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Item Rs_MEP1 is required for the pathogenesis of Rhizoctonia solani AG1-IA in plants(The American Phytopathological Society (APS), 2026) Pradhan, Amrita; Sahoo, Debashis; Bhati, Vikrant; Kumar, Rahul; Yadav, Rajni; Ghosh, Srayan; Pawar, Prashant Anupama-Mohan; Jha, GopaljeeRhizoctonia solani AGI-IA is a polyphagous necrotrophic fungal pathogen that causes sheath blight disease in rice. Efforts are being made to identify pathogenicity-associated genes in R. solani and modulate them to develop a disease control strategy. Here, we investigate the roles of some predicted pathogenicity-associated genes of R. solani that have previously been reported to be upregulated during infection in rice. The tobacco rattle virus-based host-induced gene silencing of the selected pathogenicity-associated genes revealed that silencing of Rs_MEP1, a zinc-containing Peptidase_M43 domain-metalloprotease, severely compromises R. solani infection in tomato. Moreover, double-stranded RNA-mediated silencing of Rs_MEP1 prevented R. solani infection in rice. The signal sequence trap assay indicated the secretory nature of Rs_MEP1, while the reporter assay suggested its localization in the plant apoplast. Notably, agrobacterium-mediated transient overexpression of Rs_MEP1 induces necrotic cell death responses in plants. We provide evidence that Rs_MEP1 interacts with GH19 family of rice chitinases and potentially modulates their functions. Overall, our study emphasizes that Rs_MEP1 facilitates R. solani in promoting necrotic responses and targets rice GH19 chitinases to impart disease susceptibility in plants.Item Rice PROTEIN L-ISOASPARTYL METHYLTRANSFERASES provides tolerance against sheath blight disease and repairs ALDH and PBZ1(Nature Publishing Group, 2026) Gautam, Shikha; Kamble, Nitin Uttam; Achary, Rakesh Kumar; Chandan, Ravindra Kumar; Varshney, Vishal; Hazra, Abhijit; Laha, Saroj; Mahawar, Shivangi; Mehandiratta, Sohela; Singh, Sarvanand; Jha, Gopaljee; Majee, ManojProtein L-isoaspartyl methyltransferase (PIMT) regulates key seed traits and abiotic stress tolerance in plants by repairing isoaspartyl (isoAsp) damaged proteins. However, whether PIMT-mediated repair is induced and is required during biotic stress tolerance remains unknown. Using rice lines with OsPIMT overexpression, RNAi-mediated suppression, and genome editing, we show that PIMT enhances tolerance to sheath blight (ShB) caused by Rhizoctonia solani. OsPIMT restricts fungal penetration and colonization of rice sheaths. Co-immunoprecipitation coupled with LC-MS/MS identify various proteins including antioxidant proteins, aldehyde dehydrogenases (ALDH) and pathogenesis-related protein 10 (PBZ1), that undergo isoAsp modification during R. solani infection and interact with PIMT. We show that OsALDH and OsPBZ1 exhibit intrinsic antifungal activity against R. solani, but isoAsp modification impairs their activity, making PIMT mediated repair important. Further, OsALDH enhances tolerance to R. solani by inhibiting lipid peroxidation and ROS homeostasis in rice and fungus. Overall, our study reveals that PIMT enhances ShB tolerance through the repair of isoAsp-damaged proteins important for disease tolerance.Item Glycosyltransferase-like toxin of Burkholderia gladioli strain NGJ1 is a potent antifungal protein with potential for control of sheath blight disease in rice(The American Phytopathological Society, 2025) Pradhan, Amrita; Yadav, Sunil K.; Jha, GopaljeeSheath blight disease caused by the fungal pathogen Rhizoctonia solani poses a significant challenge for sustainable rice cultivation. It is important to develop environmentally friendly measures for its control. Previously, a rice-associated Burkholderia gladioli strain NGJ1 was shown to exhibit mycophagous and antifungal activity on R. solani. Here, we report that a B. gladioli glycosyltransferase-like 1 (BGT1) protein with a canonical