3-3. We speculate that they can also be degraded by the hcaC gene. Then, 4-hydroxyphenylpyruvate undergoes a series of reactions to produce p-hydroxybenzoic acid. The pcaG and pcaH genes cause benzene epoxidation to enable a ring-opening reaction generating cis-hexadienedioic acid; this further generates β-ketoadipate, which is degraded and finally enters the tricarboxylic acid cycle. Unlike 4-hydroxyphenylpyruvate, 3-phenylpyruvic acid may not be converted only into 4-hydroxyphenylpyruvate by hcaC but could also be converted into benzoic acid and catechol, and then a ring-opening reaction takes place to enter the β-ketoadipate pathway or generate 4-hydroxy-2-oxovalerate and further degradation. The gentisate pathway The gentisate pathway usually starts from the degradation of salicylic acid. Ethyl salicylate is a precursor in the production of salicylic acid. The pathway for degradation of phthalic acid by some fungi has been explained, in which dibutyl phthalate or diisooctyl phthalate is converted to ethyl salicylate [43]. Some aromatic oxygenases may play important roles in this process. In the DF3-3 genome, the genes encoding salicylic acid-5-hydroxylase (gene 1961) and gentisic acid 1,2-dioxygenase (gene 4137) were identified (Table 6). Gentianic acid 1,2-dioxygenase oxygenates the benzene ring of gentisic acid to produce maleylpyruvate, which is then further metabolized by maleate pyruvate isomerase (gene 5219). Dibutyl phthalate and diisooctyl phthalate were detected among the metabolites of DF3-3. Phthalate dioxygenase oxygenase (gene 4131) detected in the DF3-3 genome gene also indicated that it may appear as an intermediate product of the salicylic acid metabolic pathway. The anthranilate pathway The specific mechanism of the anthranilic acid pathway in bacteria has not been fully elucidated [42, 44]. A 2-aminobenzoate-CoA ligase (abmG) and an L-kynurenine hydrolase (kynU) gene were identified in DF3-3, and a tryptophan 2,3-dioxygenase (TDO2) gene was also observed (Table 7). It is speculated that the anthranilic acid pathway of DF3-3 generates formyl kynurenine through the degradation of tryptophan, which is further converted to kynurenine and then generates anthranilic acid under the action of kynU. In addition, tryptophan may undergo a series of redox reactions at its side chain to produce indole derivatives. The pyrrole-2-carboxylic acid detected among the metabolites of DF3-3 can also be degraded by the anthranilate synthase (phzE) gene and abmG gene through a similar pathway. Catabolic pathway for resorcinol Due to the existence of the metabolite m-xylene and related genes (Table 8), it is speculated that DF3-3 has related metabolic pathways. The resorcinol pathways for other strains involve the participation of oxidoreductases. The functions of some of these genes, such as aromatic compound monooxygenase (gene 3600)-coding genes, have not been fully clarified. Aryl-alcohol dehydrogenase and extradiol dioxygenase may effect the degradation of aromatic phenols. It is speculated that the metabolism of m-xylene by DF3-3 may take place through oxidation of methyl groups to produce resorcinol. Then, resorcinol undergoes further oxygenation on the branch chain and ring-opening oxidation with the action of oxygenases (Figure 7). Homogentisic pathway The homogentisic pathway is the central pathway for catabolism of phenylalanine and tyrosine. Genomic analysis of DF3-3 shows that phenylalanine is converted to tyrosine by phenylalanine hydroxylase and auxiliary methanolamine dehydratase (PhhB), and tyrosine aminotransferase (hisC) is converted to tyrosine 4-hydroxyphenylpyruvate, which is further converted into homogentisate by 4-hydroxyphenylpyruvate dioxygenase (hppD) and degraded by the action of homogentisate 1,2-dioxygenase (hmgA) to produce maleacetoacetate (Figure 9). A fumarylacetoacetate hydrolase (fahA) gene was identified in the DF3-3 genome (Table 9), indicating that hydrolysis of maleacetoacetate occurs through the degradation of fumarate acetoacetate. The genes involved in the homogentisate pathway are scattered throughout the genome, and the processes are carried out with the joint action of hmgA and other related genes. This non-linkage also appears in other bacteria [44]. 4-Hydroxyphenylpyruvate, as the precursor of homogentisic acid, was observed among the products detected by GC-MS, and two hppD genes observed in the genome are related to the 4-hydroxy phenylpyruvate dioxygenase in Streptomyces cellulosae and Actinospica acidiphila with high similarities (97.35% and 98.69%). In addition to the above metabolic pathways, the following two possible lignin degradation pathways were found for DF3-3 through a gene search. A relatively complete set of coding genes is present in the genome to form the pathway, but the related metabolites were not observed in this study. Phenylacetate-CoA pathway Phenylacetate can be derived from lignin-related phenylpropane units [45], and the general pathway for aerobic metabolism has just been discovered and studied with some bacteria [46, 47]. There were at least 15 genes in DF3-3 involved in this process (Table 10). The phenylacetate coenzyme A oxygenase gene is organized into clusters (paaABCDE) and exists in the DF3-3 genome (Figure 9), downstream from which there are a phenylacetic acid degradation protein (paaN) and a 3-hydroxyacyl-CoA dehydrogenase (paaH) encoding gene; a 1,2-epoxyphenylacetyl-coenzyme A isomerase (paaG) gene exists a little further downstream, and the isomerase it encodes can convert 3-hydroxypropionyl-CoA into 1,2-epoxyphenylacetyl-CoA. At the same time, 3-hydroxypropionyl-CoA can also be further degraded by 3-hydroxypropionyl-CoA dehydrogenase (paaH) and 3-hydroxypropionyl-CoA dehydrogenase (paaF) and finally enter the tricarboxylic acid cycle. 2,3-Dihydroxyphenylpropionic acid pathway The 2,3-dihydroxyphenylpropionic acid pathway-related mhpABD gene cluster was observed in the DF3-3 genome (Table 11), including encoding for 3-(3-hydroxy-phenyl) propionate hydroxylase (mhpA), 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (mhpB) and fumarate acetoacetate hydrolase (mhpD) genes, which are located upstream of the 4-hydroxy-2-oxovalerate aldolase (hpaI) gene (Figure 9). DF3-3 lacks the mhpE and mhpF genes, and the generated 4-hydroxy-2-oxovalerate is decomposed by the aldolase encoded by the hpaI gene. It was also determined that other aldehyde dehydrogenases may effect the degradation of acetaldehyde and generate pyruvate and acetyl-CoA to enter the tricarboxylic acid cycle for metabolism. Discussion Biofuel production by biodegradable lignocellulose has far-reaching prospects [ 13 ]. Research on the degradation system of lignocellulose-degrading microorganisms has great significance to its practical application and development. However, few microorganisms, only white rot fungi, have been reported that can degrade lignin and cellulose at the same time [ 18 ]. In the actual degradation of biomass materials, the degradation of lignin, cellulose and hemicellulose often occurs simultaneously and is interrelated. In our research, we found that DF3-3 has good degradation performance on both lignin and cellulose. More experiments and new approaches are needed in future work to better develop and apply DF3-3. The enzymology for bacterial lignin degradation has been well-studied in recent years, and some bacterial specific enzymes for lignin degradation have been reported. Like Cα-dehydrogenase (LigD) [ 48 ], glutathione-dependent β-etherase enzymes (LigE, F, G) have been identified from Sphingomonas paucimobilis SYK-6 [ 49 ], a demethylase enzyme (LigX) from Pseudomonas paucimobilis [ 50 ], and DyP-type peroxidases from Rhodococcus jostii RHA1 [ 51 ]. Recent reports have shown multicopper oxidases that demonstrate laccase activities [ 52 , 53 ]. In our study, we found that DF3-3 had Lac, Mnp and Lip activities. Genome research identified three multicopper oxidase coding genes (gene 5348, gene 4491, gene 2609), and gene 5348 has high similarity (96.64%) to the laccase structural protein gene of Streptomyces griseorubens (GGQ64023.1) [ 54 ], showing that DF3-3 has the ability to encode laccase at the genetic level. No gene encoding manganese peroxidase has been detected, but a catalase/peroxidase gene (gene3898) was found in DF3-3, which was 99.87% similar to KatG from Streptomyces sp. Akac8 [ 8 ]. The fur gene (gene3899) encoding a transcription regulator appears downstream, and these were reported as possible manganese peroxidase-encoding genes in Streptomyces reticuli [ 43 , 44 ], suggesting that DF3-3 can exhibit manganese peroxidase activity. In addition, a gene (gene 6937) encoding a dye decolouring peroxidase was observed. The peroxidase encoded by it has a broad spectrum of substrates, which is also commonly reported in the depolymerization of lignin in some bacteria [ 22 , 45 , 46 ]. The hydrogen peroxide-producing enzyme system mainly participates in lignin degradation in the capacity of auxiliary enzymes [ 47 ]. These enzymes include glyoxal oxidase, aryl alcohol oxidase, quinone reductase and related dehydrogenases [ 48 ]. They produce hydrogen peroxide to support degradation by other peroxidases. The alcohol dehydrogenase (gene 2768), alcohol dioxygenase (gene 3045), and aldehyde dehydrogenase (aldH) annotated in the DF3-3 genome are thought to be involved in the process of lignin degradation. In addition, catalase removes the hydrogen peroxide produced by these reactions quickly enough to prevent oxidative damage to [4Fe-4S]-clusters in proteins and protect the body from toxification [ 24 , 49 ]. The catalase-encoding gene (katE) identified in DF3-3 is thought to be involved in lignin degradation. According to the GC-MS results, 2,4-di-tert-butylphenol and 2,2'-methyl bis(4-methyl-6-tert-butyl phenol) were involved in the metabolic processes of DF3-3. Recent studies have also shown that there is a 2,4-di-tert-butylphenol metabolic pathway for microbial degradation of lignin [ 55 ]. Considering the resorcinol pathway and its correlative gene, it is speculated that there may be a similar pathway in DF3-3. It may retain the structure of the tert-butyl side face and be metabolized by the meta-cleavage pathway. The formation of 2,2'-methyl bis(4-methyl-6-tert-butyl phenol) may come from the same metabolic intermediate as 2,4-di-tert-butylphenol. However, there are few studies on microbial degradation of this kind of structure at present. As an environmental pollutant, 4-tert-butylphenol can be degraded by several reported bacteria [ 56 , 57 ]. However, to better understand this purification process, its specific metabolic process and some of the enzymes involved require further study. The lignin degradation pathway of actinomycetes was first studied through research on the culture medium and metabolites [ 31 , 58 ]. As the understanding of molecular biology increased, people began to seek more direct evidence. Masai et al. [ 23 ] first established a relatively complete pathway of lignin degradation and metabolism by means of enzymology and genomics. In Sphingomonas paucimobilis SYK-6, β-aryl ether cleavage catalysis [ 59 ], the biphenyl ring cleavage pathway [ 60 ], the ferulate catabolic pathway [ 61 ], the O-demethylation systems of vanillate and syringate [ 62 ], the protocatechuate 4,5-cleavage pathway [ 63 ], and multiple 3- O -methylagallate catabolic pathways [ 64 ] were described. Eleven lignin metabolic pathways were found in the genome of Cupriavidus necator , among which the β-ketoadipate pathway also included four branches: catechol, chlorocatechol, methylcatechol and protocatechuate ortho ring-cleavage [ 42 ]. In our study, evidence of a lignin degradation pathway was found in the metabolites and genetics. The products detected by GC-MS are also related to five lignin metabolic pathways. However, some unusual products detected may point to new branches. We speculate that 4-hydroxyphenylpyruvate ( 14 ) and 3-phenylpyruvic acid ( 12 ) may be transformed from phenylalanine and enter the homologous pathway and β-ketoadipate pathway, respectively, for further metabolism. A large number of genes related to the β-ketoadipate pathway have been detected in DF3-3, but there are still some genes involved in the reaction process that have not been compared, and for some genes, the reaction process in which they specifically participate has not been further elucidate. Perhaps there are related reactions in DF3-3 which are different from those in other bacteria. The heterologous expression of these gene fragments is helpful to the establishment and production of efficient engineered bacteria with biological enzymes. Recent studies have shown that bacterial degradation of lignin has complex growth condition-specific regulation [ 65 ]. Because of the diversity of structure of lignan compounds, different reactions may occur in the degradation process of different substrate. Based on genome data alone, we predicted two other pathways the phenylacetate-CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway, but did not find the related metabolites by GC-MS. This absence might be related to the substrates. To further verify the degradation process, transcriptome analysis, proteomic analysis and other biological methods are needed to study the enzymes and the genes involved in their degradation pathways to understand the biological function of DF3-3 in the degradation of lignin. Conclusions Based on the above data and analyses, we isolated a bacterial strain identified as Streptomyces thermocarboxydus strain DF3-3 from greening litter and concluded that it degraded alkaline lignin, and the degradation efficiency reached 31% within 15 days. In total, 19 alkaline lignin degradation intermediates were identified by GC-MS, and 107 possible lignin-degrading enzyme encoding genes in the DF3-3 genome were annotated; 7 pathways for metabolism of lignin and its intermediates were predicted, including the β-ketoadipate pathway and peripheral reactions; gentisate pathway; anthranilate pathway; catabolic pathway for resorcinol; homogentisic pathway; phenylacetate-CoA pathway; and the 2,3-dihydroxyphenylpropionic acid pathway. Intermediates in the first five metabolic pathway were detected by GC-MS. The degradation products and genomics analyses show that DF3-3 has a relatively complete lignin degradation pathway. Methods Sampling, isolation and screening of bacterial strain Samples were collected from greening litter of Beijing University of Agriculture (40.0947° N, 116.3151° E). One gram of sample was placed in a 50-mL sterile centrifuge tube containing 10 mL of sterile distilled water and shaken at 120 rpm overnight. Next, 10 −1 and 10 −2 serial dilutions of each sample suspension were spread as 0.1-mL aliquots on Gause's synthetic medium with the formula (g/L): 0.5 NaCl;1 KNO 3 ༛0.5 K 2 HPO 4 ·3H 2 O༛0.5 MgSO 4 ·7H 2 O༛0.01 FeSO 4 ·7H 2 O༛20 soluble starch [ 8 ]. The plates were incubated at 30°C for one week, and distinct colonies were picked and subcultured for further analysis. Gause’s guaiacol medium and Gause’s Azure B medium used for lignin degradation screening contained 0.1% guaiacol and 0.1% aniline blue, respectively, added to Gause’s medium. Different external nitrogen sources (20 g/L), such as acrylamide and potassium nitrate, and additional carbon sources (1 g/L), such as glucose and mannose, were used to replace soluble starch culture strains in studies of their utilization of nitrogen sources and carbon sources. The culture medium for detecting lignin degradation and enzyme activity was kraft lignin-MSM medium (3 g of kraft lignin L, 2 g of [NH 4 ] 2 SO 4 , 1 g of K 2 HPO 4 , 1 g of KH 2 PO 4 , 0.2 g of MgSO 4 , 0.1 g of CaCl 2 , 0.05 g of FeSO 4 , and 0.02 g of MnSO 4 in 1 L distilled water, pH 7.0). Scanning electron microscope observations The shapes of the bacteria were observed by scanning electron microscopy. A cover glass was inserted into the solid medium to cultivate the strain, and the insert was removed after the bacterial body climbed onto the glass slide. The precipitate was washed by adding a phosphate buffer solution (pH 7.2), added to 2.5% glutaraldehyde, fixed at room temperature for 2~4 hours, and then placed in a refrigerator at 4°C overnight. After elution with a 30–95% ethanol gradient, the material was rinsed with tert-butanol, then 20 µL of tert-butanol was added and the mixture was put into a refrigerator at -20℃ until it froze and solidified. Using critical point drying (HITACHI HCP-2 Critical Point Dryer) and gold sputter coating (Eiko IB-3 ion plating machine), the sample was observed by scanning electron microscopy (SEM, JSM-6360LV, JEOL, Japan) [ 66 ]. Strain growth curve determination To assess the growth of bacteria, an equal quantity of bacteria was inserted into Gause’s liquid medium and cultured on a shaker. The culture solution was removed and centrifuged every 24 hours. The supernatant was discarded, and the filter paper was placed into an oven. The mixture was dried to a constant weight, and the filter paper and the bacteria were weighed. The weight of the filter paper was compared with the weight of the bacteria. All assays were performed with three replicates. Biodegradation of alkali lignin To determine the lignin loss from alkaline lignin cause by various strains, samples (1.5 mL) were centrifuged at 12,000 ×g for 10 min. One millilitre of supernatant was diluted by adding 2 mL of phosphate buffer (pH 7.6). The lignin concentration was determined by measuring the absorbance at 280 nm with a UV-Vis spectrophotometer (Shimadzu UN-1900i) [ 67 ]. The calculated standard curve for lignin was y = 0.0786x - 0.0245, R² = 0.9988. Enzyme assay Samples were centrifuged at 12000 rpm for 5 min, and the supernatant was used for lignin peroxidase (Lip), laccase and manganese peroxidase (MnP) enzyme assays. Laccase activity was determined by monitoring the oxidation of ABTS at 420 nm (ε420 = 36000 M −1 cm −1 ) [ 68 ]. A lignin peroxidase assay was carried out by using peroxidase oxidation of Azure B. LiP activity was determined by measuring the absorbance at 651 nm (ε651=48.8 M −1 cm −1 ) [ 69 ]. Manganese peroxidase activity was determined from the change in absorbance occurring when Mn 2+ is oxidized to Mn 3+ and forms a complex with malonate, which produced absorbance at 270 nm (ε270=11590 M −1 cm −1 ) [ 70 ]. Genome sequencing and functional annotation The genome of DF3-3 was sequenced at Major Biomedical Technology Co., Ltd. (Shanghai, China). Genomic DNA was extracted using a Wizard® Genomic DNA Purification Kit (Promega). Purified genomic DNA was quantified by a TBS-380 fluorometer (Turner BioSystems Inc., Sunnyvale, CA). The genome was sequenced by adopting the second-generation + third-generation sequencing method of Illumina HiSeq+PacBio, with a shotgun library of 400 bp insertion size. Assembly software canu, SPAdes, etc. was used for three-generation sequence assembly [ 71 ], and GeneMarkS software was used to predict the coding sequence (CDS) in the genome [ 72 ]. The prediction and annotation of genes were carried out using Prodigal Son (prokaryotic dynamic programming gene discovery algorithm). GeneMarkS was used to predict the plasmid genome. tRNAscan-SE v2.0 software was used to predict the tRNA contained in the genome, and Barrnap software was used to predict the rRNA contained in the genome. Functional annotation of the predicted coding gene was carried out by comparison with 6 major databases (NR, Swiss-Prot, Pfam, EggNOG, GO and KEGG) [ 73 – 76 ]. Alkali lignin degradation products determined by GC-MS DF3-3 was inoculated in 100 ml of medium with AL as the carbon source and cultured on a shaker for seven days. Samples were collected every 24 hours, and a number of control groups was set up. The sample was centrifuged (10,000 rpm, 15 min) to remove the bacteria, the supernatant was acidified with HCl to pH 2–3, and it was thoroughly extracted with a three-fold volume of ethyl acetate. The extract was rotary evaporated to 10 ml at 37°C and dried with anhydrous Na 2 SO 4 . After evaporating the solvent in a nitrogen stream, 100 µl of the organic layer was derivatized. Then, 100 µl of dioxane and 10 µl of pyridine were added to the sample and vortexed, and 50 µl of bis(trimethylsilyl)trifluoroacetamide (BSTFA) was added. The mixed solution was placed in a water bath at 80°C for 45 min and shaken regularly. The silanized sample was tested by GC-MS [ 77 ]. The analytical column was a DB-5 capillary column (30 m length, 0.25 mm inner diameter, 0.25 mm film thickness). The carrier gas was helium. The column temperature was initially 50°C (5 min), then it was raised to 280°C (10°C/min, holding time of 5 min). The transmission line and ion source temperatures were 200 and 250°C, respectively. The solvent delay time was 4.0 min. The injection volume was 1 µl. Electron ionization mass spectra were recorded in the range 30–550 (m/z) in full scan mode. Abbreviations AL: Alkali lignin; GC-MS: Gas chromatography-mass spectrometry; MnP: Manganese peroxidase; Lac: Laccase; LiP: Lignin peroxidase. Declarations Fangyun Tan and Jun Cheng are co-first authors. Ethics approval and consent to participate Ethical approval and consent to participate are not required. Consent for publication All authors agree to the submission and publication of the manuscript in the journal Biotechnology for Biofuel . Availability of data and materials The additional data generated during this study are available in the Additional file . Competing interests The authors declare that they have no competing interests. Funding This work was funded by the National Key Research and Development Program of China (code: 2017YFF0207800) and the Scientific Research Program of Beijing Municipal Education Commission (code: KM201810020012). Authors' contributions YQL designed the experimental strategy. FYT, JC, YZ and XFJ carried out the experiments and performed the bioinformatics data analysis. FYT and JC wrote the manuscript. YQL supervised the overall research. This manuscript was proofread by all the authors. All authors read and approved the final manuscript. Acknowledgements The authors thank Beijing Key Laboratory of New Technology in Agricultural Application for their support of the part of the work involving scanning electron microscopy. And genome analysis was performed using the free online platform of Majorbio Cloud Platform (www.majorbio.com). Author information 1 School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206 PR China; 2 School of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206 PR China; 3 Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193 PR China. References Zeng Y, Zhao S, Yang S, Ding SY. Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels. Curr Opin Biotechnol. 2014;27:38-45. Kumar M, Singhal A, Thakur IS. Comparison of submerged and solid state pretreatment of sugarcane bagasse by Pandoraea sp. ISTKB: enzymatic and structural analysis. Bioresour Technol. 2016;203:18-25. Kamimura N, Sakamoto S, Mitsuda N, Masai E, Kajita S. Advances in microbial lignin degradation and its applications. Curr Opin Biotechnol. 2019;56:179-86. Ralph J, Lundquist K, Brunow G, Lu F, Kim H, Schatz PF, et al. Lignins: natural polymers from oxidative coupling of 4-hydroxyphenyl- propanoids. Phytochem Rev. 2004;3:29-60. Abdelaziz OY, Brink DP, Prothmann J, Ravi K, Sun M, García-Hidalgo J, et al. Biological valorization of low molecular weight lignin. Biotechnol Adv. 2016;34:1318-46. Tuor U, Winterhalter K, Fiechter A. Enzymes of white-rot fungi involved in lignin degradation and ecological determinants for wood decay. J Biotechnol. 1995;41:1-17. Sánchez C. Lignocellulosic residues: biodegradation and bioconversion by fungi. Biotechnol Adv. 2009;27:185-94. Yang YS, Zhou JT, Lu H, Yuan YL, Zhao LH. Isolation and characterization of Streptomyces spp. strains F-6 and F-7 capable of decomposing alkali lignin. Environ Technol. 2012;33:2603-9. Mcleod MP, Warren RL, Hsiao W, Araki N, Myhre M, Fernandes C, et al. The complete genome of Rhodococcu s sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A. 2006;103:15582-7. Masai E, Kamimura N, Kasai D, Oguchi A, Ankai A, Fukui S, et al. Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of lignin-derived biaryls and monoaryls. J Bacteriol. 2012;194:534-5. Lin L, Cheng Y, Pu Y, Sun S, Li X, Jin M, et al. Systems biology-guided biodesign of consolidated lignin conversion. Green Chem. 2016;18:5536-47. Janshekar H, Fiechter A. On the bacterial degradation of lignin. Eur J Appl Microbiol Biotechnol. 1982;14:47-50. Bugg TD, Ahmad M, Hardiman EM, Singh R. The emerging role for bacteria in lignin degradation and bio-product formation. Curr Opin Biotechnol. 2011;22:394-400. Pasti MB, Pometto AL, Nuti MP, Crawford DL. Lignin-solubilizing ability of actinomycetes isolated from termite (Termitidae) gut. Appl Environ Microbiol. 1990;56:2213-8. 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Xu G, Li F, Wang Q. Occurrence and degradation characteristics of dibutyl phthalate (DBP) and di-(2-ethylhexyl) phthalate (DEHP) in typical agricultural soils of China. Sci Total Environ. 2008;393:333-40. Schühle K, Jahn M, Ghisla S, Fuchs G. Two similar gene clusters coding for enzymes of a new type of aerobic 2-aminobenzoate (anthranilate) metabolism in the bacterium Azoarcus evansii. J Bacteriol. 2001;183:5268-78. Liu D, Yan X, Si M, Deng X, Min X, Shi Y, et al. Bioconversion of lignin into bioplastics by Pandoraea sp. B-6: molecular mechanism. Environ Sci Pollut Res Int. 2019;26:2761-70. Mohamed Mel S, Ismail W, Heider J, Fuchs G. Aerobic metabolism of phenylacetic acids in Azoarcus evansii. Arch Microbiol. 2002;178:180-92. Ferrández A, Miñambres B, García B, Olivera ER, Luengo JM, García JL, et al. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J Biol Chem. 1998;273:25974-86. Brown ME, Chang MCY. Exploring bacterial lignin degradation. Current Opinion in Chemical Biology. 2014;19:1-7. Masai E, Katayama Y, Kubota S, Kawai S, Yamasaki M, Morohoshi N. A bacterial enzyme degrading the model lignin compound beta-etherase is a member of the glutathione-S-transferase superfamily. FEBS Lett. 1993;323:135-40. Masai E, Kubota S, Katayama Y, Kawai S, Yamasaki M, Morohoshi N. Characterization of the C alpha-dehydrogenase gene involved in the cleavage of beta-aryl ether by Pseudomonas paucimobilis. Biosci Biotechnol Biochem. 1993;57:1655-9. Colpa DI, Fraaije MW, van Bloois E. DyP-type peroxidases: a promising and versatile class of enzymes. J Ind Microbiol Biotechnol. 2014;41:1-7. Majumdar S, Lukk T, Solbiati JO, Bauer S, Nair SK, Cronan JE, et al. Roles of small laccases from Streptomyces in lignin degradation. Biochemistry. 2014;53:4047-58. Ihssen J, Reiss R, Luchsinger R, Thöny-Meyer L, Richter M. Biochemical properties and yields of diverse bacterial laccase-like multicopper oxidases expressed in Escherichia coli. Sci Rep. 2015;5:10465. Medema MH, Trefzer A, Kovalchuk A, van den Berg M, Müller U, Heijne W, et al. The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol Evol. 2010;2:212-24. Toyama T, Momotani N, Ogata Y, Miyamori Y, Inoue D, Sei K, et al. Isolation and characterization of 4-tert-butylphenol-utilizing Sphingobium fuliginis strains from Phragmites australis rhizosphere sediment. Appl Environ Microbiol. 2010;76:6733-40. Gabriel FL, Giger W, Guenther K, Kohler HPE. Differential degradation of nonylphenol isomers by Sphingomonas xenophaga Bayram. Appl Environ Microbiol. 2005;71:1123-9. Gabriel FL, Cyris M, Jonkers N, Giger W, Guenther K, Kohler HPE. Elucidation of the ipso-substitution mechanism for side-chain cleavage of α-quaternary 4-nonylphenols and 4-t-butoxyphenol in Sphingobium xenophagum Bayram. Appl Environ Microbiol. 2007;73:3320-6. Crawford DL, Pometto AL, 3rd, Crawford RL. Production of useful modified lignin polymers by bioconversion of lignocellulose with Streptomyces. Biotechnol Adv. 1984;2:217-32. Masai E, Katayama Y, Nishikawa S, Yamasaki M, Morohoshi N, Haraguchi T. Detection and localization of a new enzyme catalyzing the beta-aryl ether cleavage in the soil bacterium (Pseudomonas paucimobilis SYK-6). FEBS Lett. 1989;249:348-52. Sonoki T, Obi T, Kubota S, Higashi M, Masai E, Katayama Y. Coexistence of two different O demethylation systems in lignin metabolism by Sphingomonas paucimobilis SYK-6: cloning and sequencing of the lignin biphenyl-specific O-demethylase (LigX) gene. Appl Environ Microbiol. 2000;66:2125-32. Masai E, Harada K, Peng X, Kitayama H, Katayama Y, Fukuda M. 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Castillo U, Myers S, Browne L, Strobel G, Hess WM, Hanks J, et al. Scanning electron microscopy of some endophytic streptomycetes in snakevine‐ Kennedia nigricans. Scanning. 2005;27:305-11. Lara MA, Rodrı́guez-Malaver AJ, Rojas OJ, Holmquist O, González AM, Bullón J, et al. Black liquor lignin biodegradation by Trametes elegans. Int Biodeterior Biodegrad. 2003;52:167-73. Kinnunen A, Maijala P, JArvinen P, Hatakka A. Improved efficiency in screening for lignin-modifying peroxidases and laccases of basidiomycetes. Curr Biotechnol. 2017;6:105-15. Morya R, Kumar M, Thakur IS. Utilization of glycerol by Bacillus sp. ISTVK1 for production and characterization of polyhydroxyvalerate. Bioresour Technol Rep. 2018;2:1-6. Kumar M, Singh J, Singh MK, Singhal A, Thakur IS. Investigating the degradation process of kraft lignin by β-proteobacterium, Pandoraea sp. ISTKB. Environ Sci Pollut Res. 2015;22:15690-702. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455-77. Besemer J, Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 2005;33:W451-4. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 2000;28:45-8. Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, et al. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res. 2008;36:D250-4. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27-30. Finn RD, Alex B, Jody C, Penelope C, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Research. 2014;42:D222-30. Raj A, Chandra R, Reddy MMK, Purohit HJ, Kapley A. Biodegradation of kraft lignin by a newly isolated bacterial strain, Aneurinibacillus aneurinilyticus from the sludge of a pulp paper mill. World J Microbiol Biotechnol. 2007;23:793-9. Supplementary Files supplementarymaterial9.23.docx Cite Share Download PDF Status: Under Review Version 1 posted Reviewer # 2 agreed at journal 15 Feb, 2022 Reviews received at journal 02 Dec, 2021 Reviewer # 1 agreed at journal 01 Dec, 2021 Reviewers invited by journal 17 Nov, 2021 Editor invited by journal 21 Oct, 2021 Editor assigned by journal 21 Oct, 2021 Submission checks completed at journal 20 Oct, 2021 First submitted to journal 19 Oct, 2021 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-996090","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research","associatedPublications":[],"authors":[{"id":59805936,"identity":"bd27ee01-8e5b-4112-8f6a-550173c5330f","order_by":0,"name":"Fangyun Tan","email":"","orcid":"","institution":"Beijing University of Agriculture","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Fangyun","middleName":"","lastName":"Tan","suffix":""},{"id":59805937,"identity":"0e61b558-bcfa-4083-9b06-fdcaa83550f0","order_by":1,"name":"Jun Cheng","email":"","orcid":"","institution":"Beijing University of Agriculture","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jun","middleName":"","lastName":"Cheng","suffix":""},{"id":59805938,"identity":"aaa832a9-9790-452e-8354-aefc86557819","order_by":2,"name":"Yu Zhang","email":"","orcid":"","institution":"Beijing University of Agriculture","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Yu","middleName":"","lastName":"Zhang","suffix":""},{"id":59805939,"identity":"43e1e9f5-c17c-49b3-9632-7e0b24987a28","order_by":3,"name":"Xingfu Jiang","email":"","orcid":"","institution":"Chinese Academy of Agricultural Sciences Institute of Plant Protection","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Xingfu","middleName":"","lastName":"Jiang","suffix":""},{"id":59805940,"identity":"d0ebc909-9eff-4127-931b-636b533876f4","order_by":4,"name":"Yueqiu Liu","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA0UlEQVRIiWNgGAWjYBACPmYIzcPA3gNmMDYQ0sIG18JzhlgtcJZEDrFa2HnMpHkqrGUMbr49JvGDwUZ2wwHmZw/wOwyk5Uw6j8HtvDTJHoY04w0H2MwNCGrhbTsM1JJjJsHDcDhxwwEeNgnCWv4Btdw8Yyb5h+E/sVoagFpugFzIcIAYLWzFlnOOpfNInslLBgZCsvHMw2xmeLXw8x/eeONNjbU93/GzB2++qbCT7Tve/AyvFiBgASqARigDKKiY8SmGAOYPRCkbBaNgFIyCkQsAAao8EB3PutsAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0002-9152-4752","institution":"Beijing University of Agriculture","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Yueqiu","middleName":"","lastName":"Liu","suffix":""}],"badges":[],"createdAt":"2021-10-19 16:06:32","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-996090/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-996090/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":15094791,"identity":"07ac2a5c-31c5-40aa-a3eb-1f28a316aaf3","added_by":"auto","created_at":"2021-11-01 15:24:35","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":816222,"visible":true,"origin":"","legend":"DF3-3 colour reaction and morphological characteristics.\na Colony morphology streaked on a plate of DF3-3. b Transparent fading circle on Gause’s- Azure B medium. c Colour reaction on Gause’s-guaiacol medium. d Scanning electron micrograph of DF3-3.\n","description":"","filename":"Figure1.png","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/355c69171865555e8ca8afac.png"},{"id":15094799,"identity":"e60e4bb0-111e-4ff8-8477-2090bd2641e8","added_by":"auto","created_at":"2021-11-01 15:24:36","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1099556,"visible":true,"origin":"","legend":"ANI analysis results for DF3-3 and other bacteria.","description":"","filename":"Figure2.png","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/23d67c27676e229cf6a6d2ef.png"},{"id":15094796,"identity":"9ae9dd92-e18a-4ebe-a813-4b053a5cb16b","added_by":"auto","created_at":"2021-11-01 15:24:35","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":14381,"visible":true,"origin":"","legend":"Growth curve and alkaline lignin degradation curve for DF3-3. Average values of three replicates are shown with the standard error of the mean as error bars (data are contained in S1).","description":"","filename":"Figure3.png","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/c4dfd6c679cd4e135db9e1b3.png"},{"id":15094794,"identity":"b6416360-e9d4-4abc-8ae5-41dc935aec28","added_by":"auto","created_at":"2021-11-01 15:24:35","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":10402,"visible":true,"origin":"","legend":"Enzyme activities of LiP, Lac, and MnP of DF3-3 during 11 days of incubation. Average values of three replicates are shown with the standard errors of the mean shown as error bars.","description":"","filename":"Figure4.png","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/3e0bf04bc7d61dbef6dd5a71.png"},{"id":15095625,"identity":"ce18acac-4185-446a-9077-70a6c0e71f85","added_by":"auto","created_at":"2021-11-01 15:30:35","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":297560,"visible":true,"origin":"","legend":"Variations in peak areas for products identified by GC–MS before TAC","description":"","filename":"Figure5.png","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/698914436cf91566b76d7597.png"},{"id":15095177,"identity":"ed63813f-88cf-488e-9413-e75f5016b735","added_by":"auto","created_at":"2021-11-01 15:27:35","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":289608,"visible":true,"origin":"","legend":"Variations in the peak areas for products identified by GC–MS after TAC.","description":"","filename":"Figure6.png","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/2cabcccd6571d857c29b7c38.png"},{"id":15094800,"identity":"64fb8c10-fbdd-415c-9af5-2f2b2bfad4d7","added_by":"auto","created_at":"2021-11-01 15:24:36","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":460461,"visible":true,"origin":"","legend":"Predicted lignin degradation pathway for Streptomyces thermocarboxydus strain DF3-3. Numbers used to represent the compounds are the same as those in Table 3.","description":"","filename":"Figure7.png","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/a4b87114952db9fa75df261a.png"},{"id":15094797,"identity":"5262354e-3330-4f15-9865-7bc8490e6168","added_by":"auto","created_at":"2021-11-01 15:24:35","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":111719,"visible":true,"origin":"","legend":"Lignin metabolic pathway of DF3-3 to be further verified.","description":"","filename":"Figure8.png","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/c86683004bb7891aae24b075.png"},{"id":15095175,"identity":"a231df67-bbb3-473e-b57f-d94594848a45","added_by":"auto","created_at":"2021-11-01 15:27:35","extension":"png","order_by":9,"title":"Figure 9","display":"","copyAsset":false,"role":"figure","size":41310,"visible":true,"origin":"","legend":"Locations of genes encoding aromatic catabolic pathways are indicated in the genome of DF3-3; orange, genes for the β-ketoadipate central pathway; green, genes for the phenylacetyl-CoA ring-cleavage pathway; yellow, genes for the 2,3-dihydroxyphenylpropionate pathway; purple, genes for the anthranilate pathway; dark green, genes for the homogentisate pathway; dark blue, genes for the gentisate pathway; blue, genes for the resorcinol pathway.","description":"","filename":"Figure9.png","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/6187d9511c327bce230d8923.png"},{"id":15676023,"identity":"76c8b28b-2fa7-465d-ab39-85d5c57cdc9b","added_by":"auto","created_at":"2021-11-18 14:31:16","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2962166,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/6f92acf6-2c9f-484f-9346-9cc53e699130.pdf"},{"id":15094792,"identity":"859103bd-87ea-4b2e-8f0e-aa072e5fa950","added_by":"auto","created_at":"2021-11-01 15:24:35","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":1159041,"visible":true,"origin":"","legend":"","description":"","filename":"supplementarymaterial9.23.docx","url":"https://assets-eu.researchsquare.com/files/rs-996090/v1/9b1bf2ef6cdff476539bc226.docx"}],"financialInterests":"","formattedTitle":"\u003cp\u003eGenomics Analysis and Degradation Characteristics of Lignin by \u003cem\u003eStreptomyces Thermocarboxydus\u003c/em\u003e Strain DF3-3\u003c/p\u003e","fulltext":[{"header":"Background","content":"\u003cp\u003eLignocellulosic biomass is an easily available, low cost and renewable alternative to fossil fuels. Currently, the process for pretreatment of lignocellulosic biofuel requires removal or delocalization of lignin, which might generate aromatic compounds that inhibit enzymatic hydrolysis and fermentation [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. Due to its rich aromatic content, lignin is a valuable waste from the biomass industry [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. Researchers worldwide are focusing on lignin and its components for conversion into value-added products. Lignin is a complex aromatic heteropolymer derived from the condensation of hydroxyphenylpropane monomers and comprises various ether bonds and carbon-carbon bonds [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. It is mainly composed of three basic monomers: guaiacyl (G) units, syringyl (S) units and p-hydroxyphenyl (H) units [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. Microorganisms that degrade lignocellulose are widely distributed in nature, and known examples include bacteria, fungi and actinomycetes. Among them, fungi and some bacteria have mainly been studied, and white-rot fungi, and brown rot fungi in particular have obvious degradation effects on lignin [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e], but the development of industrial applications has been difficult [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. Some actinomycetes and bacteria also participate in lignin degradation. Several typical lignin-degrading bacteria, such as \u003cem\u003eRhodococcus\u003c/em\u003e, \u003cem\u003ePseudomonas, Sphingobium\u003c/em\u003e and \u003cem\u003eSphingomonas\u003c/em\u003e, have been identified [\u003cspan additionalcitationids=\"CR10 CR11\" citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. \u003cem\u003eStreptomyces\u003c/em\u003e are among the identified bacteria capable of degrading lignin [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. Pasti et al. [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e] isolated 11 strains of actinomycetes from the intestines of termites and analysed their ability to degrade lignocellulose, lignin and carbohydrates. Other researchers have also screened streptomyces from the soil that degrade lignin [\u003cspan additionalcitationids=\"CR16\" citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThere are many kinds of enzymes involved in the degradation of lignin, including laccase (Lac), lignin peroxidase (LiP), manganese peroxidase (MnP), multifunctional peroxidase (VP), and dye decolouring peroxidase (DyPs) [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. The specific mechanism for biological degradation of lignin needs to be studied further. Lignin is rich in high-value degradation intermediates, such as vanillin, guaiacol, catechin and protocatechin [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. At the same time, the study of the metabolic mechanism of lignin and its transformation and utilization is an important part of the research needed for production of \"second-generation biofuels\" [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eHundreds of lignin derivatives have been identified in studies of bacterial degradation of lignin [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. Because of the complex degradation mechanism, the interpretation of metabolic pathways and intermediate products is an important part of understanding the degradation of lignin. With the development of sequencing technology and bioinformatics, genomics research has become an important method for studying degradation mechanisms. Researchers are paying increasing attention to analysing metabolism of intermediate products through annotations of related degradation genes. \u003cem\u003ePseudomonas putida\u003c/em\u003e is a lignin-degrading bacterium that has been studied earlier. Lin et al. [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e] identified several lignin-degrading enzymes, including haem peroxidase, from its genome and constructed five lignin metabolic pathways. Masai et al. [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e] conducted a series of studies on lignin degradation and related genes in \u003cem\u003eSphingomonas paucimobilis\u003c/em\u003e SYK-6 and established a relatively complete lignin degradation metabolic pathway. Niewerth et al. [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e] determined and analysed the whole genome sequence of \u003cem\u003eArthrobacter\u003c/em\u003e sp. Rue61a in soil, and the results showed that it has an aromatic degradation pathway that utilizes the characteristic products of lignin degradation, reflecting the saprophytic capabilities and nutritional diversity of organisms.