Transcriptomic characterization of recombinantClostridium beijerinckiiNCIMB 8052 expressing methylglyoxal synthase and glyoxal reductase fromClostridium pasteurianumATCC 6013

ABSTRACT Bioconversion of abundant lactose-replete whey permeate to value added chemicals holds promise for valorization of this increasing food processing waste. Efficient conversion of whey-permeate-borne lactose requires adroit microbial engineering to funnel carbon to the desired chemical. Having engineered a strain of Clostridium beijerinckii NCIMB 8052 ( C. beijerinckii _mgsA+mgR) that produces 87% more butanol on lactose than the control strain, in this study, we deployed RNA sequencing to profile the global transcriptome of C. beijerinckii _mgsA+mgR. The results revealed broadly contrasting gene expression patterns in C. beijerinckii _mgsA+mgR relative to the control strain. These were characterized by widespread downregulation of Fe-S proteins in C. beijerinckii _mgsA+mgR, coupled with increased expression of lactose uptake and catabolic genes, iron and phosphate uptake genes, two component signal transduction and motility genes, and genes involved in the biosynthesis of vitamin B 5 and B 12 , aromatic amino acids, particularly tryptophan; arginine, and pyrimidines. Conversely, L-aspartate-dependent de novo biosynthesis of NAD as well as biosynthesis/metabolism of glycine, threonine, lysine, isoleucine and asparagine were downregulated. Furthermore, genes involved in cysteine and methionine biosynthesis and metabolism, including cysteine desulfurase—a central player in Fe-S cluster biosynthesis—were equally downregulated. Genes involved in biosynthesis of capsular polysaccharides and stress response were also downregulated in C. beijerinckii _mgsA+mgR. The results suggest that remodeling of cellular and metabolic networks in C. beijerinckii _mgsA+mgR to counter likely effect of methylglyoxal production following heterologous expression of methyl glyoxal synthase led to enhanced growth and butanol production in C. beijerinckii _mgsA+mgR. IMPORTANCE Biological production of commodity chemicals from abundant waste streams such as whey permeate represents a rational approach for decarbonizing chemical production. Whey permeate remains a vastly underutilized feedstock for bioproduction purposes. Thus, enhanced understanding of the cellular and metabolic repertoires of lactose-mediated production of chemicals such as butanol, promises to arm researchers with new engineering targets that can be fine-tuned in recombinant and native microbial strains to engender stronger coupling of whey permeate-borne lactose to value-added chemicals. Our results highlight new genetic targets for future engineering of C. beijerinckii _mgsA+mgR and indeed, C. beijerinckii for improved butanol production on lactose, and ultimately in whey permeate.