The GATA Gene Family in Chickpea: Structure Analysis and Transcriptional Responses to Abscisic Acid and Dehydration Treatments Revealed Potential Genes Involved in Drought Adaptation

Niu, Liangjie; Chu, Ha Duc; Tran, Cuong; Nguyen, Kien Huu; Pham, Xuan Hoi; Le, Dung Tien; Li, Weiqiang; Wang, Wei; Le, Thao Duc; Tran, Lam-Son Phan

doi:10.1007/s00344-020-10201-5

Cited by 27 publications

(41 citation statements)

References 63 publications

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“… ** Piper nigrum , Zea mays , Solanum tuberosum , and Capsicum annuum results were omitted because its paper could not be accessed [ 83 , 110 – 112 ]. ***In the case of two species, different classification, group A, B, C, and/or D, was used so that it is also omitted (group A: 15 GATA genes, group B: 5 GATA genes, group C: 7 GATA genes, and group D: 1 GATA genes in Brachypodium distachyon [ 113 ] and group A: 17 GATA genes, group B: 5 GATA genes, and group C: 3 GATA genes in Cicer arietinum [ 114 ]). …”

Section: Resultsmentioning

confidence: 99%

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

Kim¹,

Xi²,

Park³

2021

PLoS ONE

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GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.

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Section: Resultsmentioning

confidence: 99%

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

Kim¹,

Xi²,

Park³

2021

PLoS ONE

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“…JA participates in the regulation of diverse processes encompassing plant growth and development, secondary metabolite biosynthesis, wounding response, and biotic and abiotic stresses [ 83 ]. Numerous CREs such as STRE (stress-response element), DRE (dehydration responsive element), LTR (low temperature responsive), and MBS (Myb binding site) have been identified as drought inducible cis-motifs implicated in the drought responsive gene regulation in plants [ 84 ]. According to a study on sweet potatoes, STRE is involved in heat stress responses, which typically regulate genes in response to heat stress [ 85 ].…”

Section: Resultsmentioning

confidence: 99%

Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum

et al. 2021

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Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.

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“…Informatic and expression analysis of rice OsGATA family proteins demonstrated their involvement with abiotic stress responses, and several of the genes showed duplicated relationships and similar expression patterns during rice growth (Gupta et al 2017). Similarly, GATA proteins in the Chickpea were shown to be involved in the response to ABA and Drought stress (Niu et al 2020). These recent studies into GATA TFs suggest that members of the GATA gene family may be generally involved in responses to abiotic stress.…”

Section: Discussionmentioning

confidence: 99%

OsGATA16, a GATA Transcription Factor, Confers Cold Tolerance by Repressing OsWRKY45-1 at the Seedling Stage in Rice

Zhang

et al. 2021

Preprint

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BackgroundCold stress in rice is a major abiotic stress that adversely affects growth and substantially reduces rice yield. Identification of cold-related functional rice genes is important for breeding programs aimed at increasing resilience and yield in rice crops. GATA-family transcription factors involve diverse function in rice, however, their roles in the response to low-temperature stress remain unclear.ResultsA GATA-type zinc finger transcription factor, OsGATA16, that increases cold tolerance in rice. OsGATA16 is an OsGATA subfamily-II protein and contains eleven putative phosphorylation sites, NLS, and several conserved domains. Overexpression of OsGATA16 increased tolerance to cold stress at seedling stage. Transcriptional analysis showed that OsGATA16 was induced by cold and ABA treatments, but was repressed by drought, cytokinin, and JA. OsGATA16 was expressed in all plant tissues, with highest expression in panicles. Subcellular localization and transcriptional analysis indicated that OsGATA16 acted as a nuclear-targeted transcriptional suppressor. Four cold-related genes (OsWRKY45-1, OsSRFP1, OsCYL4, and OsMYB30) were repressed in OsGATA16-overexpression lines compared with wild type after low-temperature exposure. Yeast one-hybrid and Dual-luciferase reporter assays showed that OsGATA16 bound to the promoter of OsWRKY45-1 and repressed its expression. Eleven SNPs within OsGATA16 were identified and haplotype analysis showed a polarization between Japonica and Indicia subspecies. A non-synonymous SNP was identified that explained differences in cold tolerance among the 137 rice accessions.ConclusionA novel GATA transcription factor, OsGATA16, plays a positive role in cold tolerance at the seedling stage in rice by direct repression of OsWRKY45-1 expression. One SNP was identified that explained cold tolerance differences among rice accessions. These results support future breeding programs to improve cold tolerance in commercial rice crops.

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The GATA Gene Family in Chickpea: Structure Analysis and Transcriptional Responses to Abscisic Acid and Dehydration Treatments Revealed Potential Genes Involved in Drought Adaptation

Cited by 27 publications

References 63 publications

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum

OsGATA16, a GATA Transcription Factor, Confers Cold Tolerance by Repressing OsWRKY45-1 at the Seedling Stage in Rice

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