\u003c/p\u003e \u003cp\u003eSeveral Streptomyces strains, such as \u003cem\u003eStreptomyces viridosporus\u003c/em\u003e T7A [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e] and \u003cem\u003eStreptomyces setonii\u003c/em\u003e 75Vi2 [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e], have been reported to degrade lignin. However, the actual catabolic pathways of lignin derivatives and the responsible enzymes and genes have not been investigated by using molecular methods with \u003cem\u003eStreptomyces\u003c/em\u003e. In our present study, a novel isolate, DF3-3, identified as \u003cem\u003eStreptomyces thermocarboxydus\u003c/em\u003e, was found to degrade lignin. Alkali lignin is a model compound with a structure similar to that of lignocellulose and is often used as a raw material for lignin degradation studies [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. This study used alkali lignin to investigate the characteristics of alkali lignin degradation by \u003cem\u003eStreptomyces thermocarboxydus\u003c/em\u003e strain DF3-3. GC\u0026ndash;MS combined with genomics was used to identify the genes responsible for lignin degradation and explore the metabolic pathway for lignin degradation by \u003cem\u003eStreptomyces thermocarboxydus\u003c/em\u003e strain DF3-3.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv class=\"Section2\" id=\"Sec3\"\u003e\n \u003ch2\u003eMorphological and physiological characteristics of DF3-3\u003c/h2\u003e\n \u003cp\u003eA strain of actinomycete named DF3-3 was isolated from the greening litter of Beijing University of Agriculture. The scribing form of the plate shows a rough white surface, the upper and lower surfaces are inconsistent in colour, and the hyphae in the base are obvious on Gause\u0026apos;s medium. (Figure \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003ea). When DF3-3 was inoculated on Gause\u0026rsquo;s guaiacol medium, a clear colour reaction appeared. When inoculated on Gause\u0026rsquo;s-Azure B medium, a transparent fading circle appeared (Figure \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eb and c). This shows that DF3-3 has the ability to degrade lignin [\u003cspan class=\"CitationRef\"\u003e28\u003c/span\u003e]. Microscopy was used to observe the morphology of DF3-3 (Figure \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003ed). DF3-3 grew luxuriantly on the plate, hyphae were developed, and aerial hyphae were slender. The spore filaments were spiral-shaped with obvious characteristics of \u003cem\u003eStreptomyces\u003c/em\u003e. Figure \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003ed shows a scanning electron micrograph of DF3-3 grown on Gause\u0026apos;s medium. Mature spore chains were moderately long, with 40 to 80 spores per chain. The single spores were oval or cylindrical with diameters of 0.5 to 0.7 \u0026micro;m and lengths of 1.1 to 1.3 \u0026micro;m and have rough surfaces.\u003c/p\u003e\n \u003cp\u003eWhile keeping the conditions of the basal medium otherwise unchanged, different nitrogen sources and carbon sources were added to observe the growth of DF3-3 with different nitrogen sources. The results are shown in Table \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e.\u003c/p\u003e\n \u003cdiv class=\"gridtable\"\u003e\u0026nbsp;\u0026nbsp;\u003ctable border=\"1\" id=\"Tab1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eUtilization characteristics of the nitrogen source and carbon source of DF3-3.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eTrait\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eResult\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eTrait\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eResult\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eTrait\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eResult\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNitrogen source\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNH\u003csub\u003e4\u003c/sub\u003eCl\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e(NH\u003csub\u003e4\u003c/sub\u003e)\u003csub\u003e2\u003c/sub\u003eSO\u003csub\u003e4\u003c/sub\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAcrylamide\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePotassium nitrate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmmonium tartrate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePeptone\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eCarbon source\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003ctd align=\"left\"\u003e\u0026nbsp;\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGlucose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAlpha-D-methylglucoside\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSodium lactate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMannose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003etrehalose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSodium acetate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMelibiose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eCellobiose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSodium formate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eL-arabinose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eXylose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSodium malate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eStarch\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eRibose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSodium succinate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMelezitose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eInulin\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSodium malonate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eErythritol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSalicin\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSodium tartrate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMaltose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGlycerin\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSodium tyrosine\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSucrose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSodium butyrate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAmylase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003c/div\u003e\n \u003cp\u003e\u003cbr\u003e\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv class=\"Section2\" id=\"Sec4\"\u003e\n \u003ch2\u003eMolecular identification\u003c/h2\u003e\n \u003cp\u003eGenome de novo sequencing was performed on DF3-3 cells using second- and third-generation sequencing methods, namely, Illumina HiSeq+PacBio, and the gene location and sequence information of the samples were obtained through de novo assembly and gene prediction. According to the whole genome sequencing results (Table \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e), strain DF3-3 has a chromosome with a total genome length of 7311713 bp. GeneMarkS predicted and annotated a total of 6929 coding sequences (CDSs), with a G+C content of 72.24%.\u003c/p\u003e\n \u003cdiv class=\"gridtable\"\u003e\u0026nbsp;\u0026nbsp;\u003ctable border=\"1\" id=\"Tab2\" \u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenome-wide characteristics of DF3-3.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\u0026nbsp;\u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003evalue\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGenome Size (bp)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e7311713\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eChrom No.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGC Content (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e72.24\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGene No.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e6929\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGC Content in Gene Region (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e72.52\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGene Average Len(bp)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e927.29\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGene/Genome (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e87.88\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGC Content in Intergenetic Region (%)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e70.17\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003etRNA No.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e66\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003erRNA No.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003c/div\u003e\n \u003cp\u003eAt present, 95% of the average nucleotide identity (ANI) is often used as the standard for species classification and species clustering [\u003cspan class=\"CitationRef\"\u003e29\u003c/span\u003e]. The whole genomes of eight strains with high homology to strain DF3-3 were selected and compared and analysed with DF3-3 using ANI. The results are shown in Figure \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e. The similarity between DF3-3 and \u003cem\u003eStreptomyces thermocarboxydus\u003c/em\u003e reached 98.96%, and it can now be identified as \u003cem\u003eStreptomyces thermocarboxydus\u003c/em\u003e.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv class=\"Section2\" id=\"Sec5\"\u003e\n \u003ch2\u003eBiodegradation of alkali lignin by DF3-3\u003c/h2\u003e\n \u003cp\u003eTo investigate lignin degradation by strain DF3-3, cells were incubated at 30\u0026deg;C in medium with alkali lignin as the carbon source. The growth curve and degradation rate of alkali lignin are shown in Figure \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e. The degree of degradation of alkaline lignin by DF3-3 shows that the degradation rate increased significantly in days 1\u0026ndash;4, and the increase was the largest on the fourth day. After 4\u0026ndash;7 days, degradation continued, but the rate slowed down, and the efficiency for degradation of alkali lignin reached 31% on day 15. The degradation of lignin by microorganisms requires a relatively slow process to reach a significant level. The white-rot fungus \u003cem\u003ePhanerochaete chrysosporium\u003c/em\u003e was used for degradation of lignin, and the efficiency reached approximately 20% on day 15 [\u003cspan class=\"CitationRef\"\u003e30\u003c/span\u003e], so DF3-3 exhibited a better performance. This result is also similar to the degradation results seen with some \u003cem\u003eStreptomyces\u003c/em\u003e strains, such as \u003cem\u003eS. viridosporus\u003c/em\u003e T7A (lignin loss 30.9%) and \u003cem\u003eS. setonii\u003c/em\u003e 75Vi2 (lignin loss 34.1%) [\u003cspan class=\"CitationRef\"\u003e26\u003c/span\u003e, \u003cspan class=\"CitationRef\"\u003e31\u003c/span\u003e].\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv class=\"Section2\" id=\"Sec6\"\u003e\n \u003ch2\u003eAnalysis of lignin-degrading enzymes\u003c/h2\u003e\n \u003cp\u003eLignin molecules are not easily taken passively into the cell; therefore, \u003cem\u003eStreptomyces thermocarboxydus\u003c/em\u003e DF3-3 might produce extracellular enzymes for synergistic degradation. Three major types of enzymes responsible for the degradation of lignin are lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac) [\u003cspan class=\"CitationRef\"\u003e32\u003c/span\u003e]. MnPs oxidize Mn(II) to Mn(III), and Mn(III) oxidizes phenolic compounds and generates phenoxy radicals that in turn undergo a variety of reactions, resulting in depolymerization. In the presence of Mn(II), MnP oxidizes nonphenolic lignin model compounds via peroxidation of unsaturated lipids. LiP is the most effective peroxidase and can oxidize phenolic and nonphenolic compounds, amines, aromatic ethers, and polycyclic aromatics [\u003cspan class=\"CitationRef\"\u003e33\u003c/span\u003e]. Lac is a copper oxidoreductase [\u003cspan class=\"CitationRef\"\u003e34\u003c/span\u003e] that can degrade refractory polyphenols and nonphenolics in lignin, and the expression of its coding genes in bacteria has also been reported [\u003cspan class=\"CitationRef\"\u003e35\u003c/span\u003e]. The activities of these three enzymes from DF3-3 are shown in Figure \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003e. MnP and Lac activity increased constantly during the initial 6 days, with maxima of 1821.66 U/L and 1265.58 U/L seen at day 6, followed by slight decreases from day 7. Lip activity was maintained at a low level, with a maximum of 480.33 U/L on day 4. These results indicated that MnP and Lac play crucial roles during the entire process of alkaline lignin degradation by DF3-3.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv class=\"Section2\" id=\"Sec7\"\u003e\n \u003ch2\u003eAromatic intermediates identified by GC-MS analysis\u003c/h2\u003e\n \u003cp\u003eUsing ethyl acetate as the solvent for GC-MS determination [\u003cspan class=\"CitationRef\"\u003e36\u003c/span\u003e], the degradation products of alkali lignin produced in incubation with \u003cem\u003eStreptomyces thermocarboxydus\u003c/em\u003e strain DF3-3 were analysed from the first day to the 15th day. In total, 19 degradation intermediate products were identified by GC-MS, including seven different types of compounds, including eight organic acids (butanoic acid (\u003cstrong\u003e4\u003c/strong\u003e), lactic acid (\u003cstrong\u003e8\u003c/strong\u003e), 2-hydroxypropanoic acid (\u003cstrong\u003e9\u003c/strong\u003e), pyrrole-2-carboxylic acid (\u003cstrong\u003e10\u003c/strong\u003e), 3-phenylpyruvic acid (\u003cstrong\u003e12\u003c/strong\u003e), 4-hydroxybenzoic acid (\u003cstrong\u003e13\u003c/strong\u003e), 4-hydroxyphenylpyruvate (14), palmitic acid (\u003cstrong\u003e16\u003c/strong\u003e), stearic acid (\u003cstrong\u003e17\u003c/strong\u003e)), three esters (acetic acid butyl ester (\u003cstrong\u003e1\u003c/strong\u003e), dibutyl phthalate (\u003cstrong\u003e15\u003c/strong\u003e), bis(2-ethylhexyl) phthalate (\u003cstrong\u003e19\u003c/strong\u003e)), two ethers (1-(1-ethoxy)propane (\u003cstrong\u003e2\u003c/strong\u003e) and 1-(1-propoxyethoxy)propane (\u003cstrong\u003e6\u003c/strong\u003e)), two alcohols (2-ethoxyethanol (\u003cstrong\u003e5\u003c/strong\u003e) and ethylene glycol (\u003cstrong\u003e7\u003c/strong\u003e)), one alkane (m-xylene (\u003cstrong\u003e2\u003c/strong\u003e)), and 1-(1-propylene (6-di-butylphenol phenol (2,2\u003cstrong\u003e-ethylethylenes(11-methyl\u003c/strong\u003e). These 19 low molecular weight products are related to lignin metabolism, and their serial numbers, name, and retention times are shown in Table \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e. \u0026nbsp;\u003c/p\u003e\n \u003ctable border=\"1\" id=\"Tab3\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eCompounds identified from degradation of alkali lignin by DF3-3.