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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

Schematic distribution of the conserved motifs in soybean GATA factors by MEME.Each numbered box represents a conserved motif in the protein. Motifs 1 and 4 represent the conserved GATA zinc finger motifs CX2CX18CX2 and CX2CX20CX2, respectively. Multilevel consensus sequences for the MEME-defined motifs are listed in S5 Table. The length of the protein can be estimated using the scale at the bottom.
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pone.0125174.g003: Schematic distribution of the conserved motifs in soybean GATA factors by MEME.Each numbered box represents a conserved motif in the protein. Motifs 1 and 4 represent the conserved GATA zinc finger motifs CX2CX18CX2 and CX2CX20CX2, respectively. Multilevel consensus sequences for the MEME-defined motifs are listed in S5 Table. The length of the protein can be estimated using the scale at the bottom.

Mentions: To further reveal the diversification of GATA genes in soybean, putative conserved motifs were predicted by the program MEME, and 30 distinct motifs were identified in all 64 GATA proteins. The schematic distribution of the 30 motifs among the different gene subfamilies is shown in Fig 3, and the identified multilevel consensus sequence for the motifs is shown in S5 Table. Motif 1 present in 54 GmGATA proteins and motif 4 present in the other nine GmGATA proteins were the conserved GATA zinc finger domains CX2CX18CX2C and CX2CX20CX2C, respectively. The conserved GATA zinc finger domain was not found in GmGATA28 by MEME, which may be attributed to the small half GATA motif in GmGATA28. As expected, most of the closely related members in the same subfamily had common motif compositions. Motifs 2 and 5 appeared in nearly all members of subfamily I. Motif 21 was the conserved motif in subfamily II. Motifs 3 and 8 were specific to subfamily III. Motif 3 was annotated as the CCT domain. It was first discovered in transcription factor TOC1 and CONSTANS proteins, which are involved in plant photoperiodic signaling, and the CCT domain was implicated in mediating protein-protein interactions [42–43]. Motif 8 was annotated as the TIFY domain, which may be involved in jasmonic acid-related stress response and developmental processes [44]. The CCT and TIFY motifs are also conserved in the GATA factor members of subfamily III in Arabidopsis and rice. In subfamily IV, four closely related members contain motifs 9, 6, 14, 24, 30, 26, and 7. These similarities in motif patterns suggest the similar functions of the GATA factors in the same subfamily. The differences in motif distribution in the different subfamilies of GATA factors indicated the functional divergence of the GATA factors over evolutionary history.


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)

Schematic distribution of the conserved motifs in soybean GATA factors by MEME.Each numbered box represents a conserved motif in the protein. Motifs 1 and 4 represent the conserved GATA zinc finger motifs CX2CX18CX2 and CX2CX20CX2, respectively. Multilevel consensus sequences for the MEME-defined motifs are listed in S5 Table. The length of the protein 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.g003: Schematic distribution of the conserved motifs in soybean GATA factors by MEME.Each numbered box represents a conserved motif in the protein. Motifs 1 and 4 represent the conserved GATA zinc finger motifs CX2CX18CX2 and CX2CX20CX2, respectively. Multilevel consensus sequences for the MEME-defined motifs are listed in S5 Table. The length of the protein can be estimated using the scale at the bottom.
Mentions: To further reveal the diversification of GATA genes in soybean, putative conserved motifs were predicted by the program MEME, and 30 distinct motifs were identified in all 64 GATA proteins. The schematic distribution of the 30 motifs among the different gene subfamilies is shown in Fig 3, and the identified multilevel consensus sequence for the motifs is shown in S5 Table. Motif 1 present in 54 GmGATA proteins and motif 4 present in the other nine GmGATA proteins were the conserved GATA zinc finger domains CX2CX18CX2C and CX2CX20CX2C, respectively. The conserved GATA zinc finger domain was not found in GmGATA28 by MEME, which may be attributed to the small half GATA motif in GmGATA28. As expected, most of the closely related members in the same subfamily had common motif compositions. Motifs 2 and 5 appeared in nearly all members of subfamily I. Motif 21 was the conserved motif in subfamily II. Motifs 3 and 8 were specific to subfamily III. Motif 3 was annotated as the CCT domain. It was first discovered in transcription factor TOC1 and CONSTANS proteins, which are involved in plant photoperiodic signaling, and the CCT domain was implicated in mediating protein-protein interactions [42–43]. Motif 8 was annotated as the TIFY domain, which may be involved in jasmonic acid-related stress response and developmental processes [44]. The CCT and TIFY motifs are also conserved in the GATA factor members of subfamily III in Arabidopsis and rice. In subfamily IV, four closely related members contain motifs 9, 6, 14, 24, 30, 26, and 7. These similarities in motif patterns suggest the similar functions of the GATA factors in the same subfamily. The differences in motif distribution in the different subfamilies of GATA factors indicated the functional divergence of the GATA factors over evolutionary history.

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