Publications of NIPGR Scientists

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Now showing 1 - 8 of 8
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    Plant isopropylmalate synthases: in and beyond leucine biosynthesis
    (Springer Nature Publishing AG, 2026) Varghese, Mohan; Lone, Asif; Bisht, Naveen C.
    Primary metabolic enzymes in amino acid biosynthesis pathways are involved in amino acid synthesis and maintenance of metabolic homeostasis through feedback regulatory mechanisms. The genes encoding these enzymes are also known to undergo functional diversification through evolutionary processes to encode specific secondary metabolic enzymes. One such enzyme is α-isopropylmalate synthase (α-IPMS), which catalyzes and regulates leucine (Leu) biosynthesis in eubacteria, archaebacteria, fungi, and plants, and has served as an evolutionary progenitor for specialized enzymes in distinct secondary metabolic pathways. However, most information on IPMS comes from the bacterial research community, particularly in the context of Leu overproduction or as a target for developing drugs against tuberculosis. In plants, only a few studies have reported on IPMS, focusing primarily on its role in regulating Leu homeostasis. Herein, we review the complex regulatory network that exists in Leu metabolism, focusing on the regulation of its biosynthesis and its key regulatory enzyme, IPMS. This review also highlights how evolution has independently recruited IPMS for specialized metabolism in several plant lineages. Finally, we describe the emerging roles of IPMS as a candidate for engineering amino acid and yield-related traits in crop plants. We also identify important open questions in this area that remain to be addressed.
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    Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Vivek, AT; Kiran, Harikumar; Sahu, Namrata; Kalakoti, Garima; Kumar, Shailesh
    Background:- Long non-coding RNAs (lncRNAs) play key roles in regulating plant growth, development, and stress responses. Despite their increasing identification in plant transcriptomes, a systematic characterization of lncRNAs is still lacking, leaving a significant knowledge gap. To address this, we systematically identified and characterized Arabidopsis lncRNAs through integrative analysis of strand-specific RNA sequencing data and multi-omics datasets, revealing their genomic features, regulatory interactions, and evolutionary characteristics. Results:- Using a custom pipeline applied to hundreds of stranded RNA-seq datasets, we assembled a comprehensive catalog of 4,772 intergenic and antisense Arabidopsis lncRNAs. In comparing multiple key features of lncRNAs with those of protein-coding genes, we found that intergenic lncRNAs contain high transposable element-derived fragments and display broader TE diversity. Distinct DNA methylation and histone modification signatures further distinguished lncRNAs from protein-coding genes. We additionally uncovered R-loop connections and associations with sRNAs involved in post-transcriptional regulation and RNA-directed DNA methylation, with a minor subset classified as Pol V–transcribed. Of note, our results revealed lncRNAs mediating stress-responsive cis interactions and others linked to trait-associated loci. Probing further, an experimental evidence resource confirmed small peptide production from multiple lncRNA loci. Extending our investigation, comparative analyses across Brassicaceae species revealed syntenic lncRNAs enriched for shared sequence motifs despite substantial sequence divergence. Conclusions:- This study provides a valuable and extensively annotated catalog of Arabidopsis lncRNAs, revealing their diverse genomic features, regulatory interactions, and evolutionary characteristics. Altogether, our work advocates for multi-omics integrative analysis as a potent strategy to efficiently enhance lncRNA annotation, providing insights into functionality and addressing annotation limitations. Our comprehensive bioinformatic analyses of Arabidopsis lncRNAs pave the way for future functional characterization of these transcripts.
