Expression Profiling of the <Emphasis Type="Italic">CSDP</Emphasis> Transcription Factor Gene Family Points to Roles in Organ Development and Abiotic Stress Response in Tomato (<Emphasis Type="Italic">Solanum lycopersicum</Emphasis> L.)

The cold shock domain proteins (CSDPs) are small group of nucleic acid-binding proteins that act as RNA chaperones in growth regulation, development, and stress adaptation in plants. The functions of CSDPs have been studied in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), wheat (Triticum aestivum), and Chinese cabbage (Brassica rapa). To gain insight into the function of CSDPs in tomato (Solanum lycopersicum), we performed a genome-wide analysis of CSDPs through in silico characterization and expression profiling in different organs and in response to different abiotic stress and phytohormone treatments. We identified five non-redundant SlCSDP genes. The evolutionary analysis and phylogenetic classification indicated that tomato CSDPs are more closely related to potato than those of others. The five SlCSDP genes are distributed on four of the 12 tomato chromosomes and no segmental or tandem duplication events are detected among them. Expression analysis showed broad expression patterns with strong expression in fruit development and ripening. Expression of individual SlCSDP genes was significantly altered by stress and phytohormone treatments. SlCSDP2, SlCSDP3, and SlCSDP4 were highly induced by all four abiotic stresses and by phytohormone treatment in tomato. These findings provide a foundation for future research towards functional biological roles of CSDP gene in particular to develop tomato cultivars with large size, early ripening, and abiotic stress tolerance.     

Bioinformatic and expression analyses on carotenoid dioxygenase genes in fruit development and abiotic stress responses in <Emphasis Type="Italic">Fragaria vesca</Emphasis>

Carotenoid dioxygenases, including 9-cis-epoxycarotenoid dioxygenases (NCEDs) and carotenoid cleavage dioxygenases (CCDs), can selectively cleave carotenoids into various apocarotenoid products that play important roles in fleshy fruit development and abiotic stress response. In this study, we identified 12 carotenoid dioxygenase genes in diploid strawberry Fragaria vesca, and explored their evolution with orthologous genes from nine other species. Phylogenetic analyses suggested that the NCED and CCDL groups moderately expanded during their evolution, whereas gene numbers of the CCD1, CCD4, CCD7, and CCD8 groups maintained conserved. We characterized the expression profiles of FveNCED and FveCCD genes during flower and fruit development, and in response to several abiotic stresses. FveNCED1 expression positively responded to osmotic, cold, and heat stresses, whereas FveNCED2 was only induced under cold stress. In contrast, FveNCED2 was the unique gene highly and continuously increasing in receptacle during fruit ripening, which co-occurred with the increase in endogenous abscisic acid (ABA) content previously reported in octoploid strawberry. The differential expression patterns suggested that FveNCED1 and FveNCED2 were key genes for ABA biosynthesis in abiotic stress responses and fruit ripening, respectively. FveCCD1 exhibited the highest expression in most stages of flower and fruit development, while the other FveCCDs were expressed in a subset of stages and tissues. Our study suggests distinct functions of FveNCED and FveCCD genes in fruit development and stress responses and lays a foundation for future study to understand the roles of these genes and their metabolites, including ABA and other apocarotenoid products, in the growth and development of strawberry.     

Changes in plasma membrane aquaporin gene expression under osmotic stress and blue light in tomato

Divergent abiotic stresses induce osmotic stress on plant cells resulting in an imbalance in water homeostasis which is preserved by aquaporins. Since the plasma membrane aquaporins (PIPs) were shown to be involved in seed development and responses to abiotic stresses, we focused on determining the contribution of mannitol-induced osmotic stress, blue light (BL), and 7B-1 mutation to their gene expression in tomato (Solanum lycopersicum L.) seeds. To assess that, we used a quantitative RT-PCR to determine the expression profiles of genes encoding PIPs. Subsequently, a multiple linear regression analysis was used to evaluate the impact of studied stressors (mannitol and BL) and 7B-1 mutation on PIP gene expressions. We found that mannitol-induced osmotic stress and 7B-1 mutation (conferring the lower responsiveness to osmotic stress- and BL-induced inhibition of seed germination) decreased expression of PIP1;3, PIP2;3 and PIP1;2, PIP2;1 genes, respectively. This might be a way to retain water for radicle elongation and seed germination under the stress conditions. Interestingly, the expression of PIP1;3 gene was downregulated not only by osmotic stress, but also by BL. Altogether, our data indicate the existence of a link between osmotic stress and BL signalling and the involvement of the 7B-1 mutation in this crosstalk.     

