Institutional Publications
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Item OsWAKL21, a putative receptor of rice cell wall damage activates alternate signaling in rice and Arabidopsis to induce immunity(American Phytopathological Society, 2019) Malukani, K. K.; Ranjan, A.; Hota, S. J.; Patel, H. K.; Sonti, Ramesh V.Xanthomonas oryzae pv. oryzae (Xoo) causes the serious bacterial blight disease of rice. As part of its virulence repertoire, Xoo secretes various cell wall degrading enzymes (CWDEs) such as cellulases, xylanases and a Lipase/esterase (LipA). Conversely, treatment of rice tissues with any of these purified enzymes activates immune responses. Plants sense this cell wall damage as a mark of infection and induce immune responses. Very little information is available about the plant functions that are involved in the elaboration of cell wall damage induced immune responses. Transcriptome analyses revealed a rice cell wall-associated receptor kinase, OsWAKL21 that is upregulated following treatment with either LipA or Xoo. VIGS mediated downregulation of OsWAKL21 attenuates LipA induced immune responses. Overexpression of OsWAKL21 in rice mimics LipA treatment in induction of immune responses, activation of JA pathway and enhanced expression of defence related genes, indicating that it plays an important role in elaboration of LipA induced immune responses. Ectopic expression of OsWAKL21 in Arabidopsis also activates plant immune responses. OsWAKL21 is a moonlighting kinase having in vitro kinase and guanylate cyclase activities. Interestingly, OsWAKL21 needs kinase activity to activate immune responses in rice while in Arabidopsis it needs the guanylate cyclase activity. Thus OsWAKL21 is activating similar immune responses in two different species but via different mechanisms.Item Phase variation in rice pathogen Xanthomonas oryzae pv. oryzae(American Phytopathological Society, 2019) Madhavan, V. N.; Patel, H. K.; Patil, P. B.; Sonti, Ramesh V.Xanthomonas oryzae pv. oryzae (Xoo) is the causal pathogen of bacterial blight of rice. Diverse factors contribute to its virulence, e.g., secreted enzymes, protein involved in adhesion, gene regulation. Two such studied virulence factors are Exopolysaccharide (EPS) and Lipopolysaccharide (LPS). LPS is a structural component of the outer membrane of all gram-negative bacteria. LPS is necessary for the function of many outer membrane proteins and protect the bacteria from antimicrobial plant products. EPS is a complex polymer secreted by Xanthomonas genus and the known functions of EPS include biofilm formation, and suppression of the plant immune responses. In this study, we isolated non-mucoid and virulence compromised Xoo colonies from stationary phase cultures. These spontaneous mutants are called as stationary phase variants (SPV). Our data show that, SPVs arises due to insertion of endogenous Insertion Sequence (IS) elements in EPS or LPS O-antigen biosynthetic clusters or by slipped-strand mispairing (SSM) in wxoA gene of LPS O-antigen biosynthetic cluster. The SPVs reverts to wild-type colony morphology and showed true reversion, i.e. restoration of wild-type genotype. The results suggest that we are observing phase variation in Xoo. We hypothesize that similar phase variation may be a part of Xoo’s life cycle. Which may help the bacteria survive in nutrient limited conditions during late stages of infection and on rice seeds and plant debris.Item Immune response induction in rice due to co-expression of XopQ and XopX(American Phytopathological Society, 2019) Deb, S.; Patel, H. K.; Sonti, Ramesh V.Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, a serious disease of rice. Xoo uses the type III secretion system (T3SS) to suppress rice immune responses. The T3SS secreted effectors XopQ and XopX suppress rice immune responses by interaction with different rice 14-3-3 proteins. Sub-cellular localisation of XopQ and XopX mutants that are defective in 14-3-3 binding and suppression of immune responses indicates that, for suppression, XopQ requires a cytoplasmic localisation whereas XopX requires nuclear localisation. Hence, both XopQ as well as XopX individually act as suppressors of rice immune responses, probably by targeting unique pathways in different subcellular compartments. However, we find that when XopQ is delivered through Agrobacterium along with XopX, it becomes an inducer of immune responses and that it now localizes in the nucleus. We also find that XopQ and XopX can interact with each other. This raises the possibility that besides being a suppressor of immune responses, XopQ can under certain circumstances also function as an inducer of immune responses.Item Understanding the molecular intricacies of rice-Rhizoctonia solani interactions(American Phytopathological Society, 2019) Ghosh, S.; Kanwar, P.; Jha, GopaljeeSheath