Genome-wide survey of the soybean GATA transcription factor gene family and expression analysis under low nitrogen stress.

Chanjuan Zhang,Zhihui Shan,Yuqing Hou,Haifeng Chen,Dezhen Qiu,Zhonglu Yang,Wenjun Huang,Songli Yuan,Qingnan Hao,Xiaojuan Zhang,Limiao Chen,Xinan Zhou,Manoj Prasad

doi:10.1371/journal.pone.0125174

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.

Highlights

GATA transcription factors are a group of regulators that contain the highly conserved typeIV zinc finger motif
BLASTP searches in the soybean database of National Center for Biological Information (NCBI) using Arabidopsis full-length GATA1 protein sequences, as well as sequences from A. nidulans AreA, N. crassa WC1, and chicken GATA1, yielded 56 sequences
Other 14 genes involved in tetrapyrrole pathway [55] and two key genes (AtDXS and AtDXR) in methylerythritol phosphate pathway [56] for chlorophyll biosynthesis were analyzed, and they were not found to be altered significantly in the two overexpressing lines compared with the gnc mutant (S2 Fig). These results suggested that GmGATA44 played an important role in modulating chlorophyll biosynthesis, similar to the function of the ortholog AtGATA21

Summary

Introduction

GATA transcription factors are a group of regulators that contain the highly conserved typeIV zinc finger motif. These factors bind to the consensus DNA sequence (A/T)GATA(A/G) and are designated as GATA factors [1]. They were originally identified and characterized in animals and fungi, and typically encoded by multi-gene families. Animal GATA factors typically contain two CX2CX17CX2C zinc finger domains, and only the C-terminal finger is involved in DNA binding [1,2]. Most plant GATA factors contain a single CX2CX18CX2C domain, but some contain either zinc finger loops of 20 residues or more than two zinc finger domains [6]

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Results

Conclusion