Institutional Publications

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End date: 2019Has files: No

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    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.
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    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.
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    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.
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    Understanding the molecular intricacies of rice-Rhizoctonia solani interactions
    (American Phytopathological Society, 2019) Ghosh, S.; Kanwar, P.; Jha, Gopaljee
    Sheath 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.
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    Burkholderia gladioli strain NGJ1 deploys a prophage tail-like protein to feed on fungi
    (American Phytopathological Society, 2019) Swain, D.M.; Yadav, S.; Tyagi, I.; Kumar, R.; Kumar, R.; Ghosh, S.; Das, J.; Jha, Gopaljee
    Fungal pathogens are responsible for approximately two third of the infectious plant diseases. Due to extensive usages, pathogens have evolved resistance against most of the commonly used fungicides. Rice sheath blight disease caused by Rhizoctonia solani remains a serious threat to global sustainable agriculture. The pathogen has a complex biology and has been reported occurring world-wide causing necrosis and dampingoff on numerous host plant species. The pathogen is polymorphic and despite extensive efforts, till today no source of complete disease resistance has been identified against this pathogen. We have recently discovered a novel bacterium Burkholderia gladioli strain NGJ1 which has broad spectrum mycophagus ability. We also demonstrated that the bacteria NGJ1 deploys a prophage tail like protein (Bg_9562) to feed over fungi in a T3SS dependant manner. Moreover we observed that Bg_9562 protein has a broad spectrum antifungal activity on Rhizoctonia solani as well as several other phytopathogenic fungi. Furthermore, being equipped to kill and feed upon fungi, the mycophagous bacteria can serve as an experimental tool box to facilitate discovery of novel anti-fungal molecules. This opens up a new biotechnological application of this prophage tail like protein in controlling fungal diseases in rice as well as in other plants.
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    PtRFdb: Plant tRNA-derived fragments database
    (Springer Nature Publishing AG, 2019) Zahra, Shafaque; Kumar, Shailesh
    The transfer RNA-derived fragments or tRFs represent a distinct class of small non-coding RNAs, and have been detected in evolutionarily divergent organisms. The role of tRFs in human cancers and infectious diseases as well as in gene regulation has been well established in diverse organisms. However, in plants, there is a need to further consolidate the tRF research by identification and characterization of tRFs because this domain is still unexplored across the plant kingdom. This chapter discusses about PtRFdb (www.nipgr.res.in/PtRFdb), a web-based repository harbouring the valuable information related to transfer RNA derived fragments (tRFs) in 10 different plant species. This database is believed to be beneficial for molecular biologists in facilitating future survey and characterization of tRFs across the plant kingdom.
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    Whole mount in situ localization of miRNAs and target mRNA transcripts in plants
    (Springer Nature Publishing AG, 2019) Gautam, Vibhav; Singh, Archita; Verma, Swati; Singh, Sharmila; Chatterjee, Sourav; Sarkar, Ananda K.
    The functional characterization of miRNAs often involves understanding of their spatiotemporal expression, which mostly relies on reporter-based or in situ hybridization studies. The available in situ localization methods follow separate protocols for pre-hybridization, hybridization, post-hybridization, and detection steps for both miRNA and mRNA transcripts in plants. In this study, we present a single method which can be used for whole mount in situ localization of both miRNAs and mRNAs in different plant tissues. Our modified method provides enhanced sensitivity for the localization of miRNA and their target transcripts. Consequently, a less laborious, time-saving, economic and efficient method has been proposed by the modification of pre-hybridization, hybridization, post-hybridization and detection steps.
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    GC-MS-based analysis of methanol: chloroform-extracted fatty acids from plant tissues
    (Bio-protocol LLC., 2018) Patel, Manish Kumar; Das, Shubhashis; Thakur, Jitendra K.
    Fatty acids (FAs) are carboxylic acids with long aliphatic chains that may be straight, branched and saturated or unsaturated. Most of the naturally occurring plant FAs contains an even number of carbon (C4-C24). FAs are used in food and pharmacological industries due to their nutritional importance. In addition, FAs are considered as a promising alternative for the production of biodiesel from terrestrial plant biomass. To establish commercial applications, more reliable analytical methods are needed for the identification, quantification, and composition determination of FAs. Here, we describe a relatively rapid and sensitive method for the extraction, identification, and quantification of FAs from a small quantity of plant tissue. The method includes steps of lipid extraction, conversion of lipid to fatty acid methyl esters (FAMEs) by transmethylation, identification and quantification of FAMEs using gas chromatography-mass spectrometry (GC-MS). In this protocol, an internal standard is added prior to GC-MS analysis. The amount of each FA is calculated from its peak area relative to the peak area of the internal standard.
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    Robustness through regime flips in collapsing ecological networks
    (Springer Nature, 2018) Babu, Suresh; Yadav, Gitanjali
    There has been considerable progress in our perception of organized complexity in recent years. Recurrent debates on the dynamics and stability of complex systems have provided several insights, but it is very difficult to find identifiable patterns in the relationship between complex network structure and dynamics. Traditionally an arena for theoreticians, much of this research has been invigorated by demonstration of alternate stable states in real world ecosystems such as lakes, coral reefs, forests and grasslands. In this work, we use topological connectivity attributes of eighty six ecological networks and link these with random and targeted perturbations, to obtain general patterns of behaviour of complex real world systems. We have analyzed the response of each ecological network to individual, grouped and cascading extinctions, and the results suggest that most networks are robust to loss of specialists until specific thresholds are reached in terms of network geodesics. If the extinctions persist beyond these thresholds, a state change or ‘flip’ occurs and the structural properties are altered drastically, although the network does not collapse. As opposed to simpler or smaller networks, we find larger networks to contain multiple states that may in turn, ensure long-term persistence, suggesting that complexity can endow resilience to ecosystems. The concept of critical transitions in ecological networks and the implications of these findings for complex systems characterized by networks are likely to be profound with immediate significance for ecosystem conservation, invasion biology and restoration ecology.
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    Heat shock proteins and abiotic stress tolerance in plants
    (Springer Nature, 2018) Mishra, Divya; Shekhar, Shubhendu; Singh, Deepika; Chakraborty, Subhra; Chakraborty, Niranjan
    Abiotic stresses restrict plant growth and development, and reduce harvest index of many crop species worldwide. Maintenance of native conformation of proteins and reducing the accumulation of non-native proteins are imperative for survival under stress conditions as such stresses frequently lead to protein aggregation causing metabolic dysfunction. Heat shock proteins (HSP) play a key role in conferring abiotic stress tolerance. Plants protect themselves from numerous stresses by inducing HSP, besides some stress-responsive proteins, suggesting analogous response mechanisms. A close association between the HSP and ROS also co-exists, indicating that plants have evolved to gain a higher degree of regulation over ROS toxicity and can use ROS as elicitor to induce HSP for better adaptations through activating an array of molecules. Therefore, unraveling the mechanisms of plant response against various stress and the role of HSP in acquired stress tolerance is utmost important to delineate their specific function as a part of stress-responsive module. The HSP have been well characterized in different crop species, albeit the knowledge about their correlation with genome sequence information as well as their functional plasticity is limited.