A root-leaf-root signaling loop illuminates tomato's defense against root-knot nematodes

A root-leaf-root signaling loop illuminates tomato's defense against root-knot nematodes | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 20 February 2026 V1 Latest version Share on A root-leaf-root signaling loop illuminates tomato's defense against root-knot nematodes Authors : Keyan Li and Jiatu Li 0009-0008-9704-1373 [email protected] Authors Info & Affiliations https://doi.org/10.22541/au.177156731.13694105/v1 142 views 66 downloads Contents Abstract Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Root-knot nematodes (RKNs) are one of the major diseases in global agricultural production, causing significant economic losses each year. This article highlights the mechanisms by which tomato plants defend against RKNs through a “root-leaf-root” signaling loop. When RKNs infect tomato roots, electrical signals are transmitted to the leaves via GLR3.5-dependent pathways, activating the HY5 transcription factor. HY5 is not only accumulated in the leaves upon red light stimulation through the phyB receptor but can also move to the roots via the vascular system, activating GLR3.5 expression and maintaining the electrical signal transmission. Additionally, calcium signaling (Ca 2+ -CaM2) amplifies this process, promoting the synthesis of jasmonic acid (JA), thereby enhancing the plant’s defense capabilities. This complex signaling network integrates light, electrical, and hormonal signals to form a systematic defense mechanism, providing new insights for breeding nematode-resistant tomato varieties. A root-leaf-root signaling loop illuminates tomato’s defense against root-knot nematodes Keyan Li a , Jiatu Li b,c * a College of Advanced Agriculture and Ecological Enviroment; Heilongjiang University, Harbin 150080, China b College of Environmental and Resource Sciences, MOE Key Laboratory of Environment Remediation and Ecological Health, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China c Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China * Corresponding author. E-mail: [email protected] Abstract: Root-knot nematodes (RKNs) are one of the major diseases in global agricultural production, causing significant economic losses each year. This article highlights the mechanisms by which tomato plants defend against RKNs through a “root-leaf-root” signaling loop. When RKNs infect tomato roots, electrical signals are transmitted to the leaves via GLR3.5-dependent pathways, activating the HY5 transcription factor. HY5 is not only accumulated in the leaves upon red light stimulation through the phyB receptor but can also move to the roots via the vascular system, activating GLR3.5 expression and maintaining the electrical signal transmission. Additionally, calcium signaling (Ca 2+ -CaM2) amplifies this process, promoting the synthesis of jasmonic acid (JA), thereby enhancing the plant’s defense capabilities. This complex signaling network integrates light, electrical, and hormonal signals to form a systematic defense mechanism, providing new insights for breeding nematode-resistant tomato varieties. Key words: Root-knot nematodes; tomatoes; jasmonic acid; defense mechanisms; signal transduction Introduction Root-knot nematodes (RKNs), primarily of the genus Meloidogyne, are among the most destructive plant-parasitic nematodes worldwide, causing substantial economic losses in agriculture. Estimates of annual global crop losses due to RKNs range from $100 billion to $160 billion, with some sources specifying losses of approximately $157 billion and a reduction in global crop production by 5-12% or up to 10% (Shahid & Shafi, 2025; Fan et al., 2019; Haque, Thimmanagari & Chiang, 2022). These nematodes are responsible for both quantitative and qualitative losses in yield, threatening food security and agricultural productivity across diverse cropping systems (Belmouden et al., 2025). RKNs infect a vast array of plant species, including many economically important crops. They are known to parasitize over 2,000 to 5,500 plant species, affecting vegetables (such as tomato, cucumber, potato, brinjal, melon, eggplant, beans, radish, carrot, lettuce, cabbage), cereals, cotton, tobacco, rice, peanut, sweet potato, soybean, and watermelon (Azeem et al., 2025; Sakariya et al., 2024; Qiao et al., 2014). Their polyphagous nature and adaptability make them particularly challenging to control, with species like Meloidogyne incognita being the most widespread and damaging (Cao et al., 2023; Alattas et al., 2024). RKNs parasitize plant roots, leading to the formation of characteristic galls or root-knots. The nematodes penetrate the roots, establish permanent feeding sites, and induce abnormal growths (galls) that disrupt root architecture (Martinuz et al., 2025). This interference impedes the plant’s ability to absorb