Rongrong Guo

Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family

Summary Fifty-nine VvWRKY genes were identified. Phylogenetic tree and synteny analysis revealed the specific evolutionary relationship of these genes. Meanwhile, differential expression patterns indicated their possible roles in specific tissues and under different stresses.

Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape

BackgroundAspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. In plants, they are involved in many biological processes, such as senescence, stress responses, programmed cell death, and reproduction. Prior to the present study, no grape AP gene(s) had been reported, and their research on woody species was very limited.ResultsIn this study, a total of 50 AP genes (VvAP) were identified in the grape genome, among which 30 contained the complete ASP domain. Synteny analysis within grape indicated that segmental and tandem duplication events contributed to the expansion of the grape AP family. Additional analysis between grape and Arabidopsis demonstrated that several grape AP genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of grape and Arabidopsis. Phylogenetic relationships of the 30 VvAPs with the complete ASP domain and their Arabidopsis orthologs, as well as their gene and protein features were analyzed and their cellular localization was predicted. Moreover, expression profiles of VvAP genes in six different tissues were determined, and their transcript abundance under various stresses and hormone treatments were measured. Twenty-seven VvAP genes were expressed in at least one of the six tissues examined; nineteen VvAPs responded to at least one abiotic stress, 12 VvAPs responded to powdery mildew infection, and most of the VvAPs responded to SA and ABA treatments. Furthermore, integrated synteny and phylogenetic analysis identified orthologous AP genes between grape and Arabidopsis, providing a unique starting point for investigating the function of grape AP genes.ConclusionsThe genome-wide identification, evolutionary and expression analyses of grape AP genes provide a framework for future analysis of AP genes in defining their roles during stress response. Integrated synteny and phylogenetic analyses provide novel insight into the functions of less well-studied genes using information from their better understood orthologs.

Evolutionary and Expression Analyses of the Apple Basic Leucine Zipper Transcription Factor Family

Transcription factors (TFs) play essential roles in the regulatory networks controlling many developmental processes in plants. Members of the basic leucine (Leu) zipper (bZIP) TF family, which is unique to eukaryotes, are involved in regulating diverse processes, including flower and vascular development, seed maturation, stress signaling, and defense responses to pathogens. The bZIP proteins have a characteristic bZIP domain composed of a DNA-binding basic region and a Leu zipper dimerization region. In this study, we identified 112 apple (Malus domestica Borkh) bZIP TF-encoding genes, termed MdbZIP genes. Synteny analysis indicated that segmental and tandem duplication events, as well as whole genome duplication, have contributed to the expansion of the apple bZIP family. The family could be divided into 11 groups based on structural features of the encoded proteins, as well as on the phylogenetic relationship of the apple bZIP proteins to those of the model plant Arabidopsis thaliana (AtbZIP genes). Synteny analysis revealed that several paired MdbZIP genes and AtbZIP gene homologs were located in syntenic genomic regions. Furthermore, expression analyses of group A MdbZIP genes showed distinct expression levels in 10 different organs. Moreover, changes in these expression profiles in response to abiotic stress conditions and various hormone treatments identified MdbZIP genes that were responsive to high salinity and drought, as well as to different phytohormones.

Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily in apple (Malus × domestica Borkh.)

Aldehyde dehydrogenases (ALDHs) represent a protein superfamily encoding NAD(P)(+)-dependent enzymes that oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes. In plants, they are involved in many biological processes and play a role in the response to environmental stress. In this study, a total of 39 ALDH genes from ten families were identified in the apple (Malus × domestica Borkh.) genome. Synteny analysis of the apple ALDH (MdALDH) genes indicated that segmental and tandem duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of these gene families in apple. Moreover, synteny analysis between apple and Arabidopsis demonstrated that several MdALDH genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes appeared before the divergence of lineages that led to apple and Arabidopsis. In addition, phylogenetic analysis, as well as comparisons of exon-intron and protein structures, provided further insight into both their evolutionary relationships and their putative functions. Tissue-specific expression analysis of the MdALDH genes demonstrated diverse spatiotemporal expression patterns, while their expression profiles under abiotic stress and various hormone treatments indicated that many MdALDH genes were responsive to high salinity and drought, as well as different plant hormones. This genome-wide identification, as well as characterization of evolutionary relationships and expression profiles, of the apple MdALDH genes will not only be useful for the further analysis of ALDH genes and their roles in stress response, but may also aid in the future improvement of apple stress tolerance.

