Publications of NIPGR Scientists

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    Comparative transcriptome profiling reveals differential defense responses among Alternaria brassicicola resistant Sinapis alba and susceptible Brassica rapa
    (Frontiers Media S.A., 2024) Ahmed, Reshma; Dey, Kuntal Kumar; Senthil-Kumar, Muthappa; Modi, Mahendra Kumar; Sarmah, Bidyut Kumar; Bhorali, Priyadarshini
    Alternaria blight is a devastating disease that causes significant crop losses in oilseed Brassicas every year. Adoption of conventional breeding to generate disease-resistant varieties has so far been unsuccessful due to the lack of suitable resistant source germplasms of cultivated Brassica spp. A thorough understanding of the molecular basis of resistance, as well as the identification of defense-related genes involved in resistance responses in closely related wild germplasms, would substantially aid in disease management. In the current study, a comparative transcriptome profiling was performed using Illumina based RNA-seq to detect differentially expressed genes (DEGs) specifically modulated in response to Alternaria brassicicola infection in resistant Sinapis alba, a close relative of Brassicas, and the highly susceptible Brassica rapa. The analysis revealed that, at 48 hpi (hours post inoculation), 3396 genes were upregulated and 23239 were downregulated, whereas at 72 hpi, 4023 genes were upregulated and 21116 were downregulated. Furthermore, a large number of defense response genes were detected to be specifically regulated as a result of Alternaria infection. The transcriptome data was validated using qPCR-based expression profiling for selected defense-related DEGs, that revealed significantly higher fold change in gene expression in S. alba when compared to B. rapa. Expression of most of the selected genes was elevated across all the time points under study with significantly higher expression towards the later time point of 72 hpi in the resistant germplasm. S. alba activates a stronger defense response reaction against the disease by deploying an array of genes and transcription factors involved in a wide range of biological processes such as pathogen recognition, signal transduction, cell wall modification, antioxidation, transcription regulation, etc. Overall, the study provides new insights on resistance of S. alba against A. brassicicola, which will aid in devising strategies for breeding resistant varieties of oilseed Brassica.
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    Interaction of the Xanthomonas effectors XopQ and XopX results in induction of rice immune responses
    (John Wiley & Sons, 2020) Deb, Sohini; Ghosh, Palash; Patel, Hitendra K.; Sonti, Ramesh V.
    Xanthomonas oryzae pv. oryzae uses several type III secretion system (T3SS) secreted effectors, namely XopN, XopQ, XopX, and XopZ, to suppress rice immune responses that are induced following treatment with cell wall degrading enzymes. Here we show that a T3SS secreted effector XopX interacts with two of the eight rice 14‐3‐3 proteins. Mutants of XopX that are defective in 14‐3‐3 binding are also defective in suppression of immune responses, suggesting that interaction with 14‐3‐3 proteins is required for suppression of host innate immunity. However, Agrobacterium mediated delivery of both XopQ and XopX into rice cells results in induction of rice immune responses. These immune responses are not observed when either protein is individually delivered into rice cells. XopQ‐ XopX induced rice immune responses are not observed with a XopX mutant that is defective in 14‐3‐3 binding. Yeast two‐ hybrid, BiFC and co‐ IP assays indicate that XopQ and XopX interact with each other. A screen for Xanthomonas effectors which can suppress XopQ‐ XopX induced rice immune responses, led to the identification of five effectors, namely XopU, XopV, XopP, XopG and AvrBs2, that could individually suppress these immune responses. These results suggest a complex interplay of Xanthomonas T3SS effectors in suppression of both pathogen triggered immunity and effector triggered immunity to promote virulence on rice.
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    Xanthomonas oryzae pv. oryzae XopQ protein suppresses rice immune responses through interaction with two 14-3-3 proteins but its phospho-null mutant induces rice immune responses and interacts with another 14-3-3 protein
    (John Wiley & Sons, 2019) Deb, Sohini; Gupta, Mahesh K.; Patel, Hitendra K.; Sonti, Ramesh V.
    Many bacterial phytopathogens employ effectors secreted through the type-III secretion system to suppress plant innate immune responses. The Xanthomonas type-III secreted non-TAL effector protein Xanthomonas outer protein Q (XopQ) exhibits homology to nucleoside hydrolases. Previous work indicated that mutations which affect the biochemical activity of XopQ fail to affect its ability to suppress rice innate immune responses, suggesting that the effector might be acting through some other pathway or mechanism. In this study, we show that XopQ interacts in yeast and in planta with two rice 14-3-3 proteins, Gf14f and Gf14g. A serine to alanine mutation (S65A) of a 14-3-3 interaction motif in XopQ abolishes the ability of XopQ to interact with the two 14-3-3 proteins and to suppress innate immunity. Surprisingly, the S65A mutant gains the ability to interact with a third 14-3-3 protein that is a negative regulator of innate immunity. The XopQS65A mutant is an inducer of rice immune responses and this property is dominant over the wild-type function of XopQ. Taken together, these results suggest that XopQ targets the rice 14-3-3 mediated immune response pathway and that its differential phosphorylation might enable interaction with alternative 14-3-3 proteins.