water and essential nutrients, resulting in stunted growth, chlorosis (leaf yellowing), wilting, reduced photosynthetic efficiency, root dysfunction, and rot death of the plant in severe cases (Li et al., 2018). RKN infections frequently predispose plants to secondary infections by soil-borne pathogens, exacerbating crop losses. Disease complexes involving RKNs and fungi such as Fusarium spp., Verticillium spp., and Rhizoctonia solani can lead to root rots and wilts, further diminishing plant health and yield (Ramadwa, Makhubu & Eloff, 2024). Continuous cropping and soil degradation aggravate RKN infestations. Long-term monoculture practices alter soil microbiome composition and physicochemical properties, suppressing beneficial microbes and impairing key metabolic functions. This creates a self-reinforcing cycle of soil degradation, microbial dysbiosis, and increased nematode proliferation, further destabilizing plant health and biocontrol efficacy (Wang et al., 2025). However, a groundbreaking study published in Nature Communications (October 2025) unveils a sophisticated “root-leaf-root” communication mechanism that integrates light perception, electrical signals, and hormone bursts to fortify defenses. Led by researchers from Zhejiang University and the University of Birmingham, the work spotlights ELONGATED HYPOCOTYL 5 (HY5) as a central hub in this systemic resistance strategy (Sun et al., 2025). The trigger: from root invasion to leaf alert Light is a crucial environmental signal that regulates plant defense responses through its effects on hormonal signaling pathways, particularly those involving jasmonic acid (JA) and salicylic acid (SA). Light influences the production and signaling of these hormones, thereby modulating the plant’s ability to respond to biotic stresses such as pathogens and herbivores (Lazzarin et al., 2021). Light quality and intensity affect the balance between plant growth and defense, with specific wavelengths (e.g., red, blue, far-red, UV) having distinct impacts on defense-related gene expression and metabolite accumulation (Dutta, Devi & Lee, 2024; Forges et al., 2018; Klem et al., 2019). Photoreceptors such as phytochromes (including phytochrome B, phyB), cryptochromes, and phototropins perceive light signals and modulate downstream hormonal pathways, including those involving JA. The ratio of red to far-red light (R/FR) is a key environmental signal that influences the trade-off between plant growth and defense: low R/FR ratios, which signal competition (shade), are sensed by phytochrome B (phyB) and lead to the inactivation of phyB. Inactivation of phyB under low R/FR conditions attenuates JA-mediated defense responses by promoting the degradation of DELLA proteins (repressors of growth) and increasing the stability of JAZ proteins (inhibitors of JA-responsive defense), thereby shifting the balance toward growth (shade-avoidance) and away from defense. Upregulating the sulfotransferase gene ST2a , which increases the accumulation of inactive JA metabolites (e.g., 12-HSO 4 -JA), reducing the flux toward active JA-Ile and suppressing defense signaling (Li et al., 2025). Mutations in phyB can alter plant immunity, with phyB mutants showing changes in the expression of JA synthesis and signaling genes, further demonstrating the role of phyB in connecting light perception to defense regulation (Pierik & Ballaré, 2021; Kuo et al., 2015; Sun et al., 2019). Light and JA signaling are integrated through transcription factors such as MYC2 and PIFs, which coordinate the expression of defense-related genes and secondary metabolite biosynthesis. Resource allocation between growth and defense is modulated by the interplay of light signals (via phyB and other photoreceptors) and hormonal pathways, allowing plants to prioritize growth under competitive (low R/FR) conditions at the expense of defense (Klem et al., 2019; Swain, Jiang & Hsieh, 2017; Zhao et al., 2021). Other hormones such as auxin, gibberellins, ethylene, and SA are also involved in the light-mediated regulation of defense, with complex interactions and feedback loops (Xiao et al., 2022). HY5 is a basic leucine zipper (bZIP) transcription factor that acts as a central regulator in plant light signaling pathways. It functions downstream of multiple photoreceptors, including phytochromes (PHY), cryptochromes (CRY), and UVR8, to mediate light responses in plants. HY5 binds to light-responsive elements (LREs) such as the G-box in the promoters of target genes, thereby regulating their expression and promoting photomorphogenesis. The activity and stability of HY5 are tightly controlled by the E3 ubiquitin ligase COP1, which targets HY5 for degradation in darkness, while light inactivates COP1, allowing HY5 to accumulate and function in the nucleus (Shin et al., 2016; Singh et al., 2023). HY5 integrates light signals with