Characterization of the GATA gene family in Vitis vinifera: genome-wide analysis, expression profiles, and involvement in light and phytohormone response

The plant GATA family is one of the most important transcription factors involved in light-responsive development, nitrogen metabolism, phytohormone signaling, and source/sink balance. However, the function of the GATA gene is less known in grape (Vitis vinifera L.). In this study, we comprehensively analyzed the GATA family in grape, particularly the phylogenetic evolution, duplication patterns, conserved motifs, gene structures, cis-elements, tissue expression patterns, and predicted function of VvGATA genes in response to abiotic stress. The potential roles of VvGATA genes in berry development were also investigated. The GATA transcription factors displayed expression diversity among different grape organs and tissues, and some of them showed preferential expression in a specific tissue. Heterotrophic cultured cells were used as model systems for the functional characterization of the VvGATA gene and study of its response to light and phytohormone. Results indicated that some VvGATA genes displayed differential responses to light and phytohormones, suggesting their role in light and hormone signaling pathways. A thorough analysis of GATA transcription factors in grape (V. vinifera L.) presented the characterization and functional prediction of VvGATA genes. The data presented here lay the foundation for further functional studies of grape GATA transcription factors.

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Identification of GATA Transcription Factors in Brachypodium distachyon and Functional Characterization of BdGATA13 in Drought Tolerance and Response to Gibberellins

Frontiers in Plant Science ◽

10.3389/fpls.2021.763665 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jie Guo ◽

Xionghui Bai ◽

Keli Dai ◽

Xiangyang Yuan ◽

Pingyi Guo ◽

...

Keyword(s):

Transcription Factors ◽

Drought Tolerance ◽

Expression Profiles ◽

Brachypodium Distachyon ◽

Functional Characterization ◽

Primary Root ◽

Leaf Tissue ◽

Type Iv ◽

Gata Transcription Factors ◽

Gene Structures

GATA transcription factors (TFs) are type IV zinc-finger proteins that have roles in plant development and growth. The 27 GATA TFs identified in the Brachypodium distachyon genome in this study were unevenly distributed across all five chromosomes and classified into four subgroups. Phylogenesis-related GATAs shared similar gene structures and conserved motifs. Expression profiles showed that all BdGATA genes were expressed in leaves and most were induced by PEG treatment. BdGATA13 was predominantly expressed in leaf tissue and phylogenetically close to OsSNFL1, AtGNC, and AtGNL. Its protein was detected in the nucleus by subcellular localization analysis. Overexpression of BdGATA13 in transgenic Arabidopsis resulted in darker green leaves, later flowering, and more importantly, enhanced drought tolerance compared to the wild type. BdGATA13 also promoted primary root development under GA treatment. These results lay a foundation for better understanding the function of GATA genes in B. distachyon and other plants.

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Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.632509 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wei Zhao ◽

Yonghui Liu ◽

Lin Li ◽

Haijun Meng ◽

Ying Yang ◽

...

Keyword(s):

Transcription Factors ◽

Gene Family ◽

Developmental Stage ◽

Molecular Mechanisms ◽

Anthocyanin Biosynthesis ◽

Expression Profiles ◽

Juglans Regia ◽

Expression Patterns ◽

Regulatory Elements

Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut genome and were classified into 15 subfamilies according to sequence similarity and phylogenetic relationships. The gene structure, conserved domains, and chromosome location of the genes were analyzed by bioinformatic methods. Gene duplication analyses revealed that 42 JrbHLHs were involved in the expansion of the walnut bHLH gene family. We also characterized cis-regulatory elements of these genes and performed Gene Ontology enrichment analysis of gene functions, and examined protein-protein interactions. Four candidate genes (JrEGL1a, JrEGL1b, JrbHLHA1, and JrbHLHA2) were found to have high homology to genes encoding bHLH TFs involved in anthocyanin biosynthesis in other plants. RNA sequencing revealed tissue- and developmental stage-specific expression profiles and distinct expression patterns of JrbHLHs according to phenotype (red vs. green leaves) and developmental stage in red walnut hybrid progeny, which were confirmed by quantitative real-time PCR analysis. All four of the candidate JrbHLH proteins localized to the nucleus, consistent with a TF function. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in red walnut.

