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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

Chromosomal location and region duplication of soybean GATA factor genes.The schematic diagram of genome-wide chromosome organization and segmental duplication was made from the CViT genome search and synteny viewer at the Legume Information System (http://comparative-legumes.org). Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. For example, the black blocks at the bottom of Gm03 correspond with regions on the black Gm19, and vice versa. Locations of centromeric repeats are shown as black rectangles over the chromosomes. The scale on the left represents the length of the chromosome.
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pone.0125174.g002: Chromosomal location and region duplication of soybean GATA factor genes.The schematic diagram of genome-wide chromosome organization and segmental duplication was made from the CViT genome search and synteny viewer at the Legume Information System (http://comparative-legumes.org). Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. For example, the black blocks at the bottom of Gm03 correspond with regions on the black Gm19, and vice versa. Locations of centromeric repeats are shown as black rectangles over the chromosomes. The scale on the left represents the length of the chromosome.

Mentions: The physical locations of the GATA genes on soybean chromosomes are shown in Fig 2. Sixty-four soybean GATA genes were unevenly distributed on all 20 chromosomes, except for chromosome 18. Among these chromosomes, chromosome 8 had the largest number of GATA genes with six, followed by chromosomes 2, 4, 11, 16, and 17 with five. By contrast, chromosomes 3, 10, 13, 15, and 19 had two GATA genes, and chromosomes 9 and 20 only contained one. Some clustering of GATA genes occurred on several chromosomes. For example, GmGATA14 and GmGATA15 were located in a 2.7-kb segment on chromosome 4, GmGATA17 and GmGATA18 were located in a 3.6-kb segment on chromosome 5, and GmGATA21 and GmGATA22 were located in a 2.2-kb segment on chromosome 6.


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)

Chromosomal location and region duplication of soybean GATA factor genes.The schematic diagram of genome-wide chromosome organization and segmental duplication was made from the CViT genome search and synteny viewer at the Legume Information System (http://comparative-legumes.org). Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. For example, the black blocks at the bottom of Gm03 correspond with regions on the black Gm19, and vice versa. Locations of centromeric repeats are shown as black rectangles over the chromosomes. The scale on the left represents the length of the chromosome.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0125174.g002: Chromosomal location and region duplication of soybean GATA factor genes.The schematic diagram of genome-wide chromosome organization and segmental duplication was made from the CViT genome search and synteny viewer at the Legume Information System (http://comparative-legumes.org). Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. For example, the black blocks at the bottom of Gm03 correspond with regions on the black Gm19, and vice versa. Locations of centromeric repeats are shown as black rectangles over the chromosomes. The scale on the left represents the length of the chromosome.
Mentions: The physical locations of the GATA genes on soybean chromosomes are shown in Fig 2. Sixty-four soybean GATA genes were unevenly distributed on all 20 chromosomes, except for chromosome 18. Among these chromosomes, chromosome 8 had the largest number of GATA genes with six, followed by chromosomes 2, 4, 11, 16, and 17 with five. By contrast, chromosomes 3, 10, 13, 15, and 19 had two GATA genes, and chromosomes 9 and 20 only contained one. Some clustering of GATA genes occurred on several chromosomes. For example, GmGATA14 and GmGATA15 were located in a 2.7-kb segment on chromosome 4, GmGATA17 and GmGATA18 were located in a 3.6-kb segment on chromosome 5, and GmGATA21 and GmGATA22 were located in a 2.2-kb segment on chromosome 6.

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