D×D (aspartic acid × aspartic acid) motif that is homologous to the glycosyltransferase toxin of different bacteria is encoded in the antibacterial type VI secretion system-encoding gene cluster of NGJ1. The recombinant BGT1 protein purified from Escherichia coli exhibits antifungal activity on R. solani, Magnaporthe oryzae, Fusarium oxysporum, Saccharomyces cerevisiae, and Candida albicans under laboratory conditions. Using a variant of the BGT1 protein (BGT1D168L/D170L), we demonstrate that the D×D motif is important for its antifungal activity. The heterologous expression of native BGT1 but not the BGT1D168L/D170L protein prevents the growth of yeast cells. Moreover, treatment with BGT1 but not BGT1D168L/D170L significantly reduces sheath blight disease severity in rice. BGT1 treatment does not elicit adverse effects on plants. In conclusion, we emphasize that BGT1 protein-based or transgene-based biotechnological interventions can be exploited for effective control of sheath blight disease in rice.Item The host and pathogen myo-inositol-1-phosphate synthases are required for Rhizoctonia solani AG1-IA infection in tomato(John Wiley & Sons, 2024) Tyagi, Kriti; Chandan, Ravindra K.; Sahoo, Debashis; Ghosh, Srayan; Gupta, Santosh Kumar; Jha, GopaljeeThe myo-inositol-1-phosphate synthase (MIPS) catalyses the biosynthesis of myo-inositol, an important sugar that regulates various physiological and biochemical processes in plants. Here, we provide evidence that host (SlMIPS1) and pathogen (Rs_MIPS) myo-inositol-1-phosphate synthase (MIPS) genes are required for successful infection of Rhizoctonia solani, a devastating necrotrophic fungal pathogen, in tomato. Silencing of either SlMIPS1 or Rs_MIPS prevented disease, whereas an exogenous spray of myo-inositol enhanced disease severity. SlMIPS1 was upregulated upon R. solani infection, and potentially promoted source-to-sink transition, induced SWEET gene expression, and facilitated sugar availability in the infected tissues. In addition, salicylic acid (SA)-jasmonic acid homeostasis was altered and SA-mediated defence was suppressed; therefore, disease was promoted. On the other hand, silencing of SlMIPS1 limited sugar availability and induced SA-mediated defence to prevent R. solani infection. Virus-induced gene silencing of NPR1, a key gene in SA signalling, rendered SlMIPS1-silenced tomato lines susceptible to infection. These analyses suggest that induction of SA-mediated defence imparts disease tolerance in SlMIPS1-silenced tomato lines. In addition, we present evidence that SlMIPS1 and SA negatively regulate each other to modulate the defence response. SA treatment reduced SlMIPS1 expression and myo-inositol content in tomato, whereas myo-inositol treatment prevented SA-mediated defence. We emphasize that downregulation of host/pathogen MIPS can be an important strategy for controlling diseases caused by R. solani in agriculturally important crops.Item Methionine biosynthetic genes and methionine sulfoxide reductase A are required for Rhizoctonia solani AG1-IA to cause sheath blight disease in rice(John Wiley & Sons, 2024) Das, Joyati; Ghosh, Srayan; Tyagi, Kriti; Sahoo, Debashis; Jha, GopaljeeRhizoctonia solani is a polyphagous necrotrophic fungal pathogen that causes sheath blight disease in rice. It deploys effector molecules as well as carbohydrate-active enzymes and enhances the production of reactive oxygen species for killing host tissues. Understanding R. solani ability to sustain growth under an oxidative-stress-enriched environment is important for developing disease control strategies. Here, we demonstrate that R. solani upregulates methionine biosynthetic genes, including Rs_MET13 during infection in rice, and double-stranded RNA-mediated silencing of these genes impairs the pathogen's ability to cause disease. Exogenous treatment with methionine restores the disease-causing ability of Rs_MET13-silenced R. solani and facilitates