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    Cross-species expression of OsDJ-1C from rice enhances tolerance to salinity and drought stress in tomato
    (Elsevier B.V., 2026) Mishra, Manjari; Chatterjee, Yajnaseni; Gupta, Brijesh Kumar; Tomar, Surabhi; Babuta, Priyanka; Gupta, Kapuganti Jagadis; Pareek, Ashwani; Singla-Pareek, Sneh Lata
    Abiotic stresses such as salinity and drought induce the accumulation of methylglyoxal (MG), a highly cytotoxic dicarbonyl compound that disrupts cellular metabolism in plants. MG detoxification is primarily mediated by the glutathione-dependent glyoxalase pathway, classically comprising the enzymes glyoxalase I and II. In contrast, glyoxalase III (GLYIII) catalyzes detoxification of MG in a single-step without requiring glutathione. In the present study, we investigated the functional role of OsDJ-1C, a rice GLYIII enzyme, by heterologous overexpression in tomato (Solanum lycopersicum). Transgenic lines exhibited significantly enhanced stress tolerance through a more efficient antioxidant defense mechanism under stress conditions. This improvement was driven by increased GLYIII-mediated detoxification of MG, leading to effective suppression of reactive oxygen species (ROS) accumulation. Reduced ROS levels in the overexpression lines resulted in greater internal oxygen availability and enhanced cellular respiration than wild-type plants. Furthermore, transgenic plants maintained higher pyruvate levels than the wild-type controls, thereby sustaining tricarboxylic acid (TCA) cycle flux and ATP production under stress. Overall, these findings reveal a conserved, cross-species function of OsDJ-1C in enhancing abiotic stress tolerance emphasizing its relevance for improving agricultural sustainability and food security under changing climatic conditions.
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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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    Brassinosteroids-regulated nitrogen metabolism fine-tunes growth physiology and low nitrogen response in tomato
    (Elsevier B.V., 2023) Yadav, Ritesh Kumar; Analin, Benedict; Panda, Mahesh Kumar; Ranjan, Aashish; Singh, Amar Pal
    Nitrogen (N) is a crucial nutrient for plants and its limited availability in the soils significantly affects plant growth and development. To adapt under low N condition, plants undergo various changes such as root system reprogramming to explore deeper soil horizons and metabolic activity adjustment. These N dependent responses and the genetic factors governing them are poorly known in crop plants. In this study, we investigated the effect of BRs on N metabolism in tomato. BRs application improved N assimilation and metabolic responses. By using the transgenic approach, we demonstrated the essential role of tomato Brassinazole resistant (BES1/BZR1) homolog 4 (BEH4) protein in regulating N metabolic response, growth physiology, and fruit quality. Overexpression of BEH4 promoted deeper root system architecture and improved physiological performance by adjusting N metabolic activity and photosynthetic efficiency in low N-grown plants. The BEH4 transgenic lines exhibited increased expression of genes involved in N uptake and assimilation which are associated with the improved N content and assimilation (root and shoot). Altogether, data suggested an essential role of BRs in plant adaptation to altered N regimes and appears potential target for genetic manipulation to improve nitrogen use efficiency (NUE) and nutritional quality in crops.
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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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    Genomic dissection of ROS detoxifying enzyme encoding genes for their role in antioxidative defense mechanism against Tomato leaf curl New Delhi virus infection in tomato
    (Elsevier B.V., 2021) Sharma, Namisha; Muthamilarasan, Mehanathan; Dulani, Priya; Prasad, Manoj
    In the present study, genes encoding for six major classes of enzymatic antioxidants, namely superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), Peroxidase (Prx) and glutathione S-transferase (GST) are identified in tomato. Their expression was studied in tomato cultivars contrastingly tolerant to ToLCNDV during virus infection and different hormone treatments. Significant upregulation of SlGR3, SlPrx25, SlPrx75, SlPrx95, SlGST44, and SlGST96 was observed in the tolerant cultivar during disease infection. Virus-induced gene silencing of SlGR3 in the tolerant cultivar conferred disease susceptibility to the knock-out line, and higher accumulation (~80%) of viral DNA was observed in the tolerant cultivar. Further, subcellular localization of SlGR3 showed its presence in cytoplasm, and its enzymatic activity was found to be increased (~65%) during ToLCNDV infection in the tolerant cultivar. Knock-out lines showed ~3- and 3.5-fold reduction in GR activity, which altogether underlines that SlGR3 is vital component of the defense mechanism against ToLCNDV infection.
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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.
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    Using an oxygen microsensor to measure oxygen dynamics in tomato plants in response to Pseudomonas syringae infection
    (Springer, 2017) Pathak, Pradeep Kumar; Gupta, Kapuganti Jagadis
    Pathogen infection leads to induction of defense responses which includes modulation of gene expression and changes in metabolism plants. Despite of extensive research little is information known about the role of respiration and photosynthesis during pathogen infection in plants. Limited methods are available to measure oxygen dynamics in response to pathogen infection. Here by using an oxygen microsensor we measured oxygen changes in tomato plants infected with avirulent Pseudomonas syringae pv. tomato DC3000. In this method plant is placed in a closed chamber and change in oxygen levels can be measured by an oxygen sensor.
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    eQTL regulating transcript levels associated with diverse biological processes in tomato
    (American Society of Plant Biologists, 2016) Ranjan, Aashish; Budke, Jessica; Rowland, Steven D.; Chitwood, Daniel H; Kumar, Ravi; Carriedo, Leonela G.; Ichihashi, Yasunori; Zumstein, Kristina; Maloof, Julin N.; Sinha, Neelima R.
    Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression Quantitative Trait Loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato Solanum lycopersicum to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome, and identified ~7,200 eQTL regulating the steady state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hotspots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity, and hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive expression QTL analysis details the influence of these loci on plant phenotypes, and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato.
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    Proteometabolomic analysis of transgenic tomato overexpressing oxalate decarboxylase uncovers novel proteins potentially involved in defense mechanism against Sclerotinia
    (Elsevier B.V., 2016) Ghosh, Sudip; Narula, Kanika; Sinha, Arunima; Ghosh, Rajgourab; Jawa, Priyanka; Chakraborty, Niranjan; Chakraborty, Subhra
    Oxalic acid (OA) plays dual role in fungal pathogenicity in a concentration dependent manner. While at higher concentration it induces programmed cell death leading to fungal invasion, low oxalate build resistance in plant. Although OA has been identified as a virulence determinant for rot disease caused by Sclerotinia sp., our understanding of how oxalate downregulation impart host immunity is limited. We have earlier shown that ectopic expression of oxalate decarboxylase (FvOXDC) specifically degrades OA in tomato (Solanum lycopersicum). To elucidate low oxalate regulated molecular mechanism imparting immunity, a comparative proteomics approach has been applied to E8.2-OXDC tomato fruit displaying fungal resistance. Mass spectrometric analyses identified 92 OXDC-responsive immunity related protein spots (ORIRPs) presumably associated with acid metabolism, defense signaling and endoplasmic reticulum stress. Metabolome study indicated increased abundance of some of the organic acids paralleling the proteomic analysis. Further, we interrogated the proteome data using network analysis that identified modules enriched in known and novel immunity-related prognostic proteins centered around 14-3-3, translationally controlled tumor protein, annexin and chaperonin. Taken together, our data demonstrate that low oxalate may act as metabolic and immunity determinant through translational reprogramming.