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    Pangenome-wide identification, evolutionary analysis, and characterization of WOX gene family among Brassica Triangle of U's genomes
    (Elsevier B.V., 2025) Soundararajan, Prabhakaran; Vivek, AT; Suresh, Gokul Babu; Shukla, Bhavya; Singh, Kanchan B.M.; Kumar, Shailesh; Manivannan, Abinaya
    WUSCHEL-related homeobox (WOX) is an evolutionarily important gene family involved in key developmental processes such as embryo patterning, stem cell regulation, apical meristem maintenance, etc. Brassica contains several widely diversified and economically important vegetables grown worldwide. In this study, a pangenome-wide identification and characterization of the WOX gene family among all the species of Brassica Triangle of U's have been performed. WOX gene family was identified from the genomes of 31 Brassica species/morphotypes. About 26–28, 28, and 26–31 copies of WOX genes are present in diploid progenitors such as B. rapa (AA), B. nigra(BB), and B. oleracea (CC), respectively. In allotetraploid species, the number of WOX genes exceeds more than 50 copies. However, their number varies between morphotypes at the pangenome level. Motif and gene structure analysis showed distinct and conserved patterns between homoeologous genes. Non-synonymous (Ka)/Synonymous (Ks) ratio indicated that more number of modern/WUS clade orthologs underwent positive selection followed by those of the intermediate clade. Interacting networks between the WOX and miRNA showed that the CC genome has more complex network pattern compared to the AA genome. Although the WOX-miRNA interactions observed in both AABB and AACC genomes were distinct, they exhibited similarity in overlapping connections. Transcriptome data, analyzed from unfertilized ovule to seven developmental stages of embryos and their seed coat, sourced from public databases across six genomes, illustrated that WOX genes are expressed in a spatio-temporal manner throughout these developmental stages. Furthermore, qPCR analysis of WOX genes at two stages, such as 2–3 days old (leaf and root primordia) and 3 weeks old seedlings (leaf and root) in B. juncea and B. oleracea provides details of stage- and tissues-specific expression patterns between AB and C genomes. Overall, the present study sheds light on evolution and characterization of the WOX gene family in Brassica at the pangenome level for further functional validation.
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    Evolutionary and functional analysis of Two-Component System in chickpea reveals CaRR13, a TypeB RR, as positive regulator of symbiosis
    (John Wiley & Sons, 2021) Tiwari, Manish; Yadav, Manisha; Singh, Baljinder; Pandey, Vimal; Nawaz, Kashif; Bhatia, Sabhyata
    The critical role of cytokinin in early nodulation in legumes is well known. In our study, exogenous cytokinin application to roots of the important crop legume, chickpea (Cicer arietinum L.) led to the formation of pseudo nodules even in the absence of rhizobia. Hence a genome-wide analysis of the cytokinin signaling, Two-Component System (TCS) genes was conducted in chickpea, Medicago and Cajanus cajan. The integrated phylogenetic, evolutionary and expression analysis of the TCS genes was carried out which revealed that Histidine Kinases (HKs) were highly conserved, whereas, there was diversification leading to neofunctionalization at the level of Response Regulators (RRs) especially the TypeB RRs. Further, the functional role of the CaHKs in nodulation was established by complementation of the sln1Δ mutant of yeast and cre1 mutants of (Medicago) which led to restoration of the nodule deficient phenotype. Additionally, the highest expressing TypeB RR of chickpea, CaRR13 was functionally characterized. Its localization in the nucleus and its Y1H assay-based interaction with the promoter of the early nodulation gene CaNSP2 indicated its role as a transcription factor regulating early nodulation. Overexpression, RNAi lines and complementation of cre1 mutants with CaRR13 revealed its critical involvement as an important signaling molecule regulating early events of nodule organogenesis in chickpea.