temperature and hormonal cues to coordinate plant growth and development. It acts as a convergence point for multiple hormone signaling pathways, including gibberellin (GA), abscisic acid (ABA), auxin, cytokinin, ethylene, and brassinosteroids (BR). HY5 directly regulates the transcription of genes involved in these hormonal pathways, such as ABI5 in the ABA pathway and ACS2 in the ethylene biosynthesis pathway. It also modulates the expression of negative regulators of auxin signaling and is involved in the crosstalk between light and BR signaling, often acting antagonistically with BR signaling components like BZR1 (Fernando & Schroeder, 2015; Saini, Sharma & Pati, 2015; Cañibano et al., 2021; Wang et al., 2023; Lau & Deng, 2010). HY5 is involved in plant responses to low-temperature stress by integrating light and cold signaling pathways. Its abundance is regulated by both transcriptional up-regulation and protein stabilization under cold and light conditions. In Arabidopsis , the blue light-CRY system is necessary for HY5 transcript response to cold, and HY5 mediates cold acclimation by regulating anthocyanin biosynthesis genes. In tomato, HY5 has been shown to regulate the biosynthesis of steroidal glycoalkaloids (SGAs) and anthocyanins, and it coordinates the regulation of GA and ABA signaling pathways in response to low-temperature stress (Du et al., 2026; Wang et al., 2018; Imai et al., 2021). HY5 not only functions in shoots but also acts as a mobile signal that moves from shoots to roots, thereby regulating root responses to light. HY5 mediates the light promotion of nutrient absorption, nodule formation, and root growth by regulating the expression of genes involved in nutrient uptake and signaling pathways in roots. For example, HY5 binds to the promoter of the FER gene in roots, which is required for the induction of iron mobilization genes, and positively regulates the expression of YSL iron transporters in response to iron stress. HY5 also plays a role in nitrate absorption, phosphate response, and copper signaling pathways, further highlighting its integrative role in nutrient signaling (Yang & Liu, 2020; Sun et al., 2022). HY5 regulates a large portion of the Arabidopsis genome, directly or indirectly controlling the expression of genes involved in light and hormonal signaling, as well as metabolic pathways. It acts as a transcriptional activator in vivo, often in concert with other transcription factors such as BBXs, bHLHs, and MYBs, to fine-tune gene expression in response to environmental cues. HY5’s ability to bind to G-box and related motifs allows it to regulate genes involved in anthocyanin, carotenoid, and chlorophyll biosynthesis, as well as secondary metabolism and stress responses. The fine-tuning of HY5 availability is crucial for proper photomorphogenic development and plant viability (Kong et al., 2025; Yang et al., 2021; Lee & Seo, 2017). When RKNs ( Meloidogyne incognita ) attack tomato roots, they do not just cause local damage, but spark a rapid, long-distance alarm. GLUTAMATE RECEPTOR-LIKE (GLR) channels are a family of cation-permeable ion channels in plants, homologous to animal ionotropic glutamate receptors, and are activated by amino acids such as glutamate. These channels are involved in a variety of physiological processes, including defense signaling, root growth, and seed germination. Specifically, GLR3.3 and GLR3.6 have been shown to mediate long-distance defense by propagating intercellular calcium signals, and their mutations compromise pattern-triggered Ca 2+ influx and anti-bacterial immunity. GLR3.5 is expressed mostly in germinating Arabidopsis seeds, where it modulates cytosolic calcium signaling and is required for normal germination, but it also plays a role in limiting the spread of electrical signals to non-neighbor leaves, suggesting a regulatory function in systemic signaling propagation (Li, Liu & Zhou, 2024; Takahashi & Shinozaki, 2019; Fàbregas & Fernie, 2021; Hilleary & Gilroy, 2018). Upon wounding or pathogen attack, plants release glutamate, which activates GLR channels in the plasma membrane, leading to an influx of Ca 2+ and the generation of electrical signals (membrane depolarizations or action potentials). These signals propagate rapidly through the plant vasculature, particularly via the phloem and xylem, at speeds of up to 1 mm/sec. The electrical signals and Ca 2+ waves are tightly interconnected and can travel from the site of induction to distant tissues, including systemic leaves, to trigger defense responses. GLR3.3 and GLR3.6 are expressed in sieve elements and xylem contact cells, respectively, and are essential for the initiation and propagation of these signals. In glr3.3 glr3.6 double mutants, the Ca 2+ signal does not propagate to systemic leaves, highlighting the necessity of these channels for systemic signaling (Suda & Toyota, 2022; Scherzer et al., 2022; Vatsa et al., 2011; Sanden & Schulz, 2021; Todaka et al., 2019; Zhu, Wang & Li, 2025; Qiu et al., 2019). The influx of Ca 2+ through GLR channels leads to a rise in cytosolic Ca 2+ concentration, which acts as a second messenger in downstream signaling cascades. Calcium-sensing proteins, including calmodulins (CaMs), bind Ca 2+ and undergo conformational changes that enable them to interact with target proteins. Calmodulin 2 (CaM2), a Ca 2+ -binding protein, is one such sensor that can relay the Ca 2+ signal to downstream effectors. The encoded information in Ca 2+ signals is thus decrypted and transduced by Ca 2+ -binding proteins like CaM2, which can activate or modulate the activity of other proteins, including transcription factors (Yu et al., 2023; Asaf et al., 2023). While current research did not directly describe the physical interaction between CaM2 and HY5 or the enhancement of HY5’s stability and transcriptional activity, they do establish that Ca 2+ signals, decoded by calmodulins, can regulate the activity of transcription factors and gene expression involved in stress and defense responses (Fig. 1). The propagation of Ca 2+ and electrical signals through GLR channels primes defense responses in distal tissues, including the activation of defense genes and the production of defense-related hormones such as jasmonic acid. Mutations in GLR channels, such as glr3.3, result in diminished defense responses, indicating the importance of this signaling cascade in plant immunity (Qureshi et al., 2021). The burst: HY5 fuels jasmonate production While bZIP transcription factors such as ABF1-1 have been shown to enhance JA biosynthesis by activating JA biosynthetic genes, current research did not present direct evidence that HY5 specifically regulates JA biosynthesis (Zhou et al., 2025). The available evidence focuses on HY5’s role in light signaling, anthocyanin, and flavonoid biosynthesis, but not on direct regulation of JA biosynthetic pathways. However, Sun et al., 2025 demonstrated through chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assays (EMSA), and dual-luciferase reporter assays that HY5 directly binds to promoters of key JA synthesis genes like LOXF, AOS, and AOC, as well as its own promoter (HY5). This auto-activation creates a positive feedback loop, rapidly escalating JA and its active form, JA-Ile, in both leaves and roots. In RKN-infected plants, JA levels surged under red light but plummeted in darkness or far-red light, underscoring light’s modulatory influence. HY5 mutants displayed an increased number of root galls (indicative of successful nematode infection) and reduced JA levels, whereas HY5-overexpressing lines demonstrated enhanced resistance, a phenomenon reliant on the interaction between CaM2 and HY5. Altering HY5’s CaM-binding domain weakened this partnership, reducing JA output and defense efficacy. Closing the loop: HY5 travels back to roots The mechanism’s elegance lies in its bidirectionality. HY5 acts as a mobile signal, translocating downward to roots and stems, rather than continuously staying in leaves. There, it activates GLR3.5 expression, sustaining the electrical signaling pathway. This root-leaf-root feedback ensures continuous JA production and systemic resistance (Fig. 2), underscoring the intricate regulatory network involving “effector (RKN) → electrical signal (GLR3.5) → calcium signal (Ca 2+ -CaM2) → transcription factor (HY5) → JA synthesis → defense response”. HY5 plays a central role in this process by connecting light signal perception, electrical signal amplification, and JA synthesis activation. Grafting experiments further validated this: shoots with functional HY5 conferred protection to mutant roots, but not vice versa. In summary, Sun et al., 2025 integrates multiple signals, such as light (via phyB-HY5), electricity (via GLR3.5), and Ca 2+ (via CaM2) into a cohesive defense network. This reveals how plants “wire” environmental cues like light with rapid internal alerts to combat underground threats. This discovery challenges the view of plant defenses as compartmentalized, highlighting inter-organ crosstalk as key to resilience. For agriculture, it opens avenues for breeding light-responsive, nematode-resistant tomatoes, potentially reducing reliance on chemical nematicides. Concluding remarks and future perspectives Jasmonic acid (JA) is a key phytohormone mediating plant defense responses, particularly against necrotrophic pathogens, herbivorous insects, and nematodes. JA signaling is activated upon pathogen or pest attack, leading to the transcription of defense-related genes. JA biosynthesis and signaling are tightly regulated and can be modulated by light, as photoreceptors and transcription factors involved in phototransduction influence JA production. The JA pathway is also