its growth on 10 mM H2O2-containing minimal-media. Notably, the Rs_MsrA gene that encodes methionine sulfoxide reductase A, an antioxidant enzyme involved in the repair of oxidative damage of methionine, is upregulated upon H2O2 treatment and also during infection in rice. Rs_MsrA-silenced R. solani is unable to cause disease, suggesting that it is important for the repair of oxidative damage in methionine during host colonization. We propose that spray-induced gene silencing of Rs_MsrA and designing of antagonistic molecules that block MsrA activity can be exploited as a drug target for effective control of sheath blight disease in rice.Item Co-overexpression of SWEET sucrose transporters modulates sucrose synthesis and defence responses to enhance immunity against bacterial blight in rice(John Wiley & Sons, 2024) Singh, Jitender; James, Donald; Das, Shubhashis; Patel, Manish Kumar; Sutar, Rashmi Ranjan; Achary, V. Mohan Murali; Goel, Naveen; Gupta, Kapuganti Jagadis; Reddy, Malireddy K.; Jha, Gopaljee; Sonti, Ramesh V.; Foyer, Christine H.; Thakur, Jitendra K.; Tripathy, Baishnab C.Enhancing carbohydrate export from source to sink tissues is considered to be a realistic approach for improving photosynthetic efficiency and crop yield. The rice sucrose transporters OsSUT1, OsSWEET11a and OsSWEET14 contribute to sucrose phloem loading and seed filling. Crucially, Xanthomonas oryzae pv. oryzae (Xoo) infection in rice enhances the expression of OsSWEET11a and OsSWEET14 genes, and causes leaf blight. Here we show that co‐overexpression of OsSUT1, OsSWEET11a and OsSWEET14 in rice reduced sucrose synthesis and transport leading to lower growth and yield but reduced susceptibility to Xoo relative to controls. The immunity‐related hypersensitive response (HR) was enhanced in the transformed lines as indicated by the increased expression of defence genes, higher salicylic acid content and presence of HR lesions on the leaves. The results suggest that the increased expression of OsSWEET11a and OsSWEET14 in rice is perceived as a pathogen (Xoo) attack that triggers HR and results in constitutive activation of plant defences that are related to the signalling pathways of pathogen starvation. These findings provide a mechanistic basis for the trade‐off between plant growth and immunity because decreased susceptibility against Xoo compromised plant growth and yield.Item A prophage tail-like protein facilitates the endophytic growth of Burkholderia gladioli and mounting immunity in tomato(John Wiley & Sons, 2023) Chandan, Ravindra Kumar; Kumar, Rahul; Kabyashree, Kristi; Yadav, Sunil Kumar; Roy, Mandira; Swain, Durga Madhab; Jha, GopaljeeA prophage tail-like protein (Bg_9562) of Burkholderia gladioli strain NGJ1 possesses broad-spectrum antifungal activity, and it is required for the bacterial ability to forage over fungi. Here, we analyzed whether heterologous overexpression of Bg_9562 or exogenous treatment with purified protein can impart disease tolerance in tomato. The physiological relevance of Bg_9562 during endophytic growth of NGJ1 was also investigated. Bg_9562 overexpressing lines demonstrate fungal and bacterial disease tolerance. They exhibit enhanced expression of defense genes and activation of mitogen-activated protein kinases. Treatment with Bg_9562 protein induces defense responses and imparts immunity in wild-type tomato. The defense-inducing ability lies within 18-51 aa region of Bg_9562 and is due to sequence homology with the bacterial flagellin epitope. Interaction studies suggest that Bg_9562 is perceived by FLAGELLIN-SENSING 2 homologs in tomato. The silencing of SlSERK3s (BAK1 homologs) prevents Bg_9562-triggered immunity. Moreover, type III secretion system-dependent translocation of Bg_9562 into host apoplast is important for elicitation of immune responses during colonization of NGJ1. Our study emphasizes that Bg_9562 is important for the endophytic growth of