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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 tree of the amino acid sequences of zinc finger domains from soybean, Arabidopsis, and rice.The tree was conducted based on the zinc finger amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. The tree shows four major phylogenetic classes (Classes A to D) indicated with different colors.
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pone.0125174.g004: Phylogenetic tree of the amino acid sequences of zinc finger domains from soybean, Arabidopsis, and rice.The tree was conducted based on the zinc finger amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. The tree shows four major phylogenetic classes (Classes A to D) indicated with different colors.

Mentions: The phylogenetic tree showed that all the GATA zinc finger sequences from the three higher plants were divided into four major clades (Classes A, B, C, and D) (Fig 4). This result is similar to that previously reported for Arabidopsis and rice [6]. Among these classes, Class A constituted the largest clade, containing 56 members and accounting for 46% of the total GATA zinc finger sequences, Class B formed the second largest clade containing 36 members and accounting for 29% of the total GATA zinc finger sequences, and the other two clades contained 19 (Class C) and 11 (Class D) members, respectively. The zinc fingers of the soybean GATA proteins from subfamilies I, II, III, and IV belonged to Classes A, B, C, and D, respectively. Similar results were obtained in Arabidopsis [6]. The GATA zinc fingers from three higher plants distributed interspersedly in all classes, suggesting that the expansion of GATA zinc fingers occurred before the divergence of soybean, Arabidopsis, and rice. Some putative orthologs, namely, AtGATA1/GmGATA34, AtGATA7/GmGATA53, GmGATA1/AtGATA3, GmGATA31/AtGATA28, and OsGATA11/AtGATA21, were proposed based on the phylogenetic tree.


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 tree of the amino acid sequences of zinc finger domains from soybean, Arabidopsis, and rice.The tree was conducted based on the zinc finger amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. The tree shows four major phylogenetic classes (Classes A to D) indicated with different colors.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0125174.g004: Phylogenetic tree of the amino acid sequences of zinc finger domains from soybean, Arabidopsis, and rice.The tree was conducted based on the zinc finger amino acid sequences using MEGA 5.0 by the neighbor-joining method with 1000 bootstrap replicates. The tree shows four major phylogenetic classes (Classes A to D) indicated with different colors.
Mentions: The phylogenetic tree showed that all the GATA zinc finger sequences from the three higher plants were divided into four major clades (Classes A, B, C, and D) (Fig 4). This result is similar to that previously reported for Arabidopsis and rice [6]. Among these classes, Class A constituted the largest clade, containing 56 members and accounting for 46% of the total GATA zinc finger sequences, Class B formed the second largest clade containing 36 members and accounting for 29% of the total GATA zinc finger sequences, and the other two clades contained 19 (Class C) and 11 (Class D) members, respectively. The zinc fingers of the soybean GATA proteins from subfamilies I, II, III, and IV belonged to Classes A, B, C, and D, respectively. Similar results were obtained in Arabidopsis [6]. The GATA zinc fingers from three higher plants distributed interspersedly in all classes, suggesting that the expansion of GATA zinc fingers occurred before the divergence of soybean, Arabidopsis, and rice. Some putative orthologs, namely, AtGATA1/GmGATA34, AtGATA7/GmGATA53, GmGATA1/AtGATA3, GmGATA31/AtGATA28, and OsGATA11/AtGATA21, were proposed based on the phylogenetic tree.

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