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Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (Pyrus bretschneideri) Fruit

International Journal of Molecular Sciences ◽

10.3390/ijms222212492 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12492

Author(s):

Muhammad Aamir Manzoor ◽

Irfan Ali Sabir ◽

Iftikhar Hussain Shah ◽

Han Wang ◽

Zhao Yu ◽

...

Keyword(s):

Transcription Factors ◽

Comparative Analysis ◽

Gene Family ◽

Prunus Persica ◽

Expression Profiles ◽

Functional Divergence ◽

Composition Analysis ◽

Rosaceae Species ◽

Gata Transcription Factors ◽

Gata Gene

The GATA gene family is one of the most important transcription factors (TFs). It extensively exists in plants, contributes to diverse biological processes such as the development process, and responds to environmental stress. Although the GATA gene family has been comprehensively and systematically studied in many species, less is known about GATA genes in Chinese pears (Pyrus bretschneideri). In the current study, the GATA gene family in the four Rosaceae genomes was identified, its structural characteristics identified, and a comparative analysis of its properties was carried out. Ninety-two encoded GATA proteins were authenticated in the four Rosaceae genomes (Pyrus bretschneideri, Prunus avium, Prunus mume, and Prunus persica) and categorized into four subfamilies (Ⅰ–Ⅳ) according to phylogeny. The majority of GATA genes contained one to two introns and conserved motif composition analysis revealed their functional divergence. Whole-genome duplications (WGDs) and dispersed duplication (DSD) played a key role in the expansion of the GATA gene family. The microarray indicated that, among P. bretschneideri, P. avium, P. mume and P. persica, GATA duplicated regions were more conserved between Pyrus bretschneideri and Prunus persica with 32 orthologous genes pairs. The physicochemical parameters, duplication patterns, non-synonymous (ka), and synonymous mutation rate (ks) and GO annotation ontology were performed using different bioinformatics tools. cis-elements respond to various phytohormones, abiotic/biotic stress, and light-responsive were found in the promoter regions of GATA genes which were induced via stimuli. Furthermore, subcellular localization of the PbGATA22 gene product was investigated, showing that it was present in the nucleus of tobacco (Nicotiana tabacum) epidermal cells. Finally, in silico analysis was performed on various organs (bud, leaf, stem, ovary, petal, and sepal) and different developmental stages of fruit. Subsequently, the expression profiles of PbGATA genes were extensively expressed under exogenous hormonal treatments of SA (salicylic acid), MeJA (methyl jasmonate), and ABA (abscisic acid) indicating that play important role in hormone signaling pathways. A comprehensive analysis of GATA transcription factors was performed through systematic biological approaches and comparative genomics to establish a theoretical base for further structural and functional investigations in Rosaceae species.

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Genome-wide analysis and expression profiles of PdeMYB transcription factors in colored-leaf poplar (Populus deltoids)

BMC Plant Biology ◽

10.1186/s12870-021-03212-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Weibing Zhuang ◽

Xiaochun Shu ◽

Xinya Lu ◽

Tao Wang ◽

Fengjiao Zhang ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Expression Profiles ◽

Functional Characterization ◽

Green Leaf ◽

Myb Transcription Factor ◽

Pcr Analysis ◽

Genome Wide ◽

Populus Deltoids

Abstract Background MYB transcription factors, comprising one of the largest transcription factor families in plants, play many roles in secondary metabolism, especially in anthocyanin biosynthesis. However, the functions of the PdeMYB transcription factor in colored-leaf poplar remain elusive. Results In the present study, genome-wide characterization of the PdeMYB genes in colored-leaf poplar (Populus deltoids) was conducted. A total of 302 PdeMYB transcription factors were identified, including 183 R2R3-MYB, five R1R2R3-MYB, one 4R-MYB, and 113 1R-MYB transcription factor genes. Genomic localization and paralogs of PdeMYB genes mapped 289 genes on 19 chromosomes, with collinearity relationships among genes. The conserved domain, gene structure, and evolutionary relationships of the PdeMYB genes were also established and analyzed. The expression levels of PdeMYB genes were obtained from previous data in green leaf poplar (L2025) and colored leaf poplar (QHP) as well as our own qRT-PCR analysis data in green leaf poplar (L2025) and colored leaf poplar (CHP), which provide valuable clues for further functional characterization of PdeMYB genes. Conclusions The above results provide not only comprehensive insights into the structure and functions of PdeMYB genes but also provide candidate genes for the future improvement of leaf colorization in Populus deltoids.