blight disease is a devastating disease in rice that causes huge crop losses worldwide. It is caused by a necrotrophic fungus Rhizoctonia solani. In spite of global efforts till now there are no reports of complete resistance against this pathogen. We observed that R. solani has a brief biotrophic phase wherein mycelial grows parallel to rice veins without showing any morphological and anatomical changes. However, at later stage, i.e. necrotrophic phase, infection cushions along with anatomical changes are observed at the site of disease symptoms. Through transcriptome and metabolome studies we have identified several candidate host susceptibility factors and pathogenicity determinants that might play an important role during pathogenesis of R. solani in rice. Furthermore, using whole genome studies, we have identified several gene/gene families that might contribute to the aggressiveness of the R. solani strains. Although gene manipulation studies in R. solani is difficult we have devised ways wherein we can functionally characterize these pathogenicity determinants. Overall the present study will help in better understanding of the rice-R. solani pathosystem which would eventually be helpful in developing strategies for durable sheath blight disease tolerance in rice.Item 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.Item Giberellic acid-stimulated transcript proteins evolved through successive conjugation of novel motifs and their subfunctionalization(American Society of Plant Biologists, 2019) Kumar, Ashutosh; Singh, Alka; Kumar, Pramod; Sarkar, Ananda K.Gibberellic Acid Stimulated Transcript (GAST)-like genes encode small polypeptides, some of which have been implicated in diverse biological processes regulating plant growth and development. However, the occurrence of GASTs among plants, their protein structures, and the mechanisms by which they evolved remain elusive. Here, using a customized workflow, we report genes encoding GAST proteins, identify novel motifs and evolutionary patterns contributing to sub-functionalization of GAST domains, and explore functional conservation across diverse plants. We show that GAST-like sequences evolved initially in the vascular plant Selaginella moellendorffii, after the divergence from bryophytes, and later emerged in gymnosperms and angiosperms. GASTs in angiosperms are characterized by four conserved novel motifs; however, relatively fewer conserved motifs exist in pteridophytes and gymnosperms. Phylogenetic analysis revealed that the GCR1 motif evolved early in S. moellendorffii GAST, which further acquired sub-functionalization through successive conjugation of other motifs and remained conserved across plants, as supported by their collinearity. Functional characterization of two orthologues from the dicot Arabidopsis thaliana (Ath-GASA10) and the monocot rice (Oryza sativa; Osa-GAST9) suggests hormonal regulation, novel roles in seed germination, and functional conservation among diverse plant groups. Computational modelling predicts that these GAST genes are regulated by several factors, including the phytohormones GA and ABA, through conserved cis-motifs present in their promoters, and that they might act as signaling molecules in a complex feedback loop. Thus, our study identifies GASTs and their encoded proteins, uncovers their structure, novel motifs, and evolutionary pattern among plants, and suggests their functional conservation.Item Analysis of rice proteins with DLN repressor Motif/S(MDPI AG, 2019) Singh, Purnima; Mathew, Iny Elizebeth; Verma, Ankit; Tyagi, Akhilesh K.; Agarwal, PinkyTranscriptional regulation includes both activation and repression of downstream genes. In plants, a well-established class of repressors are proteins with an ERF-associated amphiphilic repression/EAR domain. They contain either DLNxxP or LxLxL as the identifying hexapeptide motif. In rice (Oryza sativa), we have identified a total of 266 DLN repressor proteins, with the former motif and its modifications thereof comprising 227 transcription factors and 39 transcriptional regulators. Apart from DLNxxP motif conservation, DLNxP and DLNxxxP motifs with variable numbers/positions of proline and those without any proline conservation have been identified. Most of the DLN repressome proteins have a single DLN motif, with higher relative percentage in the C-terminal region. We have designed a simple yeast-based experiment wherein a DLN motif can successfully cause strong repression of downstream reporter genes, when fused to a transcriptional activator of rice or yeast. The DLN hexapeptide motif is essential for repression, and at least two “DLN” residues cause maximal repression. Comparatively, rice has more DLN repressor encoding genes than Arabidopsis, and DLNSPP motif from rice is 40% stronger than the known Arabidopsis SRDX motif. The