Overexpression of ALDH2B8, an aldehyde dehydrogenase gene from grapevine, sustains Arabidopsis growth upon salt stress and protects plants against oxidative stress

Aldehyde dehydrogenases (ALDHs) belong to a family of NAD (P)+-dependent enzymes that catalyze the oxidation of various toxic aldehydes to carboxylic acids. They have been reported to play important roles in plant responses to various stresses. Here we report on the isolation of a grapevine ALDH gene, which is rapidly induced in response to NaCl treatment. When transiently expressed in Arabidopsis protoplasts, grapevine ALDH2B8 was found to be localized in mitochondria. Transgenic Arabidopsis plants overexpressing grapevine ALDH2B8 showed sustained growth upon salt stress and increased tolerance against oxidative stress, which was correlated with decreased accumulation of reactive oxygen specie and malondialdehyde derived from cellular lipid peroxidation. In addition, the transgenic line had longer roots and higher chlorophyll content than the wild type under high salinity conditions. Taken together, we suggest that grapevine ALDH2B8 is involved in plant responses to oxidative and salt stress.

Constitutive expression of a grape aspartic protease gene in transgenic Arabidopsis confers osmotic stress tolerance

Aspartic proteases are involved in various processes of plant senescence, programmed cell death, reproduction and stress responses. We previously identified a salt and drought stress induced gene, VlAP17, encoding a Group C aspartic protease. Here, we report its functional analysis through the characterization of transgenic Arabidopsisthaliana plants overexpressing VlAP17 under the control of constitutive promoter. The transgenic plants showed enhance salt and drought stress tolerance during seed germination as well as the seedling and mature plant stage. In additional, various stress responses indicators were analyzed and results suggested that osmotic stress caused less damage to the plasma membrane of transgenic seedlings than to that of wild type plants. VlAP17 overexpression also resulted in increased ABA levels, a reduction in average stomatal aperture size, and elevated expression levels of stress-response genes involved in the ABA-dependent pathway, as well as higher activities of several antioxidases: superoxide dismutase, catalase and peroxidase. Taken together, these findings suggest that VlAP17 plays a role in protecting the integrity of plasma membrane and it may also be involved in, or have a function upstream of, the ABA biosynthetic pathway.

Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines

MADS-box transcription factors are involved in many aspects of plant growth and development, such as floral organ determination, fruit ripening, and embryonic development. Yet not much is known about grape (Vitis vinifera) MADS-box genes in a relatively comprehensive genomic and functional way during ovule development. Accordingly, we identified 54 grape MADS-box genes, aiming to enhance our understanding of grape MADS-box genes from both evolutionary and functional perspectives. Synteny analysis indicated that both segmental and tandem duplication events contributed to the expansion of the grape MADS-box family. Furthermore, synteny analysis between the grape and Arabidopsis genomes suggested that several grape MADS-box genes arose before divergence of the two species. Phylogenetic analysis and comparisons of exon–intron structures provided further insight into the evolutionary relationships between the genes, as well as their putative functions. Based on phylogenetic tree analysis, grape MADS-box genes were divided into type I and type II subgroups. Tissue-specific expression analysis suggested roles in both vegetative and reproductive tissue development. Expression analysis of the MADS-box genes following gibberellic acid (GA3) treatment revealed their response to GA3 treatment and that seedlessness caused by GA3 treatment underwent a different mechanism from that of normal ovule abortion. Expression profiling of MADS-box genes from six cultivars suggests their function in ovule development and may represent potential ovule identity genes involved in parthenocarpy. The results presented provide a few candidate genes involved in ovule development for future study, which may be useful in seedlessness-related molecular breeding programs.