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Identification and Characterization of the Grape WRKY Family

BioMed Research International ◽

10.1155/2014/787680 ◽

2014 ◽

Vol 2014 ◽

pp. 1-14 ◽

Cited By ~ 8

Author(s):

Ying Zhang ◽

Jian can Feng

Keyword(s):

Transcription Factors ◽

Pathogenic Bacteria ◽

Expression Profiles ◽

Expression Patterns ◽

Structural Features ◽

Functional Identification ◽

Wrky Transcription Factors ◽

Genes Expression ◽

Wrky Proteins

WRKY transcription factors have functions in plant growth and development and in response to biotic and abiotic stresses. Many studies have focused on functional identification of WRKY transcription factors, but little is known about the molecular phylogeny or global expression patterns of the complete WRKY family. In this study, we identified 80 WRKY proteins encoded in the grape genome. Based on the structural features of these proteins, the grapeWRKYgenes were classified into three groups (groups 1–3). Analysis ofWRKYgenes expression profiles indicated that 28WRKYgenes were differentially expressed in response to biotic stress caused by grape whiterot and/or salicylic acid (SA). In that 16WRKYgenes upregulated both by whiterot pathogenic bacteria and SA. The results indicated that 16 WRKY proteins participated in SA-dependent defense signal pathway. This study provides a basis for cloning genes with specific functions from grape.

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Genome-Wide Characterization and Gene Expression Analyses of GATA Transcription Factors in Moso Bamboo (Phyllostachys edulis)

International Journal of Molecular Sciences ◽

10.3390/ijms21010014 ◽

2019 ◽

Vol 21 (1) ◽

pp. 14 ◽

Cited By ~ 2

Author(s):

Taotao Wang ◽

Yong Yang ◽

Shuaitong Lou ◽

Wei Wei ◽

Zhixin Zhao ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Plant Height ◽

Rapid Growth ◽

Expression Profiles ◽

Expression Patterns ◽

Primary Root ◽

Moso Bamboo ◽

Transcriptional Level ◽

Gata Transcription Factors

Moso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. However, the regulatory genes of these two processes are largely unexplored. GATA transcription factors regulate many developmental processes, but their roles in moso bamboo height control and rhizome development remains unexplored. Here, thirty-one bamboo GATA factors (PeGATAs) were identified, which are evolutionarily closer to rice than Arabidopsis, and their gene expression patterns were analyzed in bamboo development and phytohormone response with bioinformatics and molecular methods. Interestingly, PeGATAs could only be classified into three groups. Phytohormone responsive cis-elements were found in PeGATA promoters and the expression profiles showed that PeGATA genes might respond to gibberellin acid and abscisic acid but not to auxin at the transcriptional level. Furthermore, PeGATA genes have a tissue-specific expression pattern in bamboo rhizomes. Interestingly, most PeGATA genes were down-regulated during the rapid-growth of bamboo shoots. In addition, over-expressing one of the PeGATA genes, PeGATA26, significantly repressed the primary root length and plant height of transgenic Arabidopsis plants, which may be achieved by promoting the gibberellin acid turnover. Overall, our results provide insight into the function of GATA transcription factors in bamboo, and into genetic resources for engineering plant height.

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Genome-wide identification and characterization of the soybean SOD family during alkaline stress

PeerJ ◽

10.7717/peerj.8457 ◽

2020 ◽

Vol 8 ◽

pp. e8457 ◽

Cited By ~ 1

Author(s):

Wenxiu Lu ◽

Huizi Duanmu ◽

Yanhua Qiao ◽

Xiaoxia Jin ◽

Yang Yu ◽

...

Keyword(s):

Expression Profiles ◽

Expression Patterns ◽

Functional Characterization ◽

Soybean Genome ◽

Evolutionary Divergence ◽

Alkaline Stress ◽

Genome Database ◽

Alkaline Salt ◽

Qrt Pcr

Background Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported. Methods We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR. Results In this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1–2), FeSODs (GmFSD1–5) and Cu/ZnSODs (GmCSD1–6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future.

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