B. gladioli, while the plant perceives it as an indirect indicator of the presence of bacteria to mount immune responses. The findings have practical implications for controlling plant diseases.Item Editorial: Utilization of microbiome to develop disease resistance in crop plants against phytopathogens(Frontiers Media S.A., 2023) Ghosh, Srayan; Jha, GopaljeeSustainable agriculture is important for ensuring food security at an affordable cost. Agricultural practices heavily depend on agrochemicals, such as fertilizers, fungicides, and pesticides, to ensure optimal productivity and prevent losses due to pathogens and pests. However, with time, it has become clear that most commonly used agrochemicals have residual side effects on consumers, soil health, and the environment. Hence, developing newer environmentally friendly approaches to ensure crop productivity, with minimal usage of agrochemicals, is highly desirable. The potential of plant/rhizospheric soilassociated microbes to support the overall growth of plants and provide protection against phytopathogens has been actively studied in recent years.Item Nicotinic acid catabolism modulates bacterial mycophagy in Burkholderia gladioli strain NGJ1(American Society for Microbiology, 2023) Das, Joyati; Kumar, Rahul; Yadav, Sunil Kumar; Jha, GopaljeeBurkholderia gladioli strain NGJ1 exhibits mycophagous activity on a broad range of fungi, including Rhizoctonia solani, a devastating plant pathogen. Here, we demonstrate that the nicotinic acid (NA) catabolic pathway in NGJ1 is required for mycophagy. NGJ1 is auxotrophic to NA and it potentially senses R. solani as a NA source. Mutation in the nicC and nicX genes involved in NA catabolism renders defects in mycophagy and the mutant bacteria are unable to utilize R. solani extract as the sole nutrient source. As supplementation of NA, but not FA (fumaric acid, the end product of NA catabolism) restores the mycophagous ability of ΔnicC/ΔnicX mutants, we anticipate that NA is not required as a carbon source for the bacterium during mycophagy. Notably, nicR, a MarR-type of transcriptional regulator that functions as a negative regulator of the NA catabolic pathway is upregulated in ΔnicC/ΔnicX mutant and upon NA supplementation the nicR expression is reduced to the basal level in both the mutants. The ΔnicR mutant produces excessive biofilm and is completely defective in swimming motility. On the other hand, ΔnicC/ΔnicX mutants are compromised in swimming motility as well as biofilm formation, potentially due to the upregulation of nicR. Our data suggest that a defect in NA catabolism alters the NA pool in the bacterium and upregulates nicR which in turn suppresses bacterial motility as well as biofilm formation, leading to mycophagy defects. IMPORTANCE Mycophagy is an important trait through which certain bacteria forage over fungal mycelia and utilize fungal biomass as a nutrient source to thrive in hostile environments. The present study emphasizes that nicotinic acid (NA) is important for bacterial motility and biofilm formation during mycophagy by Burkholderia gladioli strain NGJ1. Defects in NA catabolism potentially alter the cellular NA pool, upregulate the expression of nicR, a negative regulator of biofilm, and therefore suppress bacterial motility as well as biofilm formation, leading to mycophagy defects.Item Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations(BioMed Central Ltd, 2023) Francis, Aleena; Ghosh, Srayan; Tyagi, Kriti; Prakasam, V.; Rani, Mamta; Singh, Nagendra Pratap; Pradhan, Amrita; Sundaram, R. M.; Priyanka, C.; Laha, G. S.; Kannan, C.; Prasad, M. S.; Chattopadhyay, Debasis; Jha, GopaljeeBackground: Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into the AGs and the evolution of pathogenicity-associated genes remain poorly understood. Results: We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato. Conclusions: Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.