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Author: search.filters.author.Sarkar, Ananda K.Subject: search.filters.subject.seed germination

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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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    Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination
    (Nature Publishing Group, 2018) Das, Shabari Sarkar; Yadav, Sandeep; Singh, Archita; Gautam, Vibhav; Sarkar, Ananda K.; Nandi, Asis K.; Karmakar, Prakash; Majee, Manoj; Sanan-Mishra, Neeti
    Seed germination paves the way for the dormant embryo to establish itself as a new plant marking the first critical step in postembryonic plant growth and development. Germination starts with the uptake of water (imbibition), followed by induction of transcription, translation, energy metabolism, and cell division processes. Although small RNAs have been implicated in many developmental processes, their role during seed germination stages and conditions remained elusive. Here we show that seed germination conditions, like imbibition and temperature, dynamically regulate the expression of many developmentally important miRNAs and their targets. We have identified 58 miRNAs belonging to 30 different families at different seed germination conditions. Amongst these, 15 miRNAs and their targets were significantly differentially expressed in Arabidopsis seeds in dry and 12 h, 24 h and 48 h of imbibition. Interestingly, differential expression of miR390, which targets trans-acting siRNA locus (TAS3) derived transcripts, resulted in alteration of tasiR-ARF mediated regulation of expression of target AUXIN RESPONSE FACTORs (ARF2/3/4). Our results suggest that the dynamic expression of several miRNAs, their targets, and a crosstalk between miRNA and ta-siRNA pathways contribute to the regulation of seed germination in Arabidopsis thaliana.