Genome-wide survey and expression analysis of the stress-associated protein gene family in desert poplar, <Emphasis Type="Italic">Populus euphratica</Emphasis>

Stress-associated proteins (SAPs) are a novel class of zinc finger proteins that extensively participate in abiotic stress responses. To date, no overall analysis and expression profiling of SAP genes in woody plants have been reported. Populus euphratica is distributed in desert regions and is extraordinarily adaptable to abiotic stresses. Thus, it is regarded as a promising candidate for studying abiotic stress resistance mechanisms of woody plants. In this study, 18 non-redundant SAP genes were identified from the genome of P. euphratica using basic local alignment search tool algorithms and functional domain verification. Among these 18 PeuSAP genes, 15 were intronless. To investigate the evolutionary relationships of SAP genes in P. euphratica and other Salicaceae plants, phylogenetic analyses were performed. Subsequently, the expression profiles of the 18 PeuSAP genes were analyzed in different tissues and under various stresses (drought, salt, heat, cold, and abscisic acid (ABA) treatment) using quantitative real-time PCR. Tissue expression analysis indicated that PeuSAPs showed no tissue specificity. PeuSAPs were induced by multiple abiotic stresses, especially drought, salt, and heat stresses, perhaps because of abundant cis-acting heat shock elements and drought-inducible elements in the promoter regions of the PeuSAPs. Moreover, single nucleotide polymorphisms (SNPs) variant analysis revealed many synonymous and non-synonymous SNPs in PeuSAP genes, but the zinc finger structure was conserved during evolution. These results provide an overview of the SAP gene family in P. euphratica and a reference for further functional research on PeuSAP genes.     

Genome-wide identification,systematic analysis and characterization of <Emphasis Type="Italic">SRO</Emphasis> family genes in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

SIMILAR TO RCD ONE (SRO) is a small plant-specific gene family, which play essential roles in plant growth and development as well as in abiotic stresses. However, the function of SROs in maize is still unknown. In our study, six putative SRO genes were isolated from the maize genome. A systematic analysis was performed to characterize the ZmSRO gene family. The ZmSRO gene family was divided into two groups according to the motif and intron/exon analysis. Phylogenetic analysis of them with other plants showed that the clades of SROs along with the divergence of monocot and dicot and ZmSROs were more closely with OsSROs. Many abiotic stress response and hormone-induced cis-regulatory elements were identified from the promoter region of ZmSROs. Furthermore, RNA-seq analysis indicated that SRO genes were widely expressed in different tissues and development stages in maize, and the expression divergence was also obviously observed. Analyses of expression in response to PEG6000 and NaCl treatment, in addition to exogenous application of ABA and GA hormones showed that the majority of the members display stress-induced expression patterns. Taken together, our results provide valuable reference for further functional analysis of the SRO gene family in maize, especially in abiotic stress responses.     

The <Emphasis Type="Italic">Populus trichocarpa PtHSP17.8</Emphasis> involved in heat and salt stress tolerances

Key message

PtHSP17.8 was regulated by various abiotic stresses. Overexpression of PtHSP17.8 enhanced the tolerance to heat and salt stresses through maintain ROS homeostasis and cooperate with stress-related genes in Arabidopsis.

Abstract

Small heat shock proteins (sHSPs) play important roles in response to diverse biotic and abiotic stresses, especially in heat tolerance. However, limited information is available on the stress tolerance roles of sHSPs in woody species. To explore the function of sHSPs in poplar, we isolated and characterized PtHSP17.8 from Populus trichocarpa. Phylogenetic analysis and subcellular localization revealed that PtHSP17.8 was a cytosolic class I sHSP. The gene expression profile of PtHSP17.8 in various tissues showed that it was significantly accumulated in stem and root, which was consistent with the GUS expression pattern driven by promoter of PtHSP17.8. The expression of PtHSP17.8 could be induced by various abiotic stresses and significantly activated by heat stress. Overexpression of PtHSP17.8 enhanced the tolerance to heat and salt stresses in Arabidopsis. The seedling survival rate, root length, relative water content, antioxidative enzyme activities, proline, and soluble sugar content were increased in transgenic Arabidopsis under heat and salt stresses, but not in normal condition. The co-expression network of PtHSP17.8 were constructed and demonstrated many stress responsive genes included. The stress-related genes in the co-expression network were up-regulated in the PtHSP17.8 overexpression seedlings. These results suggest that PtHSP17.8 confers heat and salt tolerances in plants.

