Genome-Wide Survey of the Soybean GATA Transcription Factor Gene Family and Expression Analysis under Low Nitrogen Stress

Abstract

GATA transcription factors are transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain and recognize the conserved GATA motif in the promoter sequence of target genes. Previous studies demonstrated that plant GATA factors possess critical functions in developmental control and responses to the environment. To date, the GATA factors in soybean (Glycine max) have yet to be characterized. Thus, this study identified 64 putative GATA factors from the entire soybean genomic sequence. The chromosomal distributions, gene structures, duplication patterns, phylogenetic tree, tissue expression patterns, and response to low nitrogen stress of the 64 GATA factors in soybean were analyzed to further investigate the functions of these factors. Results indicated that segmental duplication predominantly contributed to the expansion of the GATA factor gene family in soybean. These GATA proteins were phylogenetically clustered into four distinct subfamilies, wherein their gene structure and motif compositions were considerably conserved. A comparative phylogenetic analysis of the GATA factor zinc finger domain sequences in soybean, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa) revealed four major classes. The GATA factors in soybean exhibited expression diversity among different tissues; some of these factors showed tissue-specific expression patterns. Numerous GATA factors displayed upregulation or downregulation in soybean leaf in response to low nitrogen stress, and two GATA factors GATA44 and GATA58 were likely to be involved in the regulation of nitrogen metabolism in soybean. Overexpression of GmGATA44 complemented the reduced chlorophyll phenotype of the Arabidopsis ortholog AtGATA21 mutant, implying that GmGATA44 played an important role in modulating chlorophyll biosynthesis. Overall, our study provides useful information for the further analysis of the biological functions of GATA factors in soybean and other crops.

Genome-wide analysis of GATA factors in moso bamboo (Phyllostachys edulis) unveils that PeGATAs regulate shoot rapid-growth and rhizome development

“…1). The number of bamboo GATA factors was closer to other species, including Arabidopsis (29), rice (28) and apple (35) [9, 10, 15]. Furthermore, most of PeGATA factors have a conserved single CX 2 CX 18-20 CX 2 C zinc finger domain that is highly similar to that from Arabidopsis and rice (Fig.…”

“…However, the fungal GATA factors only contain a single zinc finger domain that is highly similar to the C-terminal zinc finger domain of the animal GATA factors [4, 8]. In plants, GATA factors contain CX 2 CX 18 CX 2 C or CX 2 CX 20 CX 2 C zinc finger domain [9, 10]. Interestingly, most of plant GATA factors have a single zinc finger domain, and very few of them also contain two zinc finger domains [9–11].…”

“…The first GATA factor identified in plant is NTL1 from Nicotiana tabacum [14]. GATA factors have been identified in many plant species, including Arabidopsis (29), rice (28), apple (35) and soybean (64) [9, 10, 15]. Plant GATA factors are involved in many developmental processes, including plant architecture [16], flowering development [17], hypocotyl elongation [18] and seed germination [19].…”

Transcriptomic reprogramming in soybean seedlings under salt stress

“…In leaf, SKP2 ( Glyma.13G036600 ; in L‐M1) encodes a homologue of an Arabidopsis auxin‐binding F‐box protein involved in cell division and its degradation is mediated by auxin (Jurado et al, ). Glyma.08G142500 (in L‐M2) encodes a GATA‐type TF that is found to be involved in the crosstalk between gibberellin (GA) and auxin in Arabidopsis thaliana and in regulating nitrogen metabolism in soybean (Richter, Behringer, Zourelidou, & Schwechheimer, ; Zhang et al, ). Lipoxygenase 1 ( LOX1 ; in L‐M13) plays an important role in JA biosynthesis and its expression can be stimulated by abscisic acid (ABA) and methyl‐JA (Melan et al, ).…”

Combining gene network, metabolic, and leaf-level models show means to future-proof soybean photosynthesis under rising CO2

“…The overexpression of Class B GATAs and GLKs in Arabidopsis roots improved photosynthesis by increasing root chlorophyll content (Ohnishi et al, 2018). GmGATA2 is annotated as NITRATE□INDUCIBLE, CARBON METABOLISM□INVOLVED (GNC) and is homologous to AtGATA5, and both are Class A GATAs that are associated with the light regulation of gene expression and photomorphogenesis (Zhang et al, 2015). The overexpression of the poplar PdGNC gene in Arabidopsis improved photosynthesis under low N levels by increasing the size and number of chloroplasts per cell.…”