Proteomic and metabolomic profiling of Valencia orange fruit after natural frost exposure

Is CRISPR/Cas9-based multi-trait enhancement of wheat forthcoming?

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have been implemented in recent years in the genome editing of eukaryotes, including plants. The original system of knocking out a single gene by causing a double-strand break (DSB), followed by non-homologous end joining (NHEJ) or Homology-directed repair (HDR) has undergone many adaptations. These adaptations include employing CRISPR/Cas9 to upregulate gene expression or to cause specific small changes to the DNA sequence of the gene-of-interest. In plants, multiplexing, i.e., inducing multiple changes by CRISPR/Cas9, is extremely relevant due to the redundancy of many plant genes, and the time- and labor-consuming generation of stable transgenic plant lines via crossing. Here we discuss relevant examples of various traits, such as yield, biofortification, gluten content, abiotic stress tolerance, and biotic stress resistance, which have been successfully manipulated using CRISPR/Cas9 in plants. While existing studies have primarily focused on proving the impact of CRISPR/Cas9 on a single trait, there is a growing interest among researchers in creating a multi-stress tolerant wheat cultivar 'super wheat', to commercially and sustainably enhance wheat yields under climate change. Due to the complexity of the technical difficulties in generating multi-target CRISPR/Cas9 lines and of the interactions between stress responses, we propose enhancing already commercial local landraces with higher yield traits along with stress tolerances specific to the respective localities, instead of generating a general 'super wheat'. We hope this will serve as the sustainable solution to commercially enhancing crop yields under both stable and challenging environmental conditions.

Integrated Transcriptomic and Metabolomics Analyses Reveal Molecular Responses to Cold Stress in Coconut (Cocos nucifera L.) Seedlings

Coconut is an important tropical and subtropical fruit and oil crop severely affected by cold temperature, limiting its distribution and application. Thus, studying its low-temperature reaction mechanism is required to expand its cultivation range. We used growth morphology and physiological analyses to characterize the response of coconuts to 10, 20, and 30 d of low temperatures, combined with transcriptome and metabolome analysis. Low-temperature treatment significantly reduced the plant height and dry weight of coconut seedlings. The contents of soil and plant analyzer development (SPAD), soluble sugar (SS), soluble protein (SP), proline (Pro), and malondialdehyde (MDA) in leaves were significantly increased, along with the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and the endogenous hormones abscisic acid (ABA), auxin (IAA), zeatin (ZR), and gibberellin (GA) contents. A large number of differentially expressed genes (DEGs) (9968) were detected under low-temperature conditions. Most DEGs were involved in mitogen-activated protein kinase (MAPK) signaling pathway-plant, plant hormone signal transduction, plant-pathogen interaction, biosynthesis of amino acids, amino sugar and nucleotide sugar metabolism, carbon metabolism, starch and sucrose metabolism, purine metabolism, and phenylpropanoid biosynthesis pathways. Transcription factors (TFs), including WRKY, AP2/ERF, HSF, bZIP, MYB, and bHLH families, were induced to significantly differentially express under cold stress. In addition, most genes associated with major cold-tolerance pathways, such as the ICE-CBF-COR, MAPK signaling, and endogenous hormones and their signaling pathways, were significantly up-regulated. Under low temperatures, a total of 205 differentially accumulated metabolites (DAMs) were enriched; 206 DAMs were in positive-ion mode and 97 in negative-ion mode, mainly including phenylpropanoids and polyketides, lipids and lipid-like molecules, benzenoids, organoheterocyclic compounds, organic oxygen compounds, organic acids and derivatives, nucleosides, nucleotides, and analogues. Comprehensive metabolome and transcriptome analysis revealed that the related genes and metabolites were mainly enriched in amino acid, flavonoid, carbohydrate, lipid, and nucleotide metabolism pathways under cold stress. Together, the results of this study provide important insights into the response of coconuts to cold stress, which will reveal the underlying molecular mechanisms and help in coconut screening and breeding.

Global crotonylatome and GWAS revealed a TaSRT1-TaPGK model regulating wheat cold tolerance through mediating pyruvate

Here, we reported the complete profiling of the crotonylation proteome in common wheat. Through a combination of crotonylation and multi-omics analysis, we identified a TaPGK associated with wheat cold stress. Then, we confirmed the positive role of TaPGK-modulating wheat cold tolerance. Meanwhile, we found that cold stress induced lysine crotonylation of TaPGK. Moreover, we screened a lysine decrotonylase TaSRT1 interacting with TaPGK and found that TaSRT1 negatively regulated wheat cold tolerance. We subsequently demonstrated TaSRT1 inhibiting the accumulation of TaPGK protein, and this inhibition was possibly resulted from decrotonylation of TaPGK by TaSRT1. Transcriptome sequencing indicated that overexpression of TaPGK activated glycolytic key genes and thereby increased pyruvate content. Moreover, we found that exogenous application of pyruvate sharply enhanced wheat cold tolerance. These findings suggest that the TaSRT1-TaPGK model regulating wheat cold tolerance is possibly through mediating pyruvate. This study provided two valuable cold tolerance genes and dissected diverse mechanism of glycolytic pathway involving in wheat cold stress.