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\u0026nbsp;\u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eRetention time\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eCompounds\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eMolecular formula\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eControl group\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e1\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e4.530\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAcetic acid, butyl ester\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e6\u003c/sub\u003eH\u003csub\u003e12\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e2\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e4.651\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1-(1-Ethoxyethoxy) propane\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e7\u003c/sub\u003eH\u003csub\u003e16\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e3\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e5.690\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eM-Xylene\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e8\u003c/sub\u003eH\u003csub\u003e10\u003c/sub\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e4\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e6.055\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eButyric acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e4\u003c/sub\u003eH\u003csub\u003e8\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e5\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e6.251\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2-Ethoxyethanol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e4\u003c/sub\u003eH\u003csub\u003e10\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e6\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e6.642\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1-(1-Propoxyethoxy) propane\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e8\u003c/sub\u003eH\u003csub\u003e18\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e7\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e8.793\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eEthylene glycol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e2\u003c/sub\u003eH\u003csub\u003e6\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e8\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e11.058\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLactic acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e3\u003c/sub\u003eH\u003csub\u003e6\u003c/sub\u003eO\u003csub\u003e3\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e9\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e13.038\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2-Hydroxybutyric acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e4\u003c/sub\u003eH\u003csub\u003e8\u003c/sub\u003eO\u003csub\u003e3\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e10\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e19.375\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePyrrole-2-carboxylic acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e5\u003c/sub\u003eH\u003csub\u003e5\u003c/sub\u003eNO\u003csub\u003e2\u003c/sub\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e11\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e23.225\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2,4-Di-tert-butylphenol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e14\u003c/sub\u003eH\u003csub\u003e22\u003c/sub\u003eO\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e12\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e25.121\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3-Phenylpyruvic acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e9\u003c/sub\u003eH\u003csub\u003e8\u003c/sub\u003eO\u003csub\u003e3\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e13\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e25.996\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-Hydroxybenzoic acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e7\u003c/sub\u003eH\u003csub\u003e6\u003c/sub\u003eO\u003csub\u003e3\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e14\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e32.028\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-Hydroxyphenylpyruvate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e9\u003c/sub\u003eH\u003csub\u003e8\u003c/sub\u003eO\u003csub\u003e4\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e15\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e32.970\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDibutyl phthalate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e16\u003c/sub\u003eH\u003csub\u003e22\u003c/sub\u003eO\u003csub\u003e4\u003c/sub\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e16\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e34.543\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePalmitic acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e16\u003c/sub\u003eH\u003csub\u003e32\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e17\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e38.084\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eStearic acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e18\u003c/sub\u003eH\u003csub\u003e36\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e+\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e18\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e41.008\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2,2\u0026apos;-Methylenebis(6-tert-butyl-4-methyl-phenol)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e23\u003c/sub\u003eH\u003csub\u003e32\u003c/sub\u003eO\u003csub\u003e2\u003c/sub\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cstrong\u003e19\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e43.033\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eBis(2-ethylhexyl) phthalate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eC\u003csub\u003e24\u003c/sub\u003eH\u003csub\u003e38\u003c/sub\u003eO\u003csub\u003e4\u003c/sub\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u003cbr\u003e\u003c/p\u003e\n \u003cp\u003e\u0026ldquo;+\u0026rdquo; indicates that the product was detected in the uninoculated control group, \u0026ldquo;-\u0026ldquo; indicates that the product was not detected in the uninoculated control group.\u003c/p\u003e\n \u003cp\u003eThe variations in the peak areas for products \u003cstrong\u003e3\u003c/strong\u003e, \u003cstrong\u003e8\u003c/strong\u003e, \u003cstrong\u003e10\u003c/strong\u003e, \u003cstrong\u003e11\u003c/strong\u003e, \u003cstrong\u003e12\u003c/strong\u003e, \u003cstrong\u003e13\u003c/strong\u003e, \u003cstrong\u003e14\u003c/strong\u003e, \u003cstrong\u003e15\u003c/strong\u003e, \u003cstrong\u003e18\u003c/strong\u003e, and \u003cstrong\u003e19\u003c/strong\u003e were plotted using the peak areas and culture times (days) as the ordinate and abscissa, respectively, and the result is shown in Figure \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003e. The peak areas for products \u003cstrong\u003e12\u003c/strong\u003e, \u003cstrong\u003e15\u003c/strong\u003e, and \u003cstrong\u003e18\u003c/strong\u003e varied greatly; in comparison, the peak areas for products \u003cstrong\u003e3\u003c/strong\u003e, \u003cstrong\u003e8\u003c/strong\u003e, \u003cstrong\u003e10\u003c/strong\u003e, \u003cstrong\u003e11\u003c/strong\u003e, \u003cstrong\u003e13\u003c/strong\u003e, \u003cstrong\u003e14\u003c/strong\u003e, and \u003cstrong\u003e19\u003c/strong\u003e exhibited small changes. The content of product \u003cstrong\u003e12\u003c/strong\u003e gradually increased within 1\u0026ndash;4 days after culture, reached a maximum on the 4th day, and then decreased to a minimum on the 6th day. The content of product \u003cstrong\u003e15\u003c/strong\u003e quickly increased to a high value on the first day of culture and then gradually decreased to the lowest value until the 7th day. The content of product \u003cstrong\u003e18\u003c/strong\u003e increased to the first high value on the 1st day after culture, dropped to the lowest point on the 3rd day, then rose to another highest point on the 4th day, and finally decreased to the lowest value. These data indicate that the contents of \u003cstrong\u003e12\u003c/strong\u003e, \u003cstrong\u003e15\u003c/strong\u003e, and \u003cstrong\u003e18\u003c/strong\u003e underwent two cycles in the first 8 days of culture.\u003c/p\u003e\n \u003cp\u003eThe process of lignin degradation can be divided into two main parts. First, through the rupture of aromatic ether bonds and carbon-carbon bonds, lignin polymers are depolymerized to form various oligomers. Then, these depolymerized aromatic organic compounds form other small molecular benzene compounds [\u003cspan class=\"CitationRef\"\u003e37\u003c/span\u003e]. Here, m-xylene (\u003cstrong\u003e3\u003c/strong\u003e), 2,4-di-tert-butylphenol (\u003cstrong\u003e11\u003c/strong\u003e), 3-phenylpyruvic acid (\u003cstrong\u003e12\u003c/strong\u003e), 4-hydroxybenzoic acid (\u003cstrong\u003e13\u003c/strong\u003e), 4-hydroxyphenylpyruvate (\u003cstrong\u003e14\u003c/strong\u003e), dibutyl phthalate (\u003cstrong\u003e15\u003c/strong\u003e), 2,2\u0026rsquo;-methylenebis(4-methyl-6-tert-butylphenol), and bis(2-ethylhexyl) phthalate (\u003cstrong\u003e19\u003c/strong\u003e) were detected among the products produced by DF3-3 in degradation of alkaline lignin. Dibutyl phthalate (\u003cstrong\u003e15\u003c/strong\u003e) is a common lignin degradation intermediate [\u003cspan class=\"CitationRef\"\u003e38\u003c/span\u003e\u0026ndash;\u003cspan class=\"CitationRef\"\u003e40\u003c/span\u003e] that can be metabolized to produce phthalic acid, which is further converted into syringyl, protocatechin and other phenolic compounds and then degraded [\u003cspan class=\"CitationRef\"\u003e41\u003c/span\u003e]. According to the metabolic pathway for formation of dibutyl phthalate (\u003cstrong\u003e15\u003c/strong\u003e) and diisooctyl phthalate (\u003cstrong\u003e19\u003c/strong\u003e), product \u003cstrong\u003e19\u003c/strong\u003e is thought to have a similar degradation process.\u003c/p\u003e\n \u003cp\u003eBoth 4-hydroxyphenylpyruvate (\u003cstrong\u003e14\u003c/strong\u003e) and 3-phenylpyruvic acid (\u003cstrong\u003e12\u003c/strong\u003e) were detected among the products of the experimental group, and their aromatic structures were related to alkali lignin. 4-Hydroxybenzoic acid is an important intermediate in many lignin metabolic pathways, including the coumaric acid pathway, gentisic acid pathway, and cinnamic acid pathway [\u003cspan class=\"CitationRef\"\u003e42\u003c/span\u003e]. This indicated that DF3-3 uses the \u0026beta;-ketoadipate metabolic pathway or other similar degradation pathways.\u003c/p\u003e\n \u003cp\u003eIn addition, small molecular compounds such as ethylene glycol (\u003cstrong\u003e7\u003c/strong\u003e) and 2-ethoxyethanol (\u003cstrong\u003e5\u003c/strong\u003e) were detected in the experiment, indicating that DF3-3 degradation of lignin has great potential for energy conversion.\u003c/p\u003e\n\u003c/div\u003e\n\u003cdiv class=\"Section2\" id=\"Sec8\"\u003e\n \u003ch2\u003eAnalyses of the lignin metabolism pathways based on whole genome sequencing and annotation\u003c/h2\u003e\n \u003cdiv class=\"Section3\" id=\"Sec9\"\u003e\n \u003ch2\u003eInitial degradation of lignin into low molecular weight compounds by extracellular phenoloxidases\u003c/h2\u003e\n \u003cp\u003eTo identify the genes related to lignin degradation by DF3-3, the genes encoding known lignin enzymes of other bacterial species were selected as query sequences, and a BLASTp search of the DF3-3 genome was carried out. The results showed that DF3-3 has abundant genes encoding lignin-degrading enzymes, and a total of 107 different genes involved in the degradation process have been annotated (Tables \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003e-\u003cspan class=\"InternalRef\"\u003e11\u003c/span\u003e).\u003c/p\u003e\n \u003cdiv class=\"gridtable\"\u003e\u0026nbsp;\u003ctable border=\"1\" id=\"Tab4\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenes responsible for lignin depolymerization.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene ID\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSize (aa)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene Name\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eEncode protein\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSpecies of reference gene\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eAccession no. (NCBI)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eBLAST identity (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2915\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e2288\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecopA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecarbonate dehydratase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eActinospica acidiphila\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_058917537.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e96.19\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5998\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e2267\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecopA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecarbonate dehydratase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_028959238.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.74\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 3898\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e2225\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ekatG\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecatalase-peroxidase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. Akac8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_136237873.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.87\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 3899\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e380\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efur\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003etranscriptional repressor\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_028958816.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.21\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0904\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1400\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eYhjG\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epentachlorophenol monooxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 4F\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eALV51870.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e95.49\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 1050\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e533\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eahpD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ealkyl hydroperoxide reductase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eActinospica acidiphila\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_163089316.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.44\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 6181\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1415\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eglcD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eFAD-linked oxidase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eActinospica acidiphila\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNEC50278.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.73\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5348\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e716\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eyfiH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003elaccase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces griseorubens\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGGQ64023.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e96.64\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4491\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e197\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003emulticopper oxidase domain-containing protein\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eunclassified \u003cem\u003eStreptomyces\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_106959434.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.46\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2609\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e989\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003emulticopper oxidase domain-containing protein\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_161108161.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.39\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2857\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e983\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePhenoxybenzoate dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces tuirus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_190903372.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e88.07\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5116\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1529\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ealdH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ealdehyde dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMXQ60577.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.61\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 1234\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1451\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ekatE\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecatalase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_028959332.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.79\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 3983\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1655\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ekatE\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecatalase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210638384.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.09\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 3220\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e2276\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ekatE\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecatalase HPII\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_161108660.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.74\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 3744\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e959\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePimeloyl-ACP methyl ester carboxylesterase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. di188\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSCD58877.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e88.43\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 6937\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1277\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eDye-decolorizing peroxidase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces pharetrae\u003c/em\u003e CZA14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOSZ61955.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e83.61\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003c/div\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003ctable border=\"1\" id=\"Tab5\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 5\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenes responsible for the \u0026beta;-ketoadipate pathway and peripheral reactions.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene ID\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSize (aa)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene Name\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eEncode protein\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSpecies of reference gene\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eAccession no. (NCBI)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eBLAST identity (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 3935\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1001\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eVanillate O-demethylase oxygenase subuni\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. SID4956\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_161232727.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.40\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2826\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e773\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ehpaI\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-hydroxy-2-oxovalerate aldolase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMXQ61669.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.61\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0228\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e335\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ephenylpropionate dioxygenase-like ring-hydroxylating dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces paradoxus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMBB6077390.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e94.59\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0557\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e599\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eubiX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003earomatic acid decarboxylase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 4F\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eALV54514.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.99\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0021\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e377\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epcaC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-carboxymuconolactone decarboxylase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. ok210\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_093930409.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.40\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0859\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e506\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecarboxymuconolactone decarboxylase family protein\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210634556.