Publications of NIPGR Scientists

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Author: search.filters.author.Mathur, SaloniSubject: search.filters.subject.Tomato

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    Functional diversification of miR172 isoforms in tomato under abiotic stress
    (Elsevier B.V., 2024) Bansal, Chandni; Kumar, Adesh; Shrivastava, Monika; Mathur, Saloni
    Plant gene families have expanded many folds as opposed to animals to compensate for being sessile as well as having unique features like ability to photosynthesise. While different protein families are well characterised in plants, similar knowledge on miRNA families is still in its infancy. The MIR172 family plays important role in various plant development processes including vegetative to reproductive phase change, floral patterning, nodulation, and fruit ripening as well as also in response to different environmental cues. However, in-depth analysis of this family in tomato (Solanum lycopersicum) is limited. In this study, we identified four new MIR172 loci (Sly-MIR172a1/a2/e/f) and two new isoforms, other than those reported at the miRBase repository. The MIR172 family has expanded by segmental duplication events and is conserved between the wild (S. pennellii and S. pimpinellifolium) and the cultivated tomato varieties. However, phylogenetic analysis showed that S. pennellii formed the most divergent member within each clade and S. pimpinellifolium is closer to the cultivated varieties. Additionally, investigations in 42 plant species highlighted that miR172a/b is the most abundant form in the plant kingdom. In addition to the classical target Apetala2 (AP2), degradome analysis identified SEC14p-like phosphatidylinositol transfer family protein (SEC14p) as a novel target of Sly-miR172 that was validated using precursor:effector and target:reporter transient assays. Further, we report dual mode of Sly-miR172-mediated silencing of targets Sly-AP2 and Sly-SEC14p by post-transcriptional transcript cleavage as well as translational repression. Different members of Sly-MIR172s:Sly-AP2s and Sly-MIR172s:Sly-SEC14p exhibit inverse expression correlation in response to different abiotic stresses, suggesting their role in stress response. Functional investigation of MIR172 showed that tomato plants performed better in different abiotic stresses (heat, drought, and salt) upon MIR172 overexpression or target knock-down by virus-induced-gene-silencing. Conversely, when miRNA is chelated using short-tandem-target-mimic, the plants exhibit sensitivity to these stresses. Thus, SlymiR172 acts as a positive regulator while its targets Sly-AP2a and Sly-SEC14p as negative regulators of different abiotic stresses.
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    Exploring the master regulator heat stress transcription factor HSFA1a-mediated transcriptional cascade of HSFs in the heat stress response of tomato
    (Springer Nature Publishing AG, 2021) Rao, Sombir; Das, Jaishri Rubina; Mathur, Saloni
    The tomato heat stress transcription factor A1a (Sly-HSFA1a) acts as the master regulator of the heat stress (HS) by directly regulating the transcription of Sly-HSFA2. However, it is unclear whether the activation of Sly-HSFA2 alone is sufficient to trigger the entire transcriptional cascade downstream of Sly-HSFA1a. Therefore, the present study aims to delineate the Sly-HSFA1a governed downstream HSFs cascade regulating the tomato heat stress response. The study identified several HSFs with common and specific roles in different HS regimes as well as in HS memory. Furthermore, the study established Sly-HSFA7, Sly-HSFA6b, Sly-HSFA4c, Sly-HSFB1 and Sly-HSFB2b as new downstream targets of SlyHSFA1a during heat stress by using virus-induced-gene-silencing (VIGS) of Sly-HSFA1a. Moreover, the silencing of downstream target Sly-HSFA7 and Sly-HSFB1 revealed the orchestration of downstream transcriptional cascade of HSFs regulated individually or in a synergistic manner by Sly-HSFA1a and Sly-HSFA7 along with co-activator Sly-HSFB1. This complex transcriptional cascade of HSFs sheds light on regulatory mechanisms that enable tomato plants to respond to various heat stress conditions to maintain cellular homeostasis.
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    Identification, evolutionary profiling, and expression analysis of F-box superfamily genes under phosphate deficiency in tomato
    (Elsevier B.V., 2021) Akash; Parida, Adwaita Prasad; Srivastava, Alok; Mathur, Saloni; Sharma, Arun Kumar; Kumar, Rahul
    F-box genes are an integral component of the Skp1-cullin-F-box (SCF) complex in eukaryotes. These genes are primarily involved in determining substrate specificities during cellular proteolysis. Here we report that 410 members constitute the F-box superfamily in tomato. Based on the incidence of C-terminal domains, these genes fell into ten subfamilies, leucine-rich repeat domain-containing F-box members constituting the largest subfamily. The F-box genes are present on all 12 chromosomes with varying gene densities. Both segmental and tandem duplication events contribute significantly to their expansion in the tomato genome. The syntenic analysis revealed close relationships among F-box homologs within Solanaceae species genomes. Transcript profiling of F-box members identified several ripening-associated genes with altered expression in the ripening mutants. RNA-sequencing data analysis showed that phosphate (Pi) deficiency affected 55 F-box transcripts in the Pi-deficient seedlings compared to their control seedlings. The persistent up-regulation of eight members, including two phloem protein 2B (PP2–B) genes, PP2–B15, and MATERNAL EFFECT EMBRYO ARREST 66 (MEE66) homologs, at multiple time-points in the roots, shoot, and seedling, point towards their pivotal roles in Pi starvation response in tomato. The attenuation of such upregulation in sucrose absence revealed the necessity of this metabolite for robust activation of these genes in the Pi-deficient seedlings. Altogether, this study identifies novel F-box genes with potential roles in fruit ripening and Pi starvation response and unlocks new avenues for functional characterization of candidate genes in tomato and other related species.
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    Novel insights into expansion and functional diversification of MIR169 family in tomato
    (Springer Nature Publishing AG, 2020) Rao, Sombir; Balyan, Sonia; Jha, Sarita; Mathur, Saloni
    MIR169 family is an evolutionarily conserved miRNA family in plants. A systematic in-depth analysis of MIR169 family in tomato is lacking. We report 18 miR169 precursors, annotating new loci for MIR169a, b and d, as well as 3 novel mature isoforms (MIR169f/g/h). The family has expanded by both tandem- and segmental-duplication events during evolution. A tandem-pair MIR169b/b-1 and MIR169b-2/h is polycistronic in nature coding for three MIR169b isoforms and a new variant miR169h, that is evidently absent in the wild relatives S. pennellii and S. pimpinellifolium. Seven novel miR169 targets including RNA-binding protein, protein-phosphatase, aminotransferase, chaperone, tetratricopeptide-repeat-protein, and transcription factors ARF-9B and SEPELLATA-3 were established by efficient target cleavage in the presence of specific precursors as well as increased target abundance upon miR169 chelation by short-tandem-target-mimic construct in transient assays. Comparative antagonistic expression profiles of MIR169:target pairs suggest MIR169 family as ubiquitous regulator of various abiotic stresses (heat, cold, dehydration and salt) and developmental pathways. This regulation is partly brought about by acquisition of new promoters as demonstrated by promoter MIR169:GUS reporter assays as well as differential processivity of different precursors and miRNA cleavage efficiencies. Thus, the current study augments the functional horizon of MIR169 family with applications for stress tolerance in crops.