interconnected with SA and ethylene (ET) signaling, with extensive crosstalk allowing plants to fine-tune their defense responses (Rizvi et al., 2026; Wu et al., 2024). Glutamate receptor-like channels (GLRs), including GLR3.5, are involved in generating calcium (Ca 2+ ) influx across the plasma membrane in response to environmental stimuli. GLRs play a role in shaping cytosolic Ca 2+ signatures, which are crucial for activating downstream defense signaling pathways. Specifically, GLR3.3 and GLR3.6 have been shown to regulate the expression of genes involved in JA synthesis and other defense-related metabolites, indicating that GLRs are important for amplifying defense responses through Ca 2+ -dependent signaling cascades (Ahmed et al., 2023). Calmodulin (CaM) proteins, such as CaM2, act as calcium sensors that relay Ca²⁺ signals to downstream effectors, including Calmodulin-Binding Transcription Activators (CAMTAs). CAMTA3, for example, decodes calcium signatures and modulates the expression of defense-related genes. In Arabidopsis , CAMTA3 mutants show altered levels of JA and salicylic acid (SA), with reduced JA and increased SA, and display enhanced tolerance to pathogens. CAMTA3 is involved in both SA- and JA-mediated defense responses and can act as a negative regulator of pathogen-triggered immunity by modulating the expression of key defense genes (Noman et al., 2021). The activation of defense responses involves a complex network where HY5 integrates light and electrical signals to trigger JA synthesis, thereby activating defense mechanisms against nematodes. GLR3.5 and CaM2 are crucial in the signal transduction pathway, amplifying the transcriptional regulation of HY5 and JA synthesis through Ca 2+ signaling. JA, in turn, orchestrates the expression of defense genes and interacts with other hormone pathways, such as SA and ET, to mount an effective response against nematode infection. There is significant crosstalk and feedback regulation among these components, ensuring a coordinated defense strategy (Wang, Du & Mou, 2016; Khan & Khan, 2021). Significant progress has been made in the field of tomato nematode resistance research, both in terms of molecular mechanisms and breeding technologies. Future research should integrate multiple aspects, from gene resource exploration to mechanism elucidation, to breeding technology innovation and multi-omics integration, ultimately achieving field application and ecological adaptability. Through these efforts, it is hoped that more efficient, stable, and broad-spectrum nematode-resistant tomato varieties can be developed, making an important contribution to sustainable agriculture and reducing reliance on chemical pesticides. Conflicts of interest The authors declare no conflict of interest. Author contributions Keyan Li and Jiatu Li conceived the manuscript. Jiatu Li wrote the manuscript. Keyan Li reviewed and edited the manuscript. All authors have read and agreed to the published version of the manuscript. Fig. 1 Fig. 2 Fig. 1 The relationship among light signals, hormone signals, and defense signals. Light signals, including high R/FR and phyB-related signals, can affect JA synthesis and JA - mediated defense through the HY5 (bZIP transcription factor). GA & ABA hormone signaling pathway is also involved. Long-distance signals from herbivores, nematodes, and necrotrophic pathogens can trigger RBOH-dependent ROS, GLR-dependent electrical signal, and Ca 2+ signal, which are related to defense and also promote JA biosynthesis. Meanwhile, light signals can also influence root growth, nodule formation, and nutrient absorption. Fig. 2 The systemic defense mechanism in tomatoes against root-knot nematodes (RKN). The above-ground part of the plant perceives a red light signal through phyB, a phytochrome that senses red light. The red light signal activates HY5, a transcription factor that can travel through the vascular system to the roots. In the roots, HY5 activates the expression of GLR3.5, a glutamate receptor that facilitates electrical signaling. GLR3.5 activation leads to a calcium signal, involving CaM2 (calmodulin), which is crucial for signal transduction. The calcium signal promotes the synthesis of jasmonic acid (JA), a key plant hormone involved in defense responses. The culmination of this signaling pathway results in a defense response against nematode infection, including reducing the number of galls formed by the nematodes. References: Ahmed, I., Kumar, A., Bheri, M., Srivastava, A.K., Pandey, G.K. (2023). Glutamate receptor like channels: Emerging players in calcium mediated signaling in plants. Int. J. Biol. Macromol., 234, p.123522. Alattas, H., Glick, B.R., Murphy, D.V. & Scott, C. (2024). Harnessing Pseudomonas spp. for sustainable plant crop protection. Front. Microbiol. 15:1485197. 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