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.40\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2323\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1199\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epcaL\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-carboxymuconolactone decarboxylase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. Akac8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_136239018.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.75\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2838\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1121\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epcaL\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3-oxoadipate enol-lactonase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. SID4956\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_161232455.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.73\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2839\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1331\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epcaB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3-carboxy-cis, cis-muconate cycloisomerase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_028959090.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.55\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2840\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e605\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epcaG\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eprotocatechuate 3,4-dioxygenase subunit alpha\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210638048.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.50\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2841\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e773\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epcaH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eprotocatechuate 3,4-dioxygenase subunit beta\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210638047.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.22\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2842\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1208\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u0026beta;-ketoadipyl CoA thiolase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. B9173\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eOQR62711.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e88.25\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2831\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1364\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epcaK\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-hydroxybenzoate transporter PcaK\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210638055.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.02\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2847\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1439\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epcaK\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-hydroxybenzoate transporter PcaK\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. Akac8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_136238348.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.79\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2852\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e734\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epcaR\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePca regulon regulatory protein\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGHE61509.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.13\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2848\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1013\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ehcaD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eTerephthalate 1,2-dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGHE61489.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.63\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4139\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1148\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ehcaD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ehypothetical protein\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210637914.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.43\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5175\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e317\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ehcaC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin subunit\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. di50b\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSCD40618.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.14\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5716\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1265\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ehcaD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epyridine nucleotide-disulfide oxidoreductase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 4F\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eALV50055.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e96.67\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5542\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1025\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces afghaniensis\u003c/em\u003e 772\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eEPJ42281.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e82.27\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4140\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e923\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4,5-dihydroxyphthalate decarboxylase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 3212.3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eREE57871.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e84.69\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4458\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1220\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epobA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-hydroxybenzoate 3-monooxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_161108189.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.01\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 6344\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1175\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epobA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-hydroxybenzoate 3-monooxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_161107724.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.49\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 6436\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1517\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ecyclohexanone monooxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 4F\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eALV51359.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.03\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 6471\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e518\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epat\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ephosphinothricin N-acetyltransferase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces werraensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGHE99025.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e94.19\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4600\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1322\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-methylmuconolactone transporter\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces afghaniensis\u003c/em\u003e 772\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eEPJ35848.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e87.02\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u003cbr\u003e\u003c/p\u003e\n \u003cp\u003e\u003cbr\u003e\u003c/p\u003e\n \u003ctable border=\"1\" id=\"Tab9\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 6\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenes responsible for gentisate pathways.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene ID\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSize (aa)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene Name\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eEncode protein\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSpecies of reference gene\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eAccession no. (NCBI)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eBLAST identity (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 1961\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e2366\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ebifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 4F\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eALV52714.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.07\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0811\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1613\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egabD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003esuccinate-semialdehyde dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_028960221.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.81\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4361\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1388\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egabD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eNADP-dependent succinic semialdehyde dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGHE69900.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.70\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 3797\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1187\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efumarylacetoacetate hydrolase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. SID8376\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_205526335.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.75\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2855\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1286\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003earomatic ring-hydroxylating dioxygenase subunit alpha\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_137208924.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.53\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4131\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1280\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePhthalate 4,5-dioxygenase oxygenase subunit\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. MBT84\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMBW8706675.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e70.79\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4137\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e620\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egentisate 1,2-dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eRobiginitomaculum\u003c/em\u003e sp.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ePHR56577.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e81.03\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4928\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1085\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efrmA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ealcohol dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGHE58756.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.23\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5219\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e689\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003emaleylpyruvate isomerase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_161107348.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.13\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u003cbr\u003e\u003c/p\u003e\n \u003ctable border=\"1\" id=\"Tab10\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 7\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenes responsible for pathways for anthranilate.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene ID\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSize (aa)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene Name\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eEncode protein\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSpecies of reference gene\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eAccession no. (NCBI)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eBLAST identity (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 1963\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1610\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eabmG\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e2-aminobenzoate-CoA ligase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 4F\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eALV52716.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e94.03\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 1964\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1128\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eacyl-CoA dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_161107119.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.47\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0037\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e638\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003epabA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eaminodeoxychorismate/anthranilate synthase component II\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210635465.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.53\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5387\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1880\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ephzE\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eanthranilate synthase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_028960786.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.52\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0262\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1202\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ekynU\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eL-kynurenine hydrolase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_028959521.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.25\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0261\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e830\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eTDO2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003etryptophan 2,3-dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210635572.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.28\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 4644\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1697\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eTryptophan 2-monooxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. di50b\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSCD87347.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.35\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0499\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1217\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAromatic-amino-acid aminotransferase 1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_064743320.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.49\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2090\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e873\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eindole-3-glycerol phosphate synthase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. I4 (2020)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_199204736.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e96.82\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5302\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e806\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003etrpC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eindole-3-glycerol phosphate synthase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. I4 (2020)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_199207289.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.63\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5306\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1493\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003etrpE\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eanthranilate synthase component I\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_161107330.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.8\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003ctable border=\"1\" id=\"Tab8\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 8\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenes responsible for pathways for resorcinol.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr \u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eGene ID\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eSize (aa)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eGene Name\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eEncode protein\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eSpecies of reference gene\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eAccession no. (NCBI)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eBLAST identity (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0128\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e971\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eLysR family transcriptional regulator\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_078611393.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.69\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 2842\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1208\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u0026beta;-ketoadipyl CoA thiolase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. B9173\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eOQR62711.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e88.25\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 1964\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1128\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eacyl-CoA dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_161107119.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.47\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 2768\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1091\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003earyl-alcohol dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. di50b\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eSCD35921.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e93.66\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 2849\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e962\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epdxA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eTerephthalate dihydrodiol dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. McG7\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_215047915.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e98.75\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 2850\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e470\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eandAd\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eterephthalate 1,2-dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eMXQ61646.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e100.00\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 2851\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1283\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eandAc\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eTerephthalate 1,2-dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eRhodococcus pyridinivorans\u003c/em\u003e AK37\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eEHK83592.