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Author: search.filters.author.Kumar, AmishHas files: Yes

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    Shared ancestry of core-histone subunits and non-histone plant proteins containing the Histone Fold Motif (HFM)
    (World Scientific Publishing Co Pte Ltd, 2021) Kumar, Amish; Yadav, Gitanjali
    The three helical Histone Fold Motif (HFM) of core histone proteins provides an evolutionarily favored site for the protein–DNA interface. Despite significant variation in sequence, the HFM retains a distinctive structural fold that has diversified into several non-histone protein families. In this work, we explore the ancestry of non-histone HFM containing families in the plant kingdom. A sequence search algorithm was developed using iterative profile Hidden Markov Models to identify remote homologs of core-histone proteins. The resulting hits were functionally annotated, classified into families, and subjected to comprehensive phylogenetic analyses via Maximum likelihood and Bayesian methods. We have identified 4390 HFM containing proteins in the plant kingdom that are not histones, mostly existing as diverse transcription factor families, distributed widely within and across taxonomic groups. Patterns of homology suggest that core histone subunit H2A has evolved into newer families like NF-YC and DRAP1, whereas the H2B subunit of core histones shares a common ancestry with NF-YB and DR1 class of TFs. Core histone subunits H3 and H4 were found to have evolved into DPE and TAF proteins, respectively. Taken together these results provide insights into diversification events during the evolution of the HFM, including sub-functionalization and neo-functionalization of the HFM.
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    Networks of function and shared ancestry provide insights into diversification of histone fold domain in the plant kingdom
    (Springer Nature Publishing AG, 2020) Kumar, Amish; Yadav, Gitanjali
    The Histone Fold Motif (HFM) of core histone proteins is one of the most highly conserved signature motifs in living organisms. Despite significant variation in sequence over millions of years of evolution, the HFM retains a distinctive structural fold that has diversified into several non-histone protein families. We have identified over 4000 HFM containing proteins in plants that are not histones, raising the question of why the family has expanded so considerably in the plant kingdom. We find that a majority of non-histone HFMs are playing regulatory roles, and that they are distributed widely within and across taxonomic groups. In this work we explore the relationships between the HFM of non-histones and that of their ancestral core histone forerunners, using a network approach. Networks of core histones and non-histone counterparts were superimposed with additional layers of complexity, like functional annotations, sub cellular locations, taxonomy and shared ancestry. HFM networks of model plants rice and Arabidopsis were investigated in terms of gene expression, interactions with other proteins as well as regulatory potential, to gain insights into diversification events during evolution that are not immediately evident from phylogenetic trees or raw data alone. Taken together, the networks elucidate diverse paths of evolution of the histone fold motif, leading to sub-functionalization and neo-functionalization of the HFM.
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    Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis
    (Springer Nature Publishing AG, 2020) Smita, Shuchi; Katiyar, Amit; Lenka, Sangram Keshari; Dalal, Monika; Kumar, Amish; Mahtha, Sanjeet Kumar; Yadav, Gitanjali; Chinnusamy, Viswanathan; Pandey, Dev Mani; Bansal, Kailash Chander
    Abiotic stress tolerance is a complex trait regulated by multiple genes and gene networks in plants. A range of abiotic stresses are known to limit rice productivity. Meta-transcriptomics has emerged as a powerful approach to decipher stress-associated molecular network in model crops. However, retaining specificity of gene expression in tolerant and susceptible genotypes during meta-transcriptome analysis is important for understanding genotype-dependent stress tolerance mechanisms. Addressing this aspect, we describe here “abiotic stress tolerant” (ASTR) genes and networks specifically and differentially expressing in tolerant rice genotypes in response to different abiotic stress conditions. We identified 6,956 ASTR genes, key hub regulatory genes, transcription factors, and functional modules having significant association with abiotic stress–related ontologies and cis-motifs. Out of the 6956 ASTR genes, 73 were co-located within the boundary of previously identified abiotic stress trait–related quantitative trait loci. Functional annotation of 14 uncharacterized ASTR genes is proposed using multiple computational methods. Around 65% of the top ASTR genes were found to be differentially expressed in at least one of the tolerant genotypes under different stress conditions (cold, salt, drought, or heat) from publicly available RNAseq data comparison. The candidate ASTR genes specifically associated with tolerance could be utilized for engineering rice and possibly other crops for broad-spectrum tolerance to abiotic stresses.