Institutional Publications

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Subject: search.filters.subject.Lignin

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    Functional characterization of WsPR-1 reveals its interplay with cytokinin and gibberellin signaling pathways
    (Elsevier B.V., 2024) Singh, Varinder; Kumar, Paramdeep; Pandey, Ashutosh; Hallan, Vipin; Pati, Pratap Kumar
    Pathogenesis-related protein 1 (PR-1) is an antimicrobial protein involved in systemic acquired resistance (SAR) in plants, but its regulatory role and interactions with other pathways remain unclear. In this study, we functionally characterize WsPR-1 gene of Withania somnifera in Nicotiana tabacum to elucidate its role in plant defense, growth, and development. Interestingly, transgenic tobacco plants with increased levels of cytokinin (CK) and decreased gibberellins (GAs) exhibited stunted shoot growth, an underdeveloped root system, modified leaf morphology, reduced seed pod production, and delayed leaf senescence. Transcriptional analysis revealed that WsPR-1 overexpression downregulated the GA 20-oxidase (GA20ox) gene involved in GA biosynthesis while upregulating GA 2-oxidase (GA2ox), a GA catabolic enzyme. Moreover, transcript levels of FRUITFULL (FUL) and LEAFY (NFL2) flowering genes exhibited a decrease in WsPR-1 plants, which could explain the delayed flowering and reduced seed pod development in transgenic plants. Confocal microscopy confirmed increased lignin deposition in stem cross-sections of WsPR-1 transgenic plants, supported by gene expression analysis and lignin content quantification. Additionally, our findings also suggest the involvement of Knotted1-like homeobox (KNOX) gene in enhancing cytokinin levels. This study highlights PR-1's regulatory role in plant growth and development, with potential to boost crop yields and enhance resilience.
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    Lignin: the building block of defense responses to stress in plants
    (Springer Nature Publishing AG, 2023) Yadav, Shalini; Chattopadhyay, Debasis
    Lignin is a complex aromatic biopolymer important for providing mechanical strength to the cell wall and resistance against both biotic and abiotic stresses. It helps in plant growth by providing physical strength and helping in long distance transport of water and minerals. Lignin biosynthetic genes are known to be induced under both biotic and abiotic stresses, and perturbations in lignin biosynthesis has shown to result in changes in plants defense responses against these stresses. It’s important to understand how these sophisticated mechanisms are employed by the plants to adapt to the adverse climatic conditions and develop more resilient plant varieties. In this review, we try to deliver a thorough comprehension of how lignin biosynthesis is altered under various environmental conditions. We believe this information will be useful in understanding the role of diferent lignin biosynthetic genes in conferring resistance against diferent stresses.
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    The R2R3-MYB gene family in banana (Musa acuminata): Genome-wide identification, classification and expression patterns
    (PLOS, 2020) Pucker, Boas; Pandey, Ashutosh; Weisshaar, Bernd; Stracke, Ralf
    The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a comprehensive, genome-wide analysis of the MYB genes from Musa acuminata DH-Pahang (A genome). A total of 285 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Organ- and development-specific expression patterns were determined from RNA-Seq data. For 280 M. acuminata MYB genes for which expression was found in at least one of the analysed samples, a variety of expression patterns were detected. The M. acuminata R2R3-MYB genes were functionally categorised, leading to the identification of seven clades containing only M. acuminata R2R3-MYBs. The encoded proteins may have specialised functions that were acquired or expanded in Musa during genome evolution. This functional classification and expression analysis of the MYB gene family in banana establishes a solid foundation for future comprehensive functional analysis of MaMYBs and can be utilized in banana improvement programmes.
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    Spodoptera litura-mediated chemical defense is differentially modulated in older and younger systemic leaves of Solanum lycopersicum
    (Springer Nature, 2018) Kundu, Anish;  Mishra, Shruti; Vadassery, Jyothilakshmi
    Main conclusion: Metabolite profling, biochemical assays, and transcript analysis revealed diferential modulation of specifc induced defense responses in local, older, and younger systemic leaves in Solanum lycopersicum upon Spodoptera litura herbivory. Plants reconfgure their metabolome upon herbivory to induce production of defense metabolites involved in both direct and indirect defenses against insect herbivores. Herbivory mediated leaf-to-leaf systemic induction pattern of primary and nonvolatile secondary metabolites is not well studied in tomato. Here, we show that, in cultivated tomato Solanum lycopersicum herbivory by generalist insect, Spodoptera litura results in diferential alteration of primary metabolites, majorly sugars and amino acids and specifc secondary metabolites in local, younger, and older systemic leaves. Cluster analysis of 55 metabolites identifed by GC–MS showed correlation between local and younger systemic leaves. Re-allocation of primary metabolites like glucose and amino acids from the local to systemic leaf was observed. Secondary metabolites chlorogenic acid, cafeic acid, and catechin were signifcantly induced during herbivory in systemic leaves. Among specifc secondary metabolites, chlorogenic acid and catechin signifcantly inhibits S. litura larval growth in all stages. Local leaf exhibited increased lignin accumulation upon herbivory. Diferential alteration of induced defense responses like reactive oxygen species, polyphenol oxidase activity, proteinase inhibitor, cell wall metabolites, and lignin accumulation was observed in systemic leaves. The metabolite alteration also resulted in increased defense in systemic leaves. Thus, comparative analysis of metabolites in local and systemic leaves of tomato revealed a constant re-allocation of primary metabolites to systemic leaves and diferential induction of secondary metabolites and induced defenses upon herbivory.
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    Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating beta-proteobacterium Pandoraea sp ISTKB
    (BioMed Central Ltd, 2018) Kumar, Madan; Verma, Sandhya; Gazara, Rajesh Kumar; Kumar, Manish; Pandey, Ashok; Verma, Praveen K.; Thakur, Indu Shekhar
    Background: Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization. Results: Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase-peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL-VA Conclusions: The unusual aerobic'-CoA'-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4-5% of total seguenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches providedvalidation to this strain's robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.