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e83.05\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 3600\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1502\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e2-polyprenyl-6-methoxyphenol hydroxylase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. di50b\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eSCD47389.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e85.06\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 5989\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1268\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003edimethylaniline monooxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 4F\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eALV54407.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e96.91\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 3045\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e383\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eextradiol dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 4F\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eALV53653.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e93.70\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 4526\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e476\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eputative dehydrochlorinase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eAUR34009.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e81.65\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 5542\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1025\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eTrans-1,2-dihydrobenzene-1,2-diol dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces afghaniensis\u003c/em\u003e 772\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eEPJ42281.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e82.27\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 6472\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e785\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eextradiol ring-cleavage dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces griseorubens\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eKEG41654.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e98.85\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u003c/p\u003e\n \n \u003ctable border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 9\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenes responsible for catabolic pathways for homogentisic.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr \u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eGene ID\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eSize (aa)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eGene Name\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eEncode protein\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eSpecies of reference gene\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eAccession no. (NCBI)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eBLAST identity (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 4937\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1361\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ehmgA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ehomogentisate 1,2-dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_161108369.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e99.78\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 1961\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e2366\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ebifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. 4F\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eALV52714.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e97.07\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0499\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1217\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eAromatic-amino-acid aminotransferase 1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_064743320.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e99.49\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 6956\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1079\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ehisC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ePutative phenylalanine aminotransferase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces werraensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eGHF12148.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e96.93\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0811\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1613\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egabD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003esuccinate-semialdehyde dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. UNC401CLCol\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_028960221.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e99.81\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 4361\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1388\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egabD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eNADP-dependent succinic semialdehyde dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eGHE69900.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e98.70\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0636\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1214\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003efahA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eFumarylacetoacetate hydrolase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. SID4956\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_161232839.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e99.01\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 3797\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1187\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003efumarylacetoacetate hydrolase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. SID8376\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_205526335.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e99.75\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 2443\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e305\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephhB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e4a-hydroxytetrahydrobiopterin dehydratase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces griseorubens\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_033273716.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e98.02\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 4811\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e2576\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epheT\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylalanine--tRNA ligase subunit beta\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_210636334.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e99.77\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 4812\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1121\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epheS\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylalanine--tRNA ligase subunit alpha\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eGHE73990.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e100\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 3632\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1814\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ehppD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e4-hydroxyphenylpyruvate dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eGHE74791.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e97.35\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 3633\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e876\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003earoE\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eshikimate dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. FxanaD5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_019522987.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e99.66\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 6183\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1145\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ehppD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e4-hydroxyphenylpyruvate dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eActinospica acidiphila\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_163089359.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e98.69\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 4928\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1085\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003efrmA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ealcohol dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eGHE58756.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e97.23\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 5219\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e689\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003emaleylpyruvate isomerase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_161107348.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e99.13\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u003c/p\u003e\n \u003ctable border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 10\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenes responsible for pathways for phenylacetate-CoA.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr \u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eGene ID\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eSize (aa)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eGene Name\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eEncode protein\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eSpecies of reference gene\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eAccession no. (NCBI)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\" \u003e\n \u003cp\u003eBLAST identity (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0050\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1061\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaE\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylacetic acid degradation protein\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eGHE31167.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.15\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0051\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e539\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylacetate-CoA oxygenase subunit\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eGHE31162.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e97.77\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0052\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e737\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaC\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylacetate-CoA oxygenase subunit\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_210635474.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e98.78\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0053\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e287\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylacetate-CoA oxygenase subunit PaaB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces griseoruber\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_055636201.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e98.95\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0054\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1016\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylacetate-CoA oxygenase subunit PaaA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. SID4956\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_161232185.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.41\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0058\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1691\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ePaaN\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylacetic acid degradation protein\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. Akac8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_136238706.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.82\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 0059\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1514\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e3-hydroxyacyl-CoA dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. SID4956\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_161233084.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e100.00\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 1159\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e803\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaG\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e1,2-epoxyphenylacetyl-CoA isomerase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eGHE51256.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e98.13\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 1381\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e848\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e3-hydroxybutyryl-CoA dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. F-7\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_093768152.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.65\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 2386\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1805\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e3-hydroxybutyryl-CoA dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. SMS_SU21\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_102640749.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e97.17\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 2736\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e764\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaF\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e3-hydroxypropionyl-CoA dehydratase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_210638121.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.61\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 4099\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1523\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaK\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylacetate-CoA ligase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_210637941.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.77\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 4804\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e860\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e3-hydroxybutyryl-CoA dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. I4 (2020)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_199207038.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.30\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 6544\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e734\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003epaaF\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eenoyl-CoA hydratase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eGHE27114.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e98.77\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 4828\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e1376\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ePad\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ePhenylacetaldehyde dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. DI166\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eSBT93309.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e87.53\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 1454\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e767\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eenoyl-CoA hydratase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. Akac8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_136239245.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e99.61\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 1960\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e827\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eenoyl-CoA hydratase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces griseorubens\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eWP_033274100.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e97.82\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr \u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003egene 1962\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e846\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ePaaX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003ephenylacetic acid degradation operon negative regulatory protein\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003e\u003cem\u003eStreptomyces aureorectus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\" \u003e\n \u003cp\u003eMBA8975440.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\" \u003e\n \u003cp\u003e90.71\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u003c/p\u003e\n \n \u003ctable border=\"1\" id=\"Tab11\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 11\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenes responsible for catabolic pathways for 2,3-dihydroxyphenylpropionate.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene ID\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSize (aa)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGene Name\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eEncode protein\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eSpecies of reference gene\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eAccession no. (NCBI)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eBLAST identity (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 3746\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1028\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3-hydroxycinnamic acid hydroxylase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces albogriseolus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGHB97425.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e91.81\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 1753\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1640\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003emhpA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3-(3-hydroxy-phenyl) propionate acid hydroxylase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. di50b\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eSCE12787.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e96.15\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2825\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1613\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003emhpA\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3-(3-hydroxy-phenyl) propionate hydroxylase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces griseorubens\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGGQ79721.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.77\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2828\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e794\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003emhpD\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003efumarylacetoacetate hydrolase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210638174.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.62\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2830\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e935\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003emhpB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3-carboxyethylcatechol 2,3-dioxygenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210638056.