Comparative Analysis of the GATA Transcription Factors in Five Solanaceae Species and Their Responses to Salt Stress in Wolfberry (Lycium barbarum L.).

GATA proteins are a class of zinc-finger DNA-binding proteins that participate in diverse regulatory processes in plants, including the development processes and responses to environmental stresses. However, a comprehensive analysis of the GATA gene family has not been performed in a wolfberry (Lycium barbarum L.) or other Solanaceae species. There are 156 GATA genes identified in five Solanaceae species (Lycium barbarum L., Solanum lycopersicum L., Capsicum annuum L., Solanum tuberosum L., and Solanum melongena L.) in this study. Based on their phylogeny, they can be categorized into four subfamilies (I-IV). Noticeably, synteny analysis revealed that dispersed- and whole-genome duplication contributed to the expansion of the GATA gene family. Purifying selection was a major force driving the evolution of GATA genes. Moreover, the predicted cis-elements revealed the potential roles of wolfberry GATA genes in phytohormone, development, and stress responses. Furthermore, the RNA-seq analysis identified 31 LbaGATA genes with different transcript profiling under salt stress. Nine candidate genes were then selected for further verification using quantitative real-time PCR. The results revealed that four candidate LbaGATA genes (LbaGATA8, LbaGATA19, LbaGATA20, and LbaGATA24) are potentially involved in salt-stress responses. In conclusion, this study contributes significantly to our understanding of the evolution and function of GATA genes among the Solanaceae species, including wolfberry.

Genome-wide identification, evolution and expression pattern analysis of the GATA gene family in Sorghum bicolor.

The GATA family of transcription factors is zinc finger DNA binding proteins involved in a variety of biological processes, including plant growth and development and response to biotic/abiotic stresses, and thus play an essential role in plant response to environmental changes. However, the GATA gene family of Sorghum (SbGATA) has not been systematically analyzed and reported yet. Herein, we used a variety of bioinformatics methods and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to explore the evolution and function of the 33 SbGATA genes identified. These SbGATA genes, distributed on 10 chromosomes, are classified into four subfamilies (I-IV) containing one pair of tandem duplications and nine pairs of segment duplications, which are more closely related to the monocot Brachypodium distachyon and Oryza sativa GATA genes. The physicochemical properties of the SbGATAs are significantly different among the subfamilies, while the protein structure and conserved protein motifs are highly conserved in the subfamilies. In addition, the transcription of SbGATAs is tissue-specific during Sorghum growth and development, which allows for functional diversity in response to stress and hormones. Collectively, our study lays a theoretical foundation for an in-depth analysis of the functions, mechanisms and evolutionary relationships of SbGATA during plant growth and development.

Genome-Wide Characterization and Expression Analysis of GATA Transcription Factors in Response to Methyl Jasmonate in Salvia miltiorrhiza.

Salvia miltiorrhiza is an important medicinal plant, which is mainly used for treatment of cardiovascular and cerebrovascular diseases. GATA transcription factors are evolutionarily conser-ved proteins that play essential roles in biological process of plants. In this study, we systematically characterized the GATA transcription factors in S. miltiorrhiza. A total 28 SmGATA genes were identified and divided into four subfamilies based on phylogenetic analysis and domain. SmGATA genes being clustered into a subfamily have similar conserved motifs and exon-intron patterns, and unevenly distribute on eight chromosomes of S. miltiorrhiza. Tissue-specific expression analysis based on transcriptome datasets showed that the majority of SmGATA genes were preferentially expressed in roots. Under methyl jasmonate (MeJA) treatment, the quantitative real-time PCR (qRT-PCR) analysis indicated that several SmGATA genes in roots showed distinct upregulation post-MeJA treatment, especially SmGATA08, which was highly responsive to MeJA, and might be involved in the jasmonate signal, thereby affecting root growth, development, tolerance to various stresses, or secondary metabolites biosynthesis. The study found that several SmGATAs, like SmGATA08, are highly responsive to MeJA, indicating that these SmGATAs might be vital in the biosynthesis of tanshinones and phenolic acids by regulating the response to MeJA in S. miltiorrhiza. Our results laid the foundation for understanding their biological roles and quality improvement in S. miltiorrhiza.

