Integrative comparative analyses of metabolite and transcript profiles uncovers complex regulatory network in tomato (Solanum lycopersicum L.) fruit undergoing chilling injury

Abstract

Tomato fruit are especially susceptible to chilling injury (CI) when continuously exposed to temperatures below 12 °C. In this study, integrative comparative analyses of transcriptomics and metabolomics data were performed to uncover the regulatory network in CI tomato fruit. Metabolite profiling analysis found that 7 amino acids, 27 organic acids, 16 of sugars and 22 other compounds had a significantly different content while transcriptomics data showed 1735 differentially expressed genes (DEGs) were down-regulated and 1369 were up-regulated in cold-stored fruit. We found that the contents of citrate, cis-aconitate and succinate were increased, which were consistent with the expression of ATP-citrate synthase (ACS) and isocitrate dehydrogenase (IDH) genes in cold-treated tomato fruit. Cold stress promotes the expression of ACS and IDH which may increase the synthesis of citrate, cis-aconitate and succinate. Alanine and leucine had increased contents, which may result from alanine aminotransferase (ALT) and branched-chain amino acid aminotransferase (BcAT)’s high expression levels, respectively. Overall the transcriptomics and metabolomics data in our study explain the molecular mechanisms of the chilling injury and expands our understanding of the complex regulatory mechanisms of a metabolic network in response to chilling injury in tomato fruit.

Combining Physiological and Metabolomic Analysis to Unravel the Regulations of Coronatine Alleviating Water Stress in Tobacco (Nicotiana tabacum L.)

“…Citrate, the first intermediate involved in the TCA cycle, is known to participate in plants responses to abiotic stress. The increase in citrate accumulation was observed in cotton under drought [52] and tomato under chilling treatment [53]. Wu et al demonstrated that citrate has the anti-oxidant capacity to modulate redox signaling through scavenging free radicals and chelating iron ions [54].…”

Combined transcriptomic and metabolomic analyses uncover rearranged gene expression and metabolite metabolism in tobacco during cold acclimation

“…Sebastian and Prasad reported that supplementation with citrate and malate could alleviate cadmium stress by reducing Cd-induced iron nutrition deficiency in rice 38 . The accumulation of citrate and malate was also detected in plants under cold conditions 29,39 . α-Ketoglutarate bridges the metabolism of carbohydrates and amino acids, serving as a precursor for the biosynthesis of glutamate and proline and subsequent protein biosynthesis.…”

“…The accumulation of amino acids is a common occurrence in many plant species when subjected to cold stress [28][29][30] , reflecting amino acid production or related protein degradation. It is thought that many amino acids that are specifically enriched in plants have a beneficial function during stress acclimation 14 .…”

“…The abundance of branched-chain amino acids (BCAAs) valine and leucine, which can be synthesized from pyruvate via de novo methods, markedly increased in our study. These BCAAs serve as compatible osmolytes and function as alternative electron donors in the mitochondrial electron transport chain to produce ATP under environmental stress conditions, including cold stress 29,36 .…”

Cold storage reveals distinct metabolic perturbations in processing and non-processing cultivars of potato (Solanum tuberosum L.)

“…role in cold tolerance in plants 45,51 . Amongst the different TCA cycle metabolites, the levels of citrate were significantly higher (p = 0.019; FC = 0.54) in the processing cultivar, FL-1533; whereas Kufri Jyoti and Kufri Pukhraj showed significantly higher levels of malate after CS (Fig.…”