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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

Relative expression profiles of soybean GATA genes in various organs.Data were obtained by real-time PCR normalized against the reference gene ACT11 and shown as a percentage of expression in leaf. Numbers on the x-axis indicate various tissues: 1 (young leaf), 2 (root), 3 (stem), 4 (flower), and 5 (immature seed).
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pone.0125174.g005: Relative expression profiles of soybean GATA genes in various organs.Data were obtained by real-time PCR normalized against the reference gene ACT