Genome-wide identification and function characterization of GATA transcription factors during development and in response to abiotic stresses and hormone treatments in pepper.

Pepper (Capsicum annuum L.) is an economically important vegetable crop whose production and quality are severely reduced under adverse environmental stress conditions. The GATA transcription factors belonging to type IV zinc-finger proteins, play a significant role in regulating light morphogenesis, nitrate assimilation, and organ development in plants. However, the functional characteristics of GATA gene family during development and in response to environmental stresses have not yet been investigated in pepper. In this study, a total of 28 pepper GATA (CaGATA) genes were identified. To gain an overview of the CaGATAs, we analyzed their chromosomal distribution, gene structure, conservative domains, cis-elements, phylogeny, and evolutionary relationship. We divided 28 CaGATAs into four groups distributed on 10 chromosomes, and identified 7 paralogs in CaGATA family of pepper and 35 orthologous gene pairs between CaGATAs and Arabidopsis GATAs (AtGATAs). The results of promoter cis-element analysis and the quantitative real-time PCR (qRT-PCR) analysis revealed that CaGATA genes were involved in regulating the plant growth and development and the responses to various abiotic stresses and hormone treatments in pepper. Tissue-specific expression analysis showed that most CaGATA genes were preferentially expressed in flower buds, flowers, and leaves. Several CaGATA genes, especially CaGATA14, were significantly regulated under multiple abiotic stresses, and CaGATA21 and CaGATA27 were highly responsive to phytohormone treatments. Taken together, our results lay a foundation for the biological function analysis of GATA gene family in pepper.

Novel mutations in the TBX5 gene in patients with Holt-Oram Syndrome.

The Holt-Oram syndrome (HOS) is an autosomal dominant condition characterized by upper limb and cardiac malformations. Mutations in the TBX5 gene cause HOS and have also been associated with isolated heart and arm defects. Interactions between the TBX5, GATA4 and NKX2.5 proteins have been reported in humans. We screened the TBX5, GATA4, and NKX2.5 genes for mutations, by direct sequencing, in 32 unrelated patients presenting classical (8) or atypical HOS (1), isolated congenital heart defects (16) or isolated upper-limb malformations (7). Pathogenic mutations in the TBX5 gene were found in four HOS patients, including two new mutations (c.374delG; c.678G > T) in typical patients, and the hotspot mutation c.835C > T in two patients, one of them with an atypical HOS phenotype involving lower-limb malformations. Two new mutations in the GATA4 gene were found in association with isolated upper-limb malformations, but their clinical significance remains to be established. A previously described possibly pathogenic mutation in the NKX2.5 gene (c.73C > 7) was detected in a patient with isolated heart malformations and also in his clinically normal father.

Novel mutations in the TBX5 gene in patients with Holt-Oram Syndrome

The Holt-Oram syndrome (HOS) is an autosomal dominant condition characterized by upper limb and cardiac malformations. Mutations in the TBX5 gene cause HOS and have also been associated with isolated heart and arm defects. Interactions between the TBX5, GATA4 and NKX2.5 proteins have been reported in humans. We screened the TBX5, GATA4, and NKX2.5 genes for mutations, by direct sequencing, in 32 unrelated patients presenting classical (8) or atypical HOS (1), isolated congenital heart defects (16) or isolated upper-limb malformations (7). Pathogenic mutations in the TBX5 gene were found in four HOS patients, including two new mutations (c.374delG; c.678G > T) in typical patients, and the hotspot mutation c.835C > T in two patients, one of them with an atypical HOS phenotype involving lower-limb malformations. Two new mutations in the GATA4 gene were found in association with isolated upper-limb malformations, but their clinical significance remains to be established. A previously described possibly pathogenic mutation in the NKX2.5 gene (c.73C > 7) was detected in a patient with isolated heart malformations and also in his clinically normal father.