     

Molecular analyses of tomato GS,GOGAT and GDH gene families and their response to abiotic stresses

Glutamine synthetase (GS), glutamate synthase (GOGAT) and glutamate dehydrogenase (GDH) are closely related enzymes in plant nitrogen metabolism and potential targets for improving nitrogen use efficiency. However, little research has focused on the enzyme-encoding genes in tomato. Here, a comprehensive study of these genes was conducted. Six GS genes, two GOGAT genes and five GDH genes were identified in tomato. Bioinformatics and gene expression analyses suggested that these genes evolved species-specific regulatory properties and biological functions in tomato. SlNADH-GOGAT, SlGS1.1 and SlNAD-GDHB1 were abundantly expressed in roots, SlGS1.1 can be induced by nitrogen deprivation, and SlGS1.2, SlGS1.3, SlNADH-GOGAT and SlNAD-GDHB1 can be induced by the re-supply of nitrogen after 5 days of deprivation, they may play key roles in primary nitrogen assimilation. SlFd-GOGAT, SlGS1.1 and SlNAD-GDHA1-A2 were also highly expressed in fruits, indicating their important roles in fruit development and ripening. Tomato GS, GOGAT and GDH may be involved in stress responsiveness, since most of these genes modified their expression levels under drought, cold or heat stress treatment. We believe these findings will assist in the exploration of the genes’ biological functions and regulatory mechanisms, as well as the studies to improve nitrogen use efficiency, stress resistance and fruit quality in tomato.     

Identification and comparative analysis of <Emphasis Type="Italic">Brassica juncea</Emphasis> pathogenesis-related genes in response to hormonal,biotic and abiotic stresses

Pathogenesis-related proteins (PRs) are the antimicrobial proteins which are commonly used as signatures of defense signaling pathways and systemic acquired resistance. However, in Brassica juncea most of the PR proteins have not been fully characterized and remains largely enigmatic. In this study, full-length cDNA sequences of SA (PR1, PR2, PR5) and JA (PR3, PR12 and PR13) marker genes were isolated from B. juncea and were named as BjPR proteins. BjPR proteins showed maximum identity with known PR proteins of Brassica species. Further, expression profiling of BjPR genes were investigated after hormonal, biotic and abiotic stresses. Pre-treatment with SA and JA stimulators downregulates each other signature genes suggesting an antagonistic relationship between SA and JA in B. juncea. After abscisic acid (ABA) treatment, SA signatures were downregulated while as JA signature genes were upregulated. During Erysiphe cruciferarum infection, SA- and JA-dependent BjPR genes showed distinct expression pattern both locally and systemically, thus suggesting the activation of SA- and JA-dependent signaling pathways. Further, expression of SA marker genes decreases while as JA-responsive genes increases during drought stress. Interestingly, both SA and JA signature genes were induced after salt stress. We also found that BjPR genes displayed ABA-independent gene expression pattern during abiotic stresses thus providing the evidence of SA/JA cross talk. Further, in silico analysis of the upstream regions (1.5 kb) of both SA and JA marker genes showed important cis-regulatory elements related to biotic, abiotic and hormonal stresses.     

A chalcone synthase gene <Emphasis Type="Italic">AeCHS</Emphasis> from <Emphasis Type="Italic">Abelmoschus esculentus</Emphasis> regulates flavonoid accumulation and abiotic stress tolerance in transgenic <Emphasis Type="Italic">Arabidopsis</Emphasis>

Chalcone synthase (CHS) is one of the key enzymes in flavonoid biosynthesis pathway in plants. However, the roles of AeCHS gene from Abelmoschus esculentus in flavonoid accumulation and tolerance to abiotic stresses have not been studied. In this study, the AeCHS gene was cloned from Abelmoschus esculentus. The open reading frame contained 1170 nucleotides encoding 389 amino acids. The coding region of AeCHS was cloned into a binary vector under the control of 35S promoter and then transformed into Arabidopsis to obtain transgenic plants. Overexpression of AeCHS increased the production of downstream flavonoids and the expression of related genes in the flavonoid biosynthesis pathway. It also improved resistance to salt and mannitol stresses during seed germination and root development. Further component and enzymatic analyses showed the decreased content of H₂O₂ and malondialdehyde and the increased activities of superoxide dismutase (SOD) and peroxidase (POD) in transgenic seedlings. Meanwhile, the expression level of AtSOD and AtPOD genes was up-regulated against salt and osmotic stresses. Together, our finding indicated that changing the expression level of AeCHS in plants alters the accumulation of flavonoids and regulates plantlet tolerance to abiotic stress by maintaining ROS homeostasis. The AeCHS gene has the potential to be used to increase the content of valuable flavonoids and improve the tolerance to abiotic stresses in plants.