Browsing by Author "Pradhan, Amrita"

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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, Gopaljee
Background: 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.
Fungal effectors, the double edge sword of phytopathogens
(Springer Nature Publishing AG, 2021) Pradhan, Amrita; Ghosh, Srayan; Sahoo, Debashis; Jha, Gopaljee
Phyto-pathogenic fungi can cause huge damage to crop production. During millions of years of coexistence, fungi have evolved diverse life-style to obtain nutrients from the host and to colonize upon them. They deploy various proteinaceous as well as non-proteinaceous secreted molecules commonly referred as efectors to sabotage host machinery during the infection process. The efectors are important virulence determinants of pathogenic fungi and play important role in successful pathogenesis, predominantly by avoiding host-surveillance system. However, besides being important for pathogenesis, the fungal efectors end-up being recognized by the resistant cultivars of the host, which mount a strong immune response to ward-of pathogens. Various recent studies involving diferent pathosystem have revealed the virulence/avirulence functions of fungal efectors and their involvement in governing the outcome of host–pathogen interactions. However, the efectors and their cognate resistance gene in the host remain elusive for several economically important fungal pathogens. In this review, using examples from some of the biotrophic, hemi-biotrophic and necrotrophic pathogens, we elaborate the double-edged functions of fungal efectors. We emphasize that knowledge of efector functions can be helpful in efective management of fungal diseases in crop plants.
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, Gopaljee
Sheath 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.
Immunity proteins of dual nuclease T6SS effectors function as transcriptional repressors
(EMBO Press, 2021) Yadav, Sunil Kumar; Magotra, Ankita; Ghosh, Srayan; Krishnan, Aiswarya; Pradhan, Amrita; Kumar, Rahul; Das, Joyati; Sharma, Mamta; Jha, Gopaljee
Bacteria utilize type VI secretion system (T6SS) to deliver antibacterial toxins to target co-habiting bacteria. Here, we report that Burkholderia gladioli strain NGJ1 deploys certain T6SS effectors (TseTBg), having both DNase and RNase activities to kill target bacteria. RNase activity is prominent on NGJ1 as well as other bacterial RNA while DNase activity is pertinent to only other bacteria. The associated immunity (TsiTBg) proteins harbor noncanonical helix–turn–helix motifs and demonstrate transcriptional repression activity, similar to the antitoxins of type II toxin– antitoxin (TA) systems. Genome analysis reveals that homologs of TseTBg are either encoded as TA or T6SS effectors in diverse bacteria. Our results indicate that a new ORF (encoding a hypothetical protein) has evolved as a result of operonic fusion of TA type TseTBg homolog with certain T6SS-related genes by the action of IS3 transposable elements. This has potentially led to the conversion of a TA into T6SS effector in Burkholderia. Our study exemplifies that bacteria can recruit toxins of TA systems as T6SS weapons to diversify its arsenal to dominate during inter-bacterial competitions.
RS_CRZ1, a C2H2 type transcription factor is required for pathogenesis of Rhizoctonia solani AG1-IA in tomato
(American Phytopathological Society, 2021) Ghosh, Srayan; Kant, Ravi; Pradhan, Amrita; Jha, Gopaljee
Rhizoctonia solani is a necrotrophic fungal pathogen which causes disease in diverse plant species. In recent years, the genomic and transcriptomic studies have identified several candidate pathogenicity determinants of R. solani; however, most of them remain to be validated. In this study, we report a viral vector-based host induced gene silencing (HIGS) as well as a dsRNA (double stranded RNA) based approach to effectively downregulate genes of R. solani AG1-IA (BRS1 strain) during pathogenesis in tomato. We tested a few of the in-planta upregulated R. solani genes and observed that silencing of one of them i.e. RS_CRZ1 (a C2H2 type Zn finger transcription factor) significantly compromises the pathogenesis of R. solani in tomato. The RS_CRZ1 silenced plants not only exhibited significant reduction in disease symptoms, but the depth of pathogen colonization was also compromised. Furthermore, we identified the R. solani genes that were co-regulated with RS_CRZ1 during pathogenicity process. The HIGS mediated silencing of a few of them (CL1756Contig1; subtilisin like protease and CL1817Contig2; 2OG- Fe(II) oxygenase) compromised the pathogenesis of R. solani in tomato. The ectopic expression of RS_CRZ1 complemented the crz1 mutant of yeast and restored tolerance against various metal ion stress. Overall, our study reveals the importance of RS_CRZ1 in managing the hostile environment encountered during host colonization. Also, it emphasizes the relevance of HIGS and dsRNA-based gene silencing approach towards functional characterization of pathogenicity determinants of R. solani.
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, Gopaljee
Rhizoctonia 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.