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.04\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 2826\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e773\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ehpaI\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4-hydroxy-2-oxovalerate aldolase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. XHT-2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eMXQ61669.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.61\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 5487\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e359\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ehpaF\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eisomerase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces cellulosae\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGHE29375.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.48\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0171\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e431\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ealdehyde dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces werraensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eGHF03416.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e88.46\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003egene 0388\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1460\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e-\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ealdehyde dehydrogenase\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eStreptomyces\u003c/em\u003e sp. GESEQ-13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eWP_210635659.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.18\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003cp\u003e\u003c/p\u003e\n \u003cp\u003eIn the initial stages of lignin degradation, extracellular enzymes are responsible for depolymerization of lignin. Degradation enzyme systems involved in lignin degradation include the lignin oxidase system, hydrogen peroxide production enzyme system and other enzyme systems. In this study, multipl lignin depolymerization-related genes were found in the genome of DF3-3 (Table \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003e), including genes encoding multicopper oxidase (gene 5348, gene 4491, gene 2609), alcohol dehydrogenase (gene 2768), alcohol dioxygenase (gene 3045), aldehyde dehydrogenase (aldH), pentachlorophenol monooxygenase (gene 0904) and terephthalate dihydrodiol dehydrogenase (pdxA).\u003c/p\u003e\n \u003c/div\u003e\n \u003cdiv class=\"Section3\" id=\"Sec10\"\u003e\n \u003ch2\u003eCatabolism pathways for lignin components\u003c/h2\u003e\n \u003cp\u003eMany low molecular weight compounds are produced by initial depolymerization of lignin. Based on GC-MS and genome analysis, 5 metabolic pathways of lignin-based derivatives were predicted: \u0026beta;-ketoadipate pathway and peripheral reactions; gentisate pathway; anthranilate pathway; homogentisic pathway; and catabolic pathway for resorcinol (shown in Figure \u003cspan class=\"InternalRef\"\u003e7\u003c/span\u003e). Based on genome data alone, we predicted two other pathways: the phenylacetate-CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway ( Figure \u003cspan class=\"InternalRef\"\u003e8\u003c/span\u003e).\u003c/p\u003e\n \u003ch2\u003e\u0026beta;-ketoadipate pathway and peripheral reactions\u003c/h2\u003e\n \u003cp\u003eThe \u0026beta;-ketoadipate pathway is an important aromatic metabolic pathway for many microorganisms. There are 26 genes involved in the degradation process of lignin in DF3-3 (Table \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003e), and they are scattered throughout the genome of DF3-3 (Figure \u003cspan class=\"InternalRef\"\u003e9\u003c/span\u003e). The key genes of the protocatechuic acid 3,4-dioxygenase (pcaG, pcaH) gene appear in the whole genome of DF3-3 and can be imagined to metabolize lignin intermediates through the \u0026beta;-ketoadipate pathway branched by protocatechin. There are two 4-hydroxycinnamic acid dioxygenases (hcaC, hcaD) in DF3-3, and 4-hydroxycinnamic acid can initially be degraded to generate 4-hydroxycinnamic acid coenzyme A and further converted into p-hydroxybenzoic acid, which was found among the degradation products of alkaline lignin produced by DF3-3. 3-Phenylpyruvic acid and 4-hydroxyphenylpyruvate were also detected as metabolites of DF3-3. We speculate that they can also be degraded by the hcaC gene. Then, 4-hydroxyphenylpyruvate undergoes a series of reactions to produce p-hydroxybenzoic acid. The pcaG and pcaH genes cause benzene epoxidation to enable a ring-opening reaction generating cis-hexadienedioic acid; this further generates \u0026beta;-ketoadipate, which is degraded and finally enters the tricarboxylic acid cycle. Unlike 4-hydroxyphenylpyruvate, 3-phenylpyruvic acid may not be converted only into 4-hydroxyphenylpyruvate by hcaC but could also be converted into benzoic acid and catechol, and then a ring-opening reaction takes place to enter the \u0026beta;-ketoadipate pathway or generate 4-hydroxy-2-oxovalerate and further degradation.\u003c/p\u003e\n \u003ch2\u003eThe gentisate pathway\u003c/h2\u003e\n \u003cp\u003eThe gentisate pathway usually starts from the degradation of salicylic acid. Ethyl salicylate is a precursor in the production of salicylic acid. The pathway for degradation of phthalic acid by some fungi has been explained, in which dibutyl phthalate or diisooctyl phthalate is converted to ethyl salicylate [\u003cspan class=\"CitationRef\"\u003e43\u003c/span\u003e]. Some aromatic oxygenases may play important roles in this process. In the DF3-3 genome, the genes encoding salicylic acid-5-hydroxylase (gene 1961) and gentisic acid 1,2-dioxygenase (gene 4137) were identified (Table \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003e). Gentianic acid 1,2-dioxygenase oxygenates the benzene ring of gentisic acid to produce maleylpyruvate, which is then further metabolized by maleate pyruvate isomerase (gene 5219). Dibutyl phthalate and diisooctyl phthalate were detected among the metabolites of DF3-3. Phthalate dioxygenase oxygenase (gene 4131) detected in the DF3-3 genome gene also indicated that it may appear as an intermediate product of the salicylic acid metabolic pathway.\u003c/p\u003e\n \u003ch2\u003eThe anthranilate pathway\u003c/h2\u003e\n \u003cp\u003eThe specific mechanism of the anthranilic acid pathway in bacteria has not been fully elucidated [\u003cspan class=\"CitationRef\"\u003e42\u003c/span\u003e, \u003cspan class=\"CitationRef\"\u003e44\u003c/span\u003e]. A 2-aminobenzoate-CoA ligase (abmG) and an L-kynurenine hydrolase (kynU) gene were identified in DF3-3, and a tryptophan 2,3-dioxygenase (TDO2) gene was also observed (Table \u003cspan class=\"InternalRef\"\u003e7\u003c/span\u003e). It is speculated that the anthranilic acid pathway of DF3-3 generates formyl kynurenine through the degradation of tryptophan, which is further converted to kynurenine and then generates anthranilic acid under the action of kynU. In addition, tryptophan may undergo a series of redox reactions at its side chain to produce indole derivatives. The pyrrole-2-carboxylic acid detected among the metabolites of DF3-3 can also be degraded by the anthranilate synthase (phzE) gene and abmG gene through a similar pathway.\u003c/p\u003e\n \u003ch2\u003eCatabolic pathway for resorcinol\u003c/h2\u003e\n \u003cp\u003eDue to the existence of the metabolite m-xylene and related genes (Table \u003cspan class=\"InternalRef\"\u003e8\u003c/span\u003e), it is speculated that DF3-3 has related metabolic pathways. The resorcinol pathways for other strains involve the participation of oxidoreductases. The functions of some of these genes, such as aromatic compound monooxygenase (gene 3600)-coding genes, have not been fully clarified. Aryl-alcohol dehydrogenase and extradiol dioxygenase may effect the degradation of aromatic phenols. It is speculated that the metabolism of m-xylene by DF3-3 may take place through oxidation of methyl groups to produce resorcinol. Then, resorcinol undergoes further oxygenation on the branch chain and ring-opening oxidation with the action of oxygenases (Figure \u003cspan class=\"InternalRef\"\u003e7\u003c/span\u003e).\u003c/p\u003e\n \u003ch2\u003eHomogentisic pathway\u003c/h2\u003e\n \u003cp\u003eThe homogentisic pathway is the central pathway for catabolism of phenylalanine and tyrosine. Genomic analysis of DF3-3 shows that phenylalanine is converted to tyrosine by phenylalanine hydroxylase and auxiliary methanolamine dehydratase (PhhB), and tyrosine aminotransferase (hisC) is converted to tyrosine 4-hydroxyphenylpyruvate, which is further converted into homogentisate by 4-hydroxyphenylpyruvate dioxygenase (hppD) and degraded by the action of homogentisate 1,2-dioxygenase (hmgA) to produce maleacetoacetate (Figure \u003cspan class=\"InternalRef\"\u003e9\u003c/span\u003e). A fumarylacetoacetate hydrolase (fahA) gene was identified in the DF3-3 genome (Table \u003cspan class=\"InternalRef\"\u003e9\u003c/span\u003e), indicating that hydrolysis of maleacetoacetate occurs through the degradation of fumarate acetoacetate. The genes involved in the homogentisate pathway are scattered throughout the genome, and the processes are carried out with the joint action of hmgA and other related genes. This non-linkage also appears in other bacteria [\u003cspan class=\"CitationRef\"\u003e44\u003c/span\u003e]. 4-Hydroxyphenylpyruvate, as the precursor of homogentisic acid, was observed among the products detected by GC-MS, and two hppD genes observed in the genome are related to the 4-hydroxy phenylpyruvate dioxygenase in \u003cem\u003eStreptomyces cellulosae\u003c/em\u003e and \u003cem\u003eActinospica acidiphila\u003c/em\u003e with high similarities (97.35% and 98.69%).\u003c/p\u003e\n \u003cp\u003eIn addition to the above metabolic pathways, the following two possible lignin degradation pathways were found for DF3-3 through a gene search. A relatively complete set of coding genes is present in the genome to form the pathway, but the related metabolites were not observed in this study.\u003c/p\u003e\n \u003ch2\u003ePhenylacetate-CoA pathway\u003c/h2\u003e\n \u003cp\u003ePhenylacetate can be derived from lignin-related phenylpropane units [\u003cspan class=\"CitationRef\"\u003e45\u003c/span\u003e], and the general pathway for aerobic metabolism has just been discovered and studied with some bacteria [\u003cspan class=\"CitationRef\"\u003e46\u003c/span\u003e, \u003cspan class=\"CitationRef\"\u003e47\u003c/span\u003e]. There were at least 15 genes in DF3-3 involved in this process (Table \u003cspan class=\"InternalRef\"\u003e10\u003c/span\u003e). The phenylacetate coenzyme A oxygenase gene is organized into clusters (paaABCDE) and exists in the DF3-3 genome (Figure \u003cspan class=\"InternalRef\"\u003e9\u003c/span\u003e), downstream from which there are a phenylacetic acid degradation protein (paaN) and a 3-hydroxyacyl-CoA dehydrogenase (paaH) encoding gene; a 1,2-epoxyphenylacetyl-coenzyme A isomerase (paaG) gene exists a little further downstream, and the isomerase it encodes can convert 3-hydroxypropionyl-CoA into 1,2-epoxyphenylacetyl-CoA. At the same time, 3-hydroxypropionyl-CoA can also be further degraded by 3-hydroxypropionyl-CoA dehydrogenase (paaH) and 3-hydroxypropionyl-CoA dehydrogenase (paaF) and finally enter the tricarboxylic acid cycle.\u003c/p\u003e\n \u003ch2\u003e2,3-Dihydroxyphenylpropionic acid pathway\u003c/h2\u003e\n \u003cp\u003eThe 2,3-dihydroxyphenylpropionic acid pathway-related mhpABD gene cluster was observed in the DF3-3 genome (Table \u003cspan class=\"InternalRef\"\u003e11\u003c/span\u003e), including encoding for 3-(3-hydroxy-phenyl) propionate hydroxylase (mhpA), 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (mhpB) and fumarate acetoacetate hydrolase (mhpD) genes, which are located upstream of the 4-hydroxy-2-oxovalerate aldolase (hpaI) gene (Figure \u003cspan class=\"InternalRef\"\u003e9\u003c/span\u003e). DF3-3 lacks the mhpE and mhpF genes, and the generated 4-hydroxy-2-oxovalerate is decomposed by the aldolase encoded by the hpaI gene. It was also determined that other aldehyde dehydrogenases may effect the degradation of acetaldehyde and generate pyruvate and acetyl-CoA to enter the tricarboxylic acid cycle for metabolism.\u003c/p\u003e\n \u003c/div\u003e\n\u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eBiofuel production by biodegradable lignocellulose has far-reaching prospects [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. Research on the degradation system of lignocellulose-degrading microorganisms has great significance to its practical application and development. However, few microorganisms, only white rot fungi, have been reported that can degrade lignin and cellulose at the same time [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. In the actual degradation of biomass materials, the degradation of lignin, cellulose and hemicellulose often occurs simultaneously and is interrelated. In our research, we found that DF3-3 has good degradation performance on both lignin and cellulose. More experiments and new approaches are needed in future work to better develop and apply DF3-3.\u003c/p\u003e \u003cp\u003eThe enzymology for bacterial lignin degradation has been well-studied in recent years, and some bacterial specific enzymes for lignin degradation have been reported. Like Cα-dehydrogenase (LigD) [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e], glutathione-dependent β-etherase enzymes (LigE, F, G) have been identified from \u003cem\u003eSphingomonas paucimobilis\u003c/em\u003e SYK-6 [\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e], a demethylase enzyme (LigX) from \u003cem\u003ePseudomonas paucimobilis\u003c/em\u003e [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e], and DyP-type peroxidases from \u003cem\u003eRhodococcus jostii\u003c/em\u003e RHA1 [\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e]. Recent reports have shown multicopper oxidases that demonstrate laccase activities [\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e, \u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e]. In our study, we found that DF3-3 had Lac, Mnp and Lip activities. Genome research identified three multicopper oxidase coding genes (gene 5348, gene 4491, gene 2609), and gene 5348 has high similarity (96.64%) to the laccase structural protein gene of \u003cem\u003eStreptomyces griseorubens\u003c/em\u003e (GGQ64023.1) [\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e], showing that DF3-3 has the ability to encode laccase at the genetic level. No gene encoding manganese peroxidase has been detected, but a catalase/peroxidase gene (gene3898) was found in DF3-3, which was 99.87% similar to KatG from \u003cem\u003eStreptomyces\u003c/em\u003e sp. Akac8 [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. The fur gene (gene3899) encoding a transcription regulator appears downstream, and these were reported as possible manganese peroxidase-encoding genes in \u003cem\u003eStreptomyces reticuli\u003c/em\u003e [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e, \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e], suggesting that DF3-3 can exhibit manganese peroxidase activity. In addition, a gene (gene 6937) encoding a dye decolouring peroxidase was observed. The peroxidase encoded by it has a broad spectrum of substrates, which is also commonly reported in the depolymerization of lignin in some bacteria [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e, \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e, \u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThe hydrogen peroxide-producing enzyme system mainly participates in lignin degradation in the capacity of auxiliary enzymes [\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e]. These enzymes include glyoxal oxidase, aryl alcohol oxidase, quinone reductase and related dehydrogenases [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e]. They produce hydrogen peroxide to support degradation by other peroxidases. The alcohol dehydrogenase (gene 2768), alcohol dioxygenase (gene 3045), and aldehyde dehydrogenase (aldH) annotated in the DF3-3 genome are thought to be involved in the process of lignin degradation. In addition, catalase removes the hydrogen peroxide produced by these reactions quickly enough to prevent oxidative damage to [4Fe-4S]-clusters in proteins and protect the body from toxification [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e, \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e]. The catalase-encoding gene (katE) identified in DF3-3 is thought to be involved in lignin degradation.\u003c/p\u003e \u003cp\u003eAccording to the GC-MS results, 2,4-di-tert-butylphenol and 2,2'-methyl bis(4-methyl-6-tert-butyl phenol) were involved in the metabolic processes of DF3-3. Recent studies have also shown that there is a 2,4-di-tert-butylphenol metabolic pathway for microbial degradation of lignin [\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e]. Considering the resorcinol pathway and its correlative gene, it is speculated that there may be a similar pathway in DF3-3. It may retain the structure of the tert-butyl side face and be metabolized by the meta-cleavage pathway. The formation of 2,2'-methyl bis(4-methyl-6-tert-butyl phenol) may come from the same metabolic intermediate as 2,4-di-tert-butylphenol. However, there are few studies on microbial degradation of this kind of structure at present. As an environmental pollutant, 4-tert-butylphenol can be degraded by several reported bacteria [\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e, \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e]. However, to better understand this purification process, its specific metabolic process and some of the enzymes involved require further study.\u003c/p\u003e \u003cp\u003eThe lignin degradation pathway of actinomycetes was first studied through research on the culture medium and metabolites [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e, \u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e]. As the understanding of molecular biology increased, people began to seek more direct evidence. Masai et al. [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e] first established a relatively complete pathway of lignin degradation and metabolism by means of enzymology and genomics. In \u003cem\u003eSphingomonas paucimobilis\u003c/em\u003e SYK-6, β-aryl ether cleavage catalysis [\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e], the biphenyl ring cleavage pathway [\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e], the ferulate catabolic pathway [\u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e61\u003c/span\u003e], the O-demethylation systems of vanillate and syringate [\u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e62\u003c/span\u003e], the protocatechuate 4,5-cleavage pathway [\u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e63\u003c/span\u003e], and multiple 3-\u003cem\u003eO\u003c/em\u003e-methylagallate catabolic pathways [\u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e64\u003c/span\u003e] were described. Eleven lignin metabolic pathways were found in the genome of \u003cem\u003eCupriavidus necator\u003c/em\u003e, among which the β-ketoadipate pathway also included four branches: catechol, chlorocatechol, methylcatechol and protocatechuate ortho ring-cleavage [\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]. In our study, evidence of a lignin degradation pathway was found in the metabolites and genetics. The products detected by GC-MS are also related to five lignin metabolic pathways. However, some unusual products detected may point to new branches. We speculate that 4-hydroxyphenylpyruvate (\u003cb\u003e14\u003c/b\u003e) and 3-phenylpyruvic acid (\u003cb\u003e12\u003c/b\u003e) may be transformed from phenylalanine and enter the homologous pathway and β-ketoadipate pathway, respectively, for further metabolism. A large number of genes related to the β-ketoadipate pathway have been detected in DF3-3, but there are still some genes involved in the reaction process that have not been compared, and for some genes, the reaction process in which they specifically participate has not been further elucidate. Perhaps there are related reactions in DF3-3 which are different from those in other bacteria. The heterologous expression of these gene fragments is helpful to the establishment and production of efficient engineered bacteria with biological enzymes.