study reports a straightforward assay to analyze repressor activity, along with the identification of a strong DLN repressor from rice.Item Cross-talk signaling in rice during combined drought and bacterial blight stress(Frontiers Media S.A., 2019) Vemanna, Ramu S; Bakade, Rahul; Bharti, Pooja; Kumar, MK Prasanna; Sreeman, Sheshshayee M; Senthil-Kumar, Muthappa; Makarla, UdayakumarDue to climatic changes, rice crop is affected by moisture deficit stress and pathogens. Tissue water limitation besides reducing growth rates, also renders the crop susceptible to the infection by Xanthomonas oryzae pv. oryzae (Xoo) that causes bacterial leaf blight. Independently, both drought adaptation and Xoo resistance have been extensively studied. Though the cross-talk between drought and Xoo stress responses have been explored from individual stress studies, examining the combinatorial stress response is limited in rice. Recently published combined stress studies showed that under the combined stress, maintenance of carbon assimilation is hindered and such response is regulated by overlapping cellular mechanisms that are different from either of the individual stresses. Several receptors, MAP kinases, transcription factors, and ribosomal proteins, are predicted for playing a role in cellular homeostasis and protects cells from combined stress effects. Here we provide a critical analysis of these aspects using information from the recently published combined stress literature. This review is useful for researchers to comprehend combinatorial stress response of rice plants to drought and Xoo.Item Comparative nuclear proteomics analysis provides insight into the mechanism of signaling and immune response to blast disease caused by Magnoporthe oryzae in rice(John Wiley & Sons, 2019) Narula, Kanika; Choudhary, Pooja; Ghosh, Sudip; Elagamey, Eman; Chakraborty, Niranjan; Chakraborty, SubhraModulation of plant immune system by extrinsic/intrinsic factors and host-specific determinants fine-tunes cellular components involving multiple organelles, particularly nucleus to mount resistance against pathogen attack. Rice blast, caused by hemibiotrophic fungus Magnaporthe oryzae, is one of the most devastating diseases that adversely affect rice productivity. However, the role of nuclear proteins and their regulation in response to M. oryzae remains unknown. Here, we elucidate the nucleus-associated immune pathways in blast resistant rice genotype. Temporal analysis of nuclear proteome was carried out using 2-DE coupled MS/MS analysis. A total of 140 immune responsive proteins (IRPs) were identified associated with nuclear reorganization, cell division, energy production/deprivation, signaling and gene regulation. We interrogated the proteome data using correlation network analysis that identified significant functional modules pointing towards immune related coinciding processes through a common mechanism of remodelling and homeostasis. Novel clues regarding blast resistance include nucleus associated redox homeostasis and glycolytic enzyme mediated chromatin organization which manipulates cell division and immunity. Taken together, our study provides evidence that coordination of nuclear function and reprogramming of host translational machinery regulate resistance mechanism against blast disease.Item Burkholderia gladioli strain NGJ1 deploys a prophage tail-like protein for mycophagy(Shared Science Publishers OG, 2018) Kumar, Rahul; Yadav, Sunil Kumar; Swain, Durga Madhab; Jha, GopaljeeFungal pathogens are responsible for approximately two third of the infectious plant diseases. Historically they have been associated with several devastating famines, causing death and disabilities in humans. Mostly fungal diseases are being controlled by using fungicides which otherwise have adverse side effects on the health of consumers as well as environment. Due to extensive usages, pathogens have evolved resistance against most of the commonly used fungicides and rendered them ineffective. Controlling fungal disease in a sustainable and eco-friendly fashion remains a challenge. The antifungal biocontrol agents are being considered as potent, alternative and ecofriendly approach to manage fungal diseases. In our recent work, we have identified a rice associated bacterium; Burkholderia gladioli strain NGJ1 which demonstrates broad spectrum fungal eating (mycophagous) property. We determined that the bacterium utilizes its type III secretion system (Injectisome) machinery to deploy a prophage tail-like protein (Bg_9562) into fungal cells to devour them. The purified Bg_9562 protein from overexpressing recombinant E. coli strain demonstrates broad spectrum antifungal activity. Overall our study opens up a new opportunity to exploit prophage taillike protein as potent antifungal compound to control plant as well as animal fungal diseases.