Institutional Publications

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    Genome-wide identification and expression, protein-protein interaction and evolutionary analysis of the seed plant-specific BIG GRAIN and BIG GRAIN LIKE gene family
    (Frontiers Media S.A., 2017) Mishra, Bhuwaneshwar S.; Jamsheer, K Muhammed; Singh, Dhriti; Sharma, Manvi; Laxmi, Ashverya
    BIG GRAIN1 (BG1) is an auxin-regulated gene which functions in auxin pathway and positively regulates biomass, grain size and yield in rice. However, the evolutionary origin and divergence of these genes are still unknown. In this study, we found that BG genes are probably originated in seed plants. We also identified that seed plants evolved a class of BIG GRAIN LIKE (BGL) genes which share conserved middle and C-terminal motifs with BG. The BG genes were present in all monocot and eudicot species analyzed; however, the BGL genes were absent in few monocot lineages. Both BG and BGL were found to be serine-rich proteins; however, differences in expansion and rates of retention after whole genome duplication events were observed. Promoters of BG and BGL genes were found to be enriched with auxin-responsive elements and the Arabidopsis thaliana BG and BGL genes were found to be auxin-regulated. The auxin-induced expression of AthBG2 was found to be dependent on the conserved ARF17/19 module. Protein-protein interaction analysis identified that AthBG2 interact with regulators of splicing, transcription and chromatin remodeling. Taken together, this study provides interesting insights about BG and BGL genes and incentivizes future work in this gene family which has the potential to be used for crop manipulation.
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    Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes
    (Frontiers Media S.A., 2015) Singh, Vikash K.; Jain, Mukesh; Garg, Rohini
    Growth hormone auxin regulates various cellular processes by altering the expression of diverse genes in plants. Among various auxin-responsive genes, GH3 genes maintain endogenous auxin homeostasis by conjugating excess of auxin with amino acids. GH3 genes have been characterized in many plant species, but not in legumes. In the present work, we identified members of GH3 gene family and analyzed their chromosomal distribution, gene structure, gene duplication and phylogenetic analysis in different legumes, including chickpea, soybean, Medicago, and Lotus. A comprehensive expression analysis in different vegetative and reproductive tissues/stages revealed that many of GH3 genes were expressed in a tissue-specific manner. Notably, chickpea CaGH3-3, soybean GmGH3-8 and -25, and Lotus LjGH3-4, -5, -9 and -18 genes were up-regulated in root, indicating their putative role in root development. In addition, chickpea CaGH3-1 and -7, and Medicago MtGH3-7, -8, and -9 were found to be highly induced under drought and/or salt stresses, suggesting their role in abiotic stress responses. We also observed the examples of differential expression pattern of duplicated GH3 genes in soybean, indicating their functional diversification. Furthermore, analyses of three-dimensional structures, active site residues and ligand preferences provided molecular insights into function of GH3 genes in legumes. The analysis presented here would help in investigation of precise function of GH3 genes in legumes during development and stress conditions.
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    Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
    (Frontiers Media S.A., 2015) Singh, Vikash K.; Jain, Mukesh
    Auxin plays a central role in many aspects of plant growth and development. Auxin/Indole-3-Acetic Acid (Aux/IAA) genes cooperate with several other components in the perception and signaling of plant hormone auxin. An investigation of chickpea and soybean genomes revealed 22 and 63 putative Aux/IAA genes, respectively. These genes were classified into six subfamilies on the basis of phylogenetic analysis. Among 63 soybean Aux/IAA genes, 57 (90.5%) were found to be duplicated via whole genome duplication (WGD)/segmental events. Transposed duplication played a significant role in tandem arrangements between the members of different subfamilies. Analysis of Ka/Ks ratio of duplicated Aux/IAA genes revealed purifying selection pressure with restricted functional divergence. Promoter sequence analysis revealed several cis-regulatory elements related to auxin, abscisic acid, desiccation, salt, seed, and endosperm, indicating their role in development and stress responses. Expression analysis of chickpea and soybean Aux/IAA genes in various tissues and stages of development demonstrated tissue/stage specific differential expression. In soybean, at least 16 paralog pairs, duplicated via WGD/segmental events, showed almost indistinguishable expression pattern, but eight pairs exhibited significantly diverse expression patterns. Under abiotic stress conditions, such as desiccation, salinity and/or cold, many Aux/IAA genes of chickpea and soybean revealed differential expression. qRT-PCR analysis confirmed the differential expression patterns of selected Aux/IAA genes in chickpea. The analyses presented here provide insights on putative roles of chickpea and soybean Aux/IAA genes and will facilitate elucidation of their precise functions during development and abiotic stress responses.
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    In silico analysis reveals 75 members of mitogen-activated protein kinase kinase kinase gene family in rice
    (Oxford University Press, 2010) Rao, Kudupudi Prabhakara; Richa, Tambi; Kumar, Kundan; Raghuram, Badmi; Sinha, Alok Krishna
    Mitogen-Activated Protein Kinase Kinase Kinases (MAPKKKs) are important components of MAPK cascades, which are universal signal transduction modules and play important role in plant growth and development. In the sequenced Arabidopsis genome 80 MAPKKKs were identified and currently being analysed for its role in different stress. In rice, economically important monocot cereal crop only five MAPKKKs were identified so far. In this study using computational analysis of sequenced rice genome we have identified 75 MAPKKKs. EST hits and full-length cDNA sequences (from KOME or Genbank database) of 75 MAPKKKs supported their existence. Phylogenetic analyses of MAPKKKs from rice and Arabidopsis have classified them into three subgroups, which include Raf, ZIK and MEKK. Conserved motifs in the deduced amino acid sequences of rice MAPKKKs strongly supported their identity as members of Raf, ZIK and MEKK subfamilies. Further expression analysis of the MAPKKKs in MPSS database revealed that their transcripts were differentially regulated in various stress and tissue-specific libraries.