Institutional Publications

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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.
Cultivar-biased regulation of HSFA7 and HSFB4a govern high-temperature tolerance in tomato
(Springer Nature Publishing AG, 2022) Rao, Sombir; Das, Jaishri Rubina; Balyan, Sonia; Verma, Radhika; Mathur, Saloni
Heat shock factors (HSFs) are at the core of heat stress (HS) response in plants. However, the contribution of HSFs governing the inherent thermo-tolerance mechanism in tomato from sub-tropical hot climates is poorly understood. With the above aim, comparative expression profiles of the HSF family in a HS-tolerant (CLN1621L) and -sensitive cultivars (CA4 and Pusa Ruby) of tomato under HS revealed cultivar-biased regulation of an activator (HSFA7) and a repressor (HSFB4a) class HSF. HSFA7 exhibited strong upregulation while HSFB4a showed downregulation in tolerant tomato cultivar upon HS. Functional characterization of HSFA7 and HSFB4a in a tolerant–sensitive cultivar pair by virus-induced gene silencing (VIGS)-based silencing and transient overexpression established them as a positive and a negative regulator of HS tolerance, respectively. Promoter:GUS reporter assays and promoter sequence analyses suggest heat-mediated transcriptional control of both the HSF genes in the contrasting cultivars. Moreover, degradome data highlighted HSFB4a is a probable target of microRNA Sly-miR4200. Transient in-planta Sly-MIR4200-effector:HSFB4a-reporter assays showed miRNA-dependent target down-regulation. Chelation of miRNA by short-tandem-target-mimic of Sly-miR4200 increased target abundance, highlighting a link between Sly-miR4200 and HSFB4a. This miRNA has induced several folds upon HS in the tolerant cultivar where HSFB4a levels are reduced, thus exhibiting the inverse miR:target expression. Thus, we speculate that the alleviation of HSFB4a and increased HSFA7 levels govern thermo-tolerance in the tolerant cultivar by regulating downstream heat stress-responsive genes.
The α-crystallin domain containing genes: identification, phylogeny and expression profiling in abiotic stress, phytohormone response and development in tomato (Solanum lycopersicum)
(Frontiers Media S.A., 2016) Paul, Asosii; Rao, Sombir; Mathur, Saloni
The α-crystallin domain (ACD) is an ancient domain conserved among all kingdoms. Plant ACD proteins have roles in abiotic stresses, transcriptional regulation, inhibiting virus movement, and DNA demethylation. An exhaustive in-silico analysis using Hidden Markov Model-based conserved motif search of the tomato proteome yielded a total of 50 ACD proteins that belonged to four groups, sub-divided further into 18 classes. One of these groups belongs to the small heat shock protein (sHSP) class of proteins, molecular chaperones implicated in heat tolerance. Both tandem and segmental duplication events appear to have shaped the expansion of this gene family with purifying selection being the primary driving force for evolution. The expression profiling of the Acd genes in two different heat stress regimes suggested that their transcripts are differentially regulated with roles in acclimation and adaptive response during recovery. The co-expression of various genes in response to different abiotic stresses (heat, low temperature, dehydration, salinity, and oxidative stress) and phytohormones (abscisic acid and salicylic acid) suggested possible cross-talk between various members to combat a myriad of stresses. Further, several genes were highly expressed in fruit, root, and flower tissues as compared to leaf signifying their importance in plant development too. Evaluation of the expression of this gene family in field grown tissues highlighted the prominent role they have in providing thermo-tolerance during daily temperature variations. The function of three putative sHSPs was established as holdase chaperones as evidenced by protection to malate-dehydrogenase against heat induced protein-aggregation. This study provides insights into the characterization of the Acd genes in tomato and forms the basis for further functional validation in-planta.

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