\u003c/p\u003e \u003cp\u003eRecent studies have shown that bacterial degradation of lignin has complex growth condition-specific regulation [\u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e65\u003c/span\u003e]. Because of the diversity of structure of lignan compounds, different reactions may occur in the degradation process of different substrate. Based on genome data alone, we predicted two other pathways the phenylacetate-CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway, but did not find the related metabolites by GC-MS. This absence might be related to the substrates. To further verify the degradation process, transcriptome analysis, proteomic analysis and other biological methods are needed to study the enzymes and the genes involved in their degradation pathways to understand the biological function of DF3-3 in the degradation of lignin.\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eBased on the above data and analyses, we isolated a bacterial strain identified as \u003cem\u003eStreptomyces thermocarboxydus\u003c/em\u003e strain DF3-3 from greening litter and concluded that it degraded alkaline lignin, and the degradation efficiency reached 31% within 15 days. In total, 19 alkaline lignin degradation intermediates were identified by GC-MS, and 107 possible lignin-degrading enzyme encoding genes in the DF3-3 genome were annotated; 7 pathways for metabolism of lignin and its intermediates were predicted, including the β-ketoadipate pathway and peripheral reactions; gentisate pathway; anthranilate pathway; catabolic pathway for resorcinol; homogentisic pathway; phenylacetate-CoA pathway; and the 2,3-dihydroxyphenylpropionic acid pathway. Intermediates in the first five metabolic pathway were detected by GC-MS. The degradation products and genomics analyses show that DF3-3 has a relatively complete lignin degradation pathway.\u003c/p\u003e"},{"header":"Methods","content":"\u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eSampling, isolation and screening of bacterial strain\u003c/h2\u003e \u003cp\u003eSamples were collected from greening litter of Beijing University of Agriculture (40.0947\u0026deg; N, 116.3151\u0026deg; E). One gram of sample was placed in a 50-mL sterile centrifuge tube containing 10 mL of sterile distilled water and shaken at 120 rpm overnight. Next, 10\u003csup\u003e\u0026minus;1\u003c/sup\u003e and 10\u003csup\u003e\u0026minus;2\u003c/sup\u003e serial dilutions of each sample suspension were spread as 0.1-mL aliquots on Gause's synthetic medium with the formula (g/L): 0.5 NaCl;1 KNO\u003csub\u003e3\u003c/sub\u003e༛0.5 K\u003csub\u003e2\u003c/sub\u003eHPO\u003csub\u003e4\u003c/sub\u003e\u0026middot;3H\u003csub\u003e2\u003c/sub\u003eO༛0.5 MgSO\u003csub\u003e4\u003c/sub\u003e\u0026middot;7H\u003csub\u003e2\u003c/sub\u003eO༛0.01 FeSO\u003csub\u003e4\u003c/sub\u003e\u0026middot;7H\u003csub\u003e2\u003c/sub\u003eO༛20 soluble starch [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. The plates were incubated at 30\u0026deg;C for one week, and distinct colonies were picked and subcultured for further analysis. Gause\u0026rsquo;s guaiacol medium and Gause\u0026rsquo;s Azure B medium used for lignin degradation screening contained 0.1% guaiacol and 0.1% aniline blue, respectively, added to Gause\u0026rsquo;s medium. Different external nitrogen sources (20 g/L), such as acrylamide and potassium nitrate, and additional carbon sources (1 g/L), such as glucose and mannose, were used to replace soluble starch culture strains in studies of their utilization of nitrogen sources and carbon sources. The culture medium for detecting lignin degradation and enzyme activity was kraft lignin-MSM medium (3 g of kraft lignin L, 2 g of [NH\u003csub\u003e4\u003c/sub\u003e]\u003csub\u003e2\u003c/sub\u003eSO\u003csub\u003e4\u003c/sub\u003e, 1 g of K\u003csub\u003e2\u003c/sub\u003eHPO\u003csub\u003e4\u003c/sub\u003e, 1 g of KH\u003csub\u003e2\u003c/sub\u003ePO\u003csub\u003e4\u003c/sub\u003e, 0.2 g of MgSO\u003csub\u003e4\u003c/sub\u003e, 0.1 g of CaCl\u003csub\u003e2\u003c/sub\u003e, 0.05 g of FeSO\u003csub\u003e4\u003c/sub\u003e, and 0.02 g of MnSO\u003csub\u003e4\u003c/sub\u003e in 1 L distilled water, pH 7.0).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec15\" class=\"Section2\"\u003e \u003ch2\u003eScanning electron microscope observations\u003c/h2\u003e \u003cp\u003eThe shapes of the bacteria were observed by scanning electron microscopy. A cover glass was inserted into the solid medium to cultivate the strain, and the insert was removed after the bacterial body climbed onto the glass slide. The precipitate was washed by adding a phosphate buffer solution (pH 7.2), added to 2.5% glutaraldehyde, fixed at room temperature for 2~4 hours, and then placed in a refrigerator at 4\u0026deg;C overnight. After elution with a 30\u0026ndash;95% ethanol gradient, the material was rinsed with tert-butanol, then 20 \u0026micro;L of tert-butanol was added and the mixture was put into a refrigerator at -20℃ until it froze and solidified. Using critical point drying (HITACHI HCP-2 Critical Point Dryer) and gold sputter coating (Eiko IB-3 ion plating machine), the sample was observed by scanning electron microscopy (SEM, JSM-6360LV, JEOL, Japan) [\u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec16\" class=\"Section2\"\u003e \u003ch2\u003eStrain growth curve determination\u003c/h2\u003e \u003cp\u003eTo assess the growth of bacteria, an equal quantity of bacteria was inserted into Gause\u0026rsquo;s liquid medium and cultured on a shaker. The culture solution was removed and centrifuged every 24 hours. The supernatant was discarded, and the filter paper was placed into an oven. The mixture was dried to a constant weight, and the filter paper and the bacteria were weighed. The weight of the filter paper was compared with the weight of the bacteria. All assays were performed with three replicates.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec17\" class=\"Section2\"\u003e \u003ch2\u003eBiodegradation of alkali lignin\u003c/h2\u003e \u003cp\u003eTo determine the lignin loss from alkaline lignin cause by various strains, samples (1.5 mL) were centrifuged at 12,000 \u0026times;g for 10 min. One millilitre of supernatant was diluted by adding 2 mL of phosphate buffer (pH 7.6). The lignin concentration was determined by measuring the absorbance at 280 nm with a UV-Vis spectrophotometer (Shimadzu UN-1900i) [\u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e67\u003c/span\u003e]. The calculated standard curve for lignin was y = 0.0786x - 0.0245, R\u0026sup2; = 0.9988.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec18\" class=\"Section2\"\u003e \u003ch2\u003eEnzyme assay\u003c/h2\u003e \u003cp\u003eSamples were centrifuged at 12000 rpm for 5 min, and the supernatant was used for lignin peroxidase (Lip), laccase and manganese peroxidase (MnP) enzyme assays. Laccase activity was determined by monitoring the oxidation of ABTS at 420 nm (ε420\u0026thinsp;=\u0026thinsp;36000 M\u003csup\u003e\u0026minus;1\u003c/sup\u003e cm\u003csup\u003e\u0026minus;1\u003c/sup\u003e) [\u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e68\u003c/span\u003e]. A lignin peroxidase assay was carried out by using peroxidase oxidation of Azure B. LiP activity was determined by measuring the absorbance at 651 nm (ε651=48.8 M\u003csup\u003e\u0026minus;1\u003c/sup\u003e cm\u003csup\u003e\u0026minus;1\u003c/sup\u003e) [\u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e69\u003c/span\u003e]. Manganese peroxidase activity was determined from the change in absorbance occurring when Mn\u003csup\u003e2+\u003c/sup\u003e is oxidized to Mn\u003csup\u003e3+\u003c/sup\u003e and forms a complex with malonate, which produced absorbance at 270 nm (ε270=11590 M\u003csup\u003e\u0026minus;1\u003c/sup\u003e cm\u003csup\u003e\u0026minus;1\u003c/sup\u003e) [\u003cspan citationid=\"CR70\" class=\"CitationRef\"\u003e70\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec19\" class=\"Section2\"\u003e \u003ch2\u003eGenome sequencing and functional annotation\u003c/h2\u003e \u003cp\u003eThe genome of DF3-3 was sequenced at Major Biomedical Technology Co., Ltd. (Shanghai, China). Genomic DNA was extracted using a Wizard\u0026reg; Genomic DNA Purification Kit (Promega). Purified genomic DNA was quantified by a TBS-380 fluorometer (Turner BioSystems Inc., Sunnyvale, CA). The genome was sequenced by adopting the second-generation + third-generation sequencing method of Illumina HiSeq+PacBio, with a shotgun library of 400 bp insertion size. Assembly software canu, SPAdes, etc. was used for three-generation sequence assembly [\u003cspan citationid=\"CR71\" class=\"CitationRef\"\u003e71\u003c/span\u003e], and GeneMarkS software was used to predict the coding sequence (CDS) in the genome [\u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e72\u003c/span\u003e]. The prediction and annotation of genes were carried out using Prodigal Son (prokaryotic dynamic programming gene discovery algorithm). GeneMarkS was used to predict the plasmid genome. tRNAscan-SE v2.0 software was used to predict the tRNA contained in the genome, and Barrnap software was used to predict the rRNA contained in the genome. Functional annotation of the predicted coding gene was carried out by comparison with 6 major databases (NR, Swiss-Prot, Pfam, EggNOG, GO and KEGG) [\u003cspan additionalcitationids=\"CR74 CR75\" citationid=\"CR73\" class=\"CitationRef\"\u003e73\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR76\" class=\"CitationRef\"\u003e76\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec20\" class=\"Section2\"\u003e \u003ch2\u003eAlkali lignin degradation products determined by GC-MS\u003c/h2\u003e \u003cp\u003eDF3-3 was inoculated in 100 ml of medium with AL as the carbon source and cultured on a shaker for seven days. Samples were collected every 24 hours, and a number of control groups was set up. The sample was centrifuged (10,000 rpm, 15 min) to remove the bacteria, the supernatant was acidified with HCl to pH 2\u0026ndash;3, and it was thoroughly extracted with a three-fold volume of ethyl acetate. The extract was rotary evaporated to 10 ml at 37\u0026deg;C and dried with anhydrous Na\u003csub\u003e2\u003c/sub\u003eSO\u003csub\u003e4\u003c/sub\u003e. After evaporating the solvent in a nitrogen stream, 100 \u0026micro;l of the organic layer was derivatized. Then, 100 \u0026micro;l of dioxane and 10 \u0026micro;l of pyridine were added to the sample and vortexed, and 50 \u0026micro;l of bis(trimethylsilyl)trifluoroacetamide (BSTFA) was added. The mixed solution was placed in a water bath at 80\u0026deg;C for 45 min and shaken regularly. The silanized sample was tested by GC-MS [\u003cspan citationid=\"CR77\" class=\"CitationRef\"\u003e77\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThe analytical column was a DB-5 capillary column (30 m length, 0.25 mm inner diameter, 0.25 mm film thickness). The carrier gas was helium. The column temperature was initially 50\u0026deg;C (5 min), then it was raised to 280\u0026deg;C (10\u0026deg;C/min, holding time of 5 min). The transmission line and ion source temperatures were 200 and 250\u0026deg;C, respectively. The solvent delay time was 4.0 min. The injection volume was 1 \u0026micro;l. Electron ionization mass spectra were recorded in the range 30\u0026ndash;550 (m/z) in full scan mode.\u003c/p\u003e \u003c/div\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eAL: Alkali lignin; GC-MS: Gas chromatography-mass spectrometry; MnP: Manganese peroxidase; Lac: Laccase; LiP: Lignin peroxidase.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003eFangyun Tan and Jun Cheng are co-first authors.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eEthics approval and consent to participate\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eEthical approval and consent to participate are not required.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eConsent for publication\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll authors agree to the submission and publication of the manuscript in the journal \u003cem\u003eBiotechnology for Biofuel\u003c/em\u003e.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eAvailability of data and materials\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe additional data generated during this study are available in the Additional file\u003cstrong\u003e\u003cem\u003e.\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eCompeting interests\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eFunding\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was funded by the National Key Research and Development Program of China (code: 2017YFF0207800) and the Scientific Research Program of Beijing Municipal Education Commission (code: KM201810020012).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eAuthors\u0026apos; contributions\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eYQL designed the experimental strategy. FYT, JC, YZ and XFJ carried out the experiments and performed the bioinformatics data analysis. FYT and JC wrote the manuscript. YQL supervised the overall research. This manuscript was proofread by all the authors. All authors read and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eAcknowledgements\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors thank Beijing Key Laboratory of New Technology in Agricultural Application for their support of the part of the work involving scanning electron microscopy. And genome analysis was performed using the free online platform of Majorbio Cloud Platform (www.majorbio.com).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eAuthor information\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003csup\u003e1\u003c/sup\u003eSchool of Landscape Architecture, Beijing University of Agriculture, Beijing 102206 PR China;\u0026nbsp;\u003csup\u003e2\u003c/sup\u003eSchool of Bioscience and\u0026nbsp;Resource Environment, Beijing University of Agriculture, Beijing 102206 PR China;\u0026nbsp;\u003csup\u003e3\u003c/sup\u003eInstitute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193 PR China.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eZeng Y, Zhao S, Yang S, Ding SY. Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels. Curr Opin Biotechnol. 2014;27:38-45.\u003c/li\u003e\n\u003cli\u003eKumar M, Singhal A, Thakur IS. 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World J Microbiol Biotechnol. 2007;23:793-9.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":true,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"biotechnology-for-biofuels-and-bioproducts","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"bbio","sideBox":"Learn more about [Biotechnology for Biofuels](http://biotechnologyforbiofuels.biomedcentral.com/)","snPcode":"13068","submissionUrl":"https://submission.nature.com/new-submission/13068/3","title":"Biotechnology for Biofuels and Bioproducts","twitterHandle":"@BioMedCentral","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"BMC/SO AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Streptomyces thermocarboxydus strain DF3-3, alkali lignin, enzyme activity, genomics, metabolic pathways","lastPublishedDoi":"10.21203/rs.3.rs-996090/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-996090/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground: \u003c/strong\u003eLignocellulose is an important raw material for biomass-to-energy conversion, and it exhibits a complex but inefficient degradation mechanism. Microbial degradation is promising due to its environmental adaptability and biochemical versatility, but the pathways used by microbes for lignin degradation have not been fully studied. Degradation intermediates and complex metabolic pathways require more study.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eResults:\u003c/strong\u003e A novel actinomycete DF3-3, with the potential for lignin degradation, was screened and isolated. After morphological and molecular identification, DF3-3 was determined to be \u003cem\u003eStreptomyces thermocarboxydus\u003c/em\u003e. The degradation of alkali lignin reached 31% within 15 days. Manganese peroxidase and laccase demonstrated their greatest activity levels, 1821.66 UL\u003csup\u003e-1 \u003c/sup\u003eand 1265.58 UL\u003csup\u003e-1\u003c/sup\u003e, respectively, on the sixth day. The highest lignin peroxidase activity was 480.33 UL\u003csup\u003e-1\u003c/sup\u003e on the fourth day. A total of 19 lignin degradation intermediates were identified by gas chromatography-mass spectrometry (GC-MS), including 10 aromatic compounds. Genome sequencing and annotation identified 107 lignin-degrading enzyme-coding genes containing three core enzymatic systems for lignin depolymerization: laccases, peroxidases and manganese peroxidase. In total, 7 lignin metabolic pathways were predicted.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eConclusions:\u003c/strong\u003e \u003cem\u003eStreptomyces thermocarboxydus \u003c/em\u003estrain DF3-3 has good lignin degradation ability. Degradation products and genomics analyses of DF3-3 show that it has a relatively complete lignin degradation pathway, including the β-ketoadipate pathway and peripheral reactions; gentisate pathway; anthranilate pathway; homogentisic pathway; and catabolic pathway for resorcinol. Two other pathways, the phenylacetate-CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway, are predicted based on genome data alone. This study provides the basis for future characterization of potential biotransformation enzyme systems for biomass energy conversion.\u003c/p\u003e","manuscriptTitle":"Genomics Analysis and Degradation Characteristics of Lignin by Streptomyces Thermocarboxydus Strain DF3-3","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2021-11-01 15:24:33","doi":"10.21203/rs.3.rs-996090/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"reviewerAgreed","content":"","date":"2022-02-16T00:00:00+00:00","index":2,"fulltext":""},{"type":"editorInvitedReview","content":"","date":"2021-12-03T02:49:39+00:00","index":0,"fulltext":""},{"type":"reviewerAgreed","content":"","date":"2021-12-02T00:00:00+00:00","index":1,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2021-11-18T03:32:53+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"Biotechnology for Biofuels","date":"2021-10-21T15:49:17+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2021-10-21T04:27:35+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2021-10-20T23:00:00+00:00","index":"","fulltext":""},{"type":"submitted","content":"Biotechnology for Biofuels","date":"2021-10-19T12:06:05+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"biotechnology-for-biofuels-and-bioproducts","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"bbio","sideBox":"Learn more about [Biotechnology for Biofuels](http://biotechnologyforbiofuels.biomedcentral.com/)","snPcode":"13068","submissionUrl":"https://submission.nature.com/new-submission/13068/3","title":"Biotechnology for Biofuels and Bioproducts","twitterHandle":"@BioMedCentral","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"BMC/SO AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"7742c12f-6db9-4daa-a1ba-d110abc7d600","owner":[],"postedDate":"November 1st, 2021","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":8224904,"name":"Biotechnology and Bioengineering"},{"id":8224905,"name":"Applied Biochemistry"},{"id":8224906,"name":"Renewable Resources"}],"tags":[],"updatedAt":"2022-07-01T15:25:56+00:00","versionOfRecord":[],"versionCreatedAt":"2021-11-01 15:24:33","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-996090","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-996090","identity":"rs-996090","version":["v1"]},"buildId":"ehx78VzkSd0WSzXnipQa-","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}