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

Zhang C, Hou Y, Hao Q, Chen H, Chen L, Yuan S, Shan Z, Zhang X, Yang Z, Qiu D, Zhou X, Huang W - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.

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.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic analysis and gene structure of soybean GATA factors.(a) Phylogenetic tree construction of soybean GATA factors based on the full-length deduced amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap values are shown as percentages (>50%) on the branches. GmGATA48 was not presented in this tree because its sequence is partial. The tree showed four major phylogenetic subfamilies (subfamilies I to IV) indicated with different colored backgrounds.(b) Exon/intron structures of GmGATA genes. Green boxes represent exons, and black lines indicate introns. GmGATA48 was not displayed in this figure because its sequence is partial. The 7 kb length base pair was represented with slash–slash. The sizes of exons and introns can be estimated using the scale at the bottom.
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pone.0125174.g001: Phylogenetic analysis and gene structure of soybean GATA factors.(a) Phylogenetic tree construction of soybean GATA factors based on the full-length deduced amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap values are shown as percentages (>50%) on the branches. GmGATA48 was not presented in this tree because its sequence is partial. The tree showed four major phylogenetic subfamilies (subfamilies I to IV) indicated with different colored backgrounds.(b) Exon/intron structures of GmGATA genes. Green boxes represent exons, and black lines indicate introns. GmGATA48 was not displayed in this figure because its sequence is partial. The 7 kb length base pair was represented with slash–slash. The sizes of exons and introns can be estimated using the scale at the bottom.

Mentions: To determine the phylogenetic relationships among the different members of the GATA factor family in soybean, a phylogenetic analysis based on alignments of the 63 full-length GATA protein sequences was performed, except GmGATA48. As shown in Fig 1A, the neighbor-joining phylogenetic tree divided 63 GmGATA genes into four clades. Previous reports classified seven subfamilies (I, II, III, IV, V, VI, and VII) of GATA factors from Arabidopsis and rice GATA factor gene families [6]. Subfamilies I, II, III, and IV were present in soybean. The gene structures of the corresponding genes are shown in Fig 1B. The members within each subfamily showed similar exon/intron structures.


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

Zhang C, Hou Y, Hao Q, Chen H, Chen L, Yuan S, Shan Z, Zhang X, Yang Z, Qiu D, Zhou X, Huang W - PLoS ONE (2015)

Phylogenetic analysis and gene structure of soybean GATA factors.(a) Phylogenetic tree construction of soybean GATA factors based on the full-length deduced amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap values are shown as percentages (>50%) on the branches. GmGATA48 was not presented in this tree because its sequence is partial. The tree showed four major phylogenetic subfamilies (subfamilies I to IV) indicated with different colored backgrounds.(b) Exon/intron structures of GmGATA genes. Green boxes represent exons, and black lines indicate introns. GmGATA48 was not displayed in this figure because its sequence is partial. The 7 kb length base pair was represented with slash–slash. The sizes of exons and introns can be estimated using the scale at the bottom.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401516&req=5

pone.0125174.g001: Phylogenetic analysis and gene structure of soybean GATA factors.(a) Phylogenetic tree construction of soybean GATA factors based on the full-length deduced amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. Bootstrap values are shown as percentages (>50%) on the branches. GmGATA48 was not presented in this tree because its sequence is partial. The tree showed four major phylogenetic subfamilies (subfamilies I to IV) indicated with different colored backgrounds.(b) Exon/intron structures of GmGATA genes. Green boxes represent exons, and black lines indicate introns. GmGATA48 was not displayed in this figure because its sequence is partial. The 7 kb length base pair was represented with slash–slash. The sizes of exons and introns can be estimated using the scale at the bottom.
Mentions: To determine the phylogenetic relationships among the different members of the GATA factor family in soybean, a phylogenetic analysis based on alignments of the 63 full-length GATA protein sequences was performed, except GmGATA48. As shown in Fig 1A, the neighbor-joining phylogenetic tree divided 63 GmGATA genes into four clades. Previous reports classified seven subfamilies (I, II, III, IV, V, VI, and VII) of GATA factors from Arabidopsis and rice GATA factor gene families [6]. Subfamilies I, II, III, and IV were present in soybean. The gene structures of the corresponding genes are shown in Fig 1B. The members within each subfamily showed similar exon/intron structures.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.

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.

No MeSH data available.


Related in: MedlinePlus