Publications of NIPGR Scientists

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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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    A conserved HSF:miR169:NF-YA loop involved in tomato and Arabidopsis heat stress tolerance
    (John Wiley & Sons, 2022) Rao, Sombir; Gupta, Apoorva; Bansal, Chandni; Sorin, Celine; Crespi, Martin; Mathur, Saloni
    Heat stress transcription factors (HSFs) and microRNAs (miRNAs) regulate different stress and developmental networks in plants. Regulatory feedbacks are at the basis of these networks. Here, we report that plants improve their heat stress tolerance through HSF-mediated transcriptional regulation of MIR169 and post-transcriptional regulation of Nuclear Factor- YA (NF-YA) transcription factors. We show that HSFs recognize tomato and Arabidopsis MIR169 promoters using yeast-one-hybrid/ChIP-qPCR. Silencing tomato HSFs using virus induced gene silencing (VIGS) reduced Sly-MIR169 levels and enhanced Sly-NF- YA9/A10 target expression. Further, Sly-NF-YA9/A10-VIGS knock-down tomato plants and Arabidopsis plants overexpressing At-MIR169d or At-nf-ya2 mutants showed a link with increased heat tolerance. In contrast, Arabidopsis plants overexpressing At-NF-YA2, or those expressing a non-cleavable At-NF-YA2 form (miR169d-resistant At-NF-YA2) as well as plants inhibited for At-miRNA169d regulation (miR169d mimic plants) were more sensitive to heat stress, highlighting NF-YA as negative regulator of heat tolerance. Furthermore, post-transcriptional cleavage of NF-YA by elevated miR169 levels resulted in alleviating the repression of heat stress effectors HSFA7 in tomato and Arabidopsis revealing a retroactive control of HSFs by the miR169:NF-YA node. Hence, a regulatory feedback loop involving HSFs, miR169s and NF-YAs plays a critical role in the regulation of heat stress response in tomato and Arabidopsis plants.
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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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    RS_CRZ1, a C2H2 type transcription factor is required for pathogenesis of Rhizoctonia solani AG1-IA in tomato
    (American Phytopathological Society, 2021) Ghosh, Srayan; Kant, Ravi; Pradhan, Amrita; Jha, Gopaljee
    Rhizoctonia solani is a necrotrophic fungal pathogen which causes disease in diverse plant species. In recent years, the genomic and transcriptomic studies have identified several candidate pathogenicity determinants of R. solani; however, most of them remain to be validated. In this study, we report a viral vector-based host induced gene silencing (HIGS) as well as a dsRNA (double stranded RNA) based approach to effectively downregulate genes of R. solani AG1-IA (BRS1 strain) during pathogenesis in tomato. We tested a few of the in-planta upregulated R. solani genes and observed that silencing of one of them i.e. RS_CRZ1 (a C2H2 type Zn finger transcription factor) significantly compromises the pathogenesis of R. solani in tomato. The RS_CRZ1 silenced plants not only exhibited significant reduction in disease symptoms, but the depth of pathogen colonization was also compromised. Furthermore, we identified the R. solani genes that were co-regulated with RS_CRZ1 during pathogenicity process. The HIGS mediated silencing of a few of them (CL1756Contig1; subtilisin like protease and CL1817Contig2; 2OG- Fe(II) oxygenase) compromised the pathogenesis of R. solani in tomato. The ectopic expression of RS_CRZ1 complemented the crz1 mutant of yeast and restored tolerance against various metal ion stress. Overall, our study reveals the importance of RS_CRZ1 in managing the hostile environment encountered during host colonization. Also, it emphasizes the relevance of HIGS and dsRNA-based gene silencing approach towards functional characterization of pathogenicity determinants of R. solani.
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    Silencing of tomato CTR1 provides enhanced tolerance against Tomato leaf curl virus infection
    (Taylor & Francis Group, 2019) Chandan, Ravindra K.; Singh, Achuit K.; Patel, Sunita; Swain, Durga Madhab; Tuteja, Narendra; Jha, Gopaljee
    Tomato leaf curl virus(ToLCV) belonging to Begomovirus family of Geminivirus is known to cause one of the most destructive diseases in tomato. Amongst variousToLCVs, a monopartite Tomato leaf curl Joydebpur virus (ToLCJoV) is most prevalent in eastern part of India. In the present study, we observed induced expression of one of the negative regulators of ethylene signaling pathway gene (LeCTR1)in ToLCJoVinfected plants. TheTobacco rattle virus(TRV) induced silencing of theLeCTR1gene provided enhanced tolerance toToLCJoVinfections. The leaf curling as well as ROS accumulation was significantly reduced in the viral infectedLeCTR1silenced plants. Induction of several defense marker genes (NPR1, PR1, PR5, AOS2, EIN2, EIN3and ERF5) reinforced enhanced tolerance againstToLCJoVinfection in the LeCTR1silenced tomato. Overall, the present study provides evidence that silencing ofLeCTR1can be deployed to protect tomato fromToLCJoVinfections.
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    Plant ribosomal proteins, RPL12 and RPL19, play a role in nonhost disease resistance against bacterial pathogens
    (Frontiers Media S.A., 2015) Nagaraj, Satish; Senthil-Kumar, Muthappa; Ramu, Vemanna S.; Wang, Keri; Mysore, Kirankumar S.
    Characterizing the molecular mechanism involved in nonhost disease resistance is important to understand the adaptations of plant-pathogen interactions. In this study, virus-induced gene silencing (VIGS)-based forward genetics screen was utilized to identify genes involved in nonhost resistance in Nicotiana benthamiana. Genes encoding ribosomal proteins, RPL12 and RPL19, were identified in the screening. These genes when silenced in N. benthamiana caused a delay in nonhost bacteria induced hypersensitive response (HR) with concurrent increase in nonhost bacterial multiplication. Arabidopsis mutants of AtRPL12 and AtRPL19 also compromised nonhost resistance. The studies on NbRPL12 and NbRPL19 double silenced plants suggested that both RPL12 and RPL19 act in the same pathway to confer nonhost resistance. Our work suggests a role for RPL12 and RPL19 in nonhost disease resistance in N. benthamiana and Arabidopsis. In addition, we show that these genes also play a minor role in basal resistance against virulent pathogens.