Expression of a grape bZIP transcription factor, VqbZIP39, in transgenic Arabidopsis thaliana confers tolerance of multiple abiotic stresses

The basic region/leucine zipper (bZIP) transcription factors are known to play key roles in response to abiotic stress. In this study, a bZIP gene (VqbZIP39) was isolated from grape (Vitis quinquangularis) and constitutively expressed in Arabidopsis under control of the cauliflower mosaic virus 35S promoter. The transgenic Arabidopsis thaliana plants showed enhance salt and drought stress tolerance during seed germination and in the seedling and mature plant stages. Various physiological parameters related to stress responses were analyzed to gain further insight into the role of VqbZIP39 and it was found that osmotic stress caused less damage to the transgenic seedlings than to the corresponding wild type plants. This correlated with an increase in endogenous ABA content as a consequence of the constitutive over-expression of VqbZIP39, and the up-regulated expression of stress-inducible target genes associated with tolerance of drought, high-salt, and oxidative stresses. Our results suggest that the expression of VqbZIP39 in A. thaliana likely enhances the tolerance to multiple abiotic stresses through the ABA signaling pathway, and may therefore have a similar function in the response to abiotic stresses in grape.

Ectopic Expression of the Wild Grape WRKY Transcription Factor VqWRKY52 in Arabidopsis thaliana Enhances Resistance to the Biotrophic Pathogen Powdery Mildew But Not to the Necrotrophic Pathogen Botrytis cinerea

WRKY transcription factors are known to play important roles in plant responses to biotic stresses. We previously showed that the expression of the WRKY gene, VqWRKY52, from Chinese wild Vitis quinquangularis was strongly induced 24 h post inoculation with powdery mildew. In this study, we analyzed the expression levels of VqWRKY52 following treatment with the defense related hormones salicylic acid (SA) and methyl jasmonate, revealing that VqWRKY52 was strongly induced by SA but not JA. We characterized the VqWRKY52 gene, which encodes a WRKY III gene family member, and found that ectopic expression in Arabidopsis thaliana enhanced resistance to powdery mildew and Pseudomonas syringae pv. tomato DC3000, but increased susceptibility to Botrytis cinerea, compared with wild type (WT) plants. The transgenic A. thaliana lines displayed strong cell death induced by the biotrophic powdery mildew pathogen, the hemibiotrophic P. syringe pathogen and the necrotrophic pathogen B. cinerea. In addition, the relative expression levels of various defense-related genes were compared between the transgenic A. thaliana lines and WT plants following the infection by different pathogens. Collectively, the results indicated that VqWRKY52 plays essential roles in the SA dependent signal transduction pathway and that it can enhance the hypersensitive response cell death triggered by microbial pathogens.

Over-expression of a grape WRKY transcription factor gene, VlWRKY48, in Arabidopsis thaliana increases disease resistance and drought stress tolerance

Members of the plant WRKY transcription factor family play important roles in regulating response to various biotic and abiotic stresses. A previous gene expression study suggested that the grape gene, WRKY48, was up-regulated during drought stress and fungal infection, as well as in response to exogenous addition of plant hormones. To examine this relationship in more details, we over-expressed VlWRKY48 from V. labrusca × V. vinifera (cv. Kyoho) in Arabidopsis thaliana. Root length and the rate of seed germination were greater in three transgenic lines than that in wild type (WT) plants, the seedlings and adult plants displayed fewer stress-related symptoms following drought treatment than WT, in addition to lower water loss rate. Moreover, over-expression of VlWRKY48 resulted in an increase in the activities of the antioxidant enzymes of catalase, peroxidase and superoxide dismutase after drought treatment, as well as in the expression of several stress-related genes. We also observed that the VlWRKY48 over-expressing lines exhibited higher resistance to powdery mildew, as evidenced by fewer disease symptoms and an increased expression of defense-related genes following infection. Taken together, the results suggest that VlWRKY48 regulates a range of responses to drought stresses, and enhances resistance to powdery mildew infection.