Cold Stress in Citrus: A Molecular, Physiological and Biochemical Perspective

Due to climate change, we are forced to face new abiotic stress challenges like cold and heat waves that currently result from global warming. Losses due to frost and low temperatures force us to better understand the physiological, hormonal, and molecular mechanisms of response to such stress to face losses, especially in tropical and subtropical crops like citrus fruit, which are well adapted to certain weather conditions. Many of the responses to cold stress that are found are also conserved in citrus. Hence, this review also intends to show the latest work on citrus. In addition to basic research, there is a great need to employ and cultivate new citrus rootstocks to better adapt to environmental conditions.

Biochemical differences in the skin of two blueberries (Vaccinium corymbosum) varieties with contrasting firmness: Implication of ions, metabolites and cell wall related proteins in two developmental stages

The pursuit of firmer and better-quality blueberries is a continuous task that aims at a more profitable production. To this end it is essential to understand the biological processes linked to fruit firmness, which may diverge among tissues. By contrasting varieties with opposing firmness, we were able to elucidate events that, taking place at immature stage, lay the foundation to produce a firmer ripe fruit. A deep analysis of blueberry skin was carried out, involving diverse comparative approaches including proteomics and metabolomics coupled to immunolocalization assays. In'O'Neal' (low firmness) enhanced levels of aquaporins, expansins and pectin esterases at the green stage were found to be critical in distinguishing it from 'Emerald' (high firmness). The latter featured higher levels of ABA, low methyl esterified pectins in tricellular junctions and high levels of catechin at this stage. Meanwhile, in 'Emerald' 's ripe fruit epicarp, several mechanisms of cell wall reinforcement such as calcium and probably boron bridges, appear to be more prominent than in 'O'Neal'. This study highlights the importance of cell wall reorganization and structure, abundance of specific metabolites, water status, and hormonal signalling in connection to fruit firmness. These findings result particularly valuable in order to improve the fertilization procedures or in the search of molecular markers related with firmness.

Integrated transcriptomic and metabolomic analyses of yellow horn (Xanthoceras sorbifolia) in response to cold stress

Xanthoceras sorbifolia, a medicinal and oil-rich woody plant, has great potential for biodiesel production. However, little study explores the link between gene expression level and metabolite accumulation of X. sorbifolia in response to cold stress. Herein, we performed both transcriptomic and metabolomic analyses of X. sorbifolia seedlings to investigate the regulatory mechanism of resistance to low temperature (4 °C) based on physiological profile analyses. Cold stress resulted in a significant increase in the malondialdehyde content, electrolyte leakage and activity of antioxidant enzymes. A total of 1,527 common differentially expressed genes (DEGs) were identified, of which 895 were upregulated and 632 were downregulated. Annotation of DEGs revealed that amino acid metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, galactose metabolism, fructose and mannose metabolism, and the citrate cycle (TCA) were strongly affected by cold stress. In addition, DEGs within the plant mitogen-activated protein kinase (MAPK) signaling pathway and TF families of ERF, WRKY, NAC, MYB, and bHLH were transcriptionally activated. Through metabolomic analysis, we found 51 significantly changed metabolites, particularly with the analysis of primary metabolites, such as sugars, amino acids, and organic acids. Moreover, there is an overlap between transcript and metabolite profiles. Association analysis between key genes and altered metabolites indicated that amino acid metabolism and sugar metabolism were enhanced. A large number of specific cold-responsive genes and metabolites highlight a comprehensive regulatory mechanism, which will contribute to a deeper understanding of the highly complex regulatory program under cold stress in X. sorbifolia.

Proteomic analysis of differentially expressed proteins involved in ethylene-induced chilling tolerance in harvested banana fruit

To better understand the mechanism involved in ethylene-induced chilling tolerance in harvested banana fruit, a gel-based proteomic study followed by MALDI-TOF-TOF MS was carried out. Banana fruit were treated with 500 ppm ethylene for 12 h and then stored at 6°C. During cold storage, the chilling tolerance was assessed and the proteins from the peel were extracted for proteomic analysis. It was observed that ethylene pretreatment significantly induced the chilling tolerance in harvested banana fruit, manifesting as increases in maximal chlorophyll fluorescence (Fv/Fm) and decreased electrolyte leakage. Sixty-four proteins spots with significant differences in abundance were identified, most of which were induced by ethylene pretreatment during cold storage. The up-regulated proteins induced by ethylene pretreatment were mainly related to energy metabolism, stress response and defense, methionine salvage cycle and protein metabolism. These proteins were involved in ATP synthesis, ROS scavenging, protective compounds synthesis, protein refolding and degradation, and polyamine biosynthesis. It is suggested that these up-regulated proteins might play a role in the ethylene-induced chilling tolerance in harvested banana fruit.