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    High throughput identification of miRNAs reveal novel interacting targets regulating chickpea-rhizobia symbiosis
    (Elsevier B.V., 2021) Tiwari, Manish; Singh, Baljinder; Yadav, Manisha; Pandey, Vimal; Bhatia, Sabhyata
    Legumes developed symbiotic associations to meet its nitrogen requirement. The nitrogen fixation takes place in root nodules which involves bacterial colonization, organogenesis and nitrogen fixation. In order to unravel the miRNA mediated regulation of chickpea symbiosis, one microRNA and four parallel analysis of RNA ends (PARE) libraries were sequenced. Analysis of microRNA library identified a set of 91 miRNAs comprising of 84 conserved and 7 novel miRNAs. Additionally, PARE library analysis revealed 564 genes being targeted by 85 miRNAs. Phylogenetic analysis of the precursor sequences of the 91 miRNAs was carried out which revealed their ancestral relationships. Further, the mechanism of miRNAs biogenesis was predicted using the miRNAs information from other legumes. Reads from the nodule library were mapped to bacterial genomes to predict bacterial-encoded small RNAs. Real time expression analysis was used to validate the antagonistic expression pattern of important miRNA-mRNA target pairs. Four candidate miRNAs were selected for in planta study based on the antagonistic expression profiling as well as the novelty of their respective targets. miR171f, miR172c, miR394 and miR1509 targeted nodulation receptor kinase, Apetala2, histidine phosphotransferase, adenylate kinase respectively and were ectopically expressed in chickpea roots. The overexpression lines showed significant change in nodule numbers, the miR172c, miR394 and miR1509 resulted in an increase in nodule number whereas, miR171f overexpression led to a decrease in nodule number. Our analysis lays the foundation for functional characterization of novel miRNAs and their respective target pairs which control nodulation in chickpea and other leguminous crops.
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    Genomic dissection and expression analysis of stress-responsive genes in C4 panicoid models, Setaria italica and Setaria viridis
    (Elsevier B.V., 2020) Muthamilarasan, Mehanathan; Singh, Roshan Kumar; Suresh, Bonthala Venkata; Rana, Sumi; Dulani, Priya; Prasad, Manoj
    The study reports the identification and expression profiling of five major classes of C4 pathway-specific genes, namely, carbonic anhydrase (CaH), phosphoenolpyruvate carboxylase (PEPC), pyruvate orthophosphate dikinase (PPDK), NADP-dependent malate dehydrogenase (MDH) and NADP-dependent malic enzyme (NADP-ME), in the model species, Setaria italica and Setaria viridis. A total of 42 and 41 genes were identified in S. italica and S. viridis, respectively. Further analysis revealed that segmental and tandem duplications have contributed to the expansion of these gene families. RNA-Seq derived expression profiles of the gene family members showed their differential expression pattern in tissues and dehydration stress. Comparative genome mapping and Ks dating provided insights into their duplication and divergence in the course of evolution. Expression profiling of candidate genes in contrasting S. italica cultivars subjected to abiotic stresses and hormone treatments showed distinct stress-specific upregulation of SiαCaH1, SiβCaH5, SiPEPC2, SiPPDK2, SiMDH8, and SiNADP-ME5 in the tolerant cultivar. Overexpression of SiNADP-ME5 in heterologous yeast system enabled the transgenic cells to survive and grow in dehydration stress conditions, which highlights the putative role of SiNADP-ME5 in conferring tolerance to dehydration stress. Altogether, the study highlights key genes that could be potential candidates for elucidating their functional roles in abiotic stress response.
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    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.
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    Phylogenetic analysis reveals conservation and diversification of micro RNA166 genes among diverse plant species
    (Elsevier B.V., 2014) Barik, Suvakanta; SarkarDas, Shabari; Singh, Archita; Gautam, Vibhav; Kumar, Pramod; Majee, Manoj; Sarkar, Ananda K.
    Similar to the majority of the microRNAs, mature miR166s are derived from multiple members of MIR166 genes (precursors) and regulate various aspects of plant development by negatively regulating their target genes (Class III HD-ZIP). The evolutionary conservation or functional diversification of miRNA166 family members remains elusive. Here, we show the phylogenetic relationships among MIR166 precursor and mature sequences from three diverse model plant species. Despite strong conservation, some mature miR166 sequences, such as ppt-miR166m, have undergone sequence variation. Critical sequence variation in ppt-miR166m has led to functional diversification, as it targets non-HD-ZIPIII gene transcript (s). MIR166 precursor sequences have diverged in a lineage specific manner, and both precursors and mature osa-miR166i/j are highly conserved. Interestingly, polycistronic MIR166s were present in Physcomitrella and Oryza but not in Arabidopsis. The nature of cis-regulatory motifs on the upstream promoter sequences of MIR166 genes indicates their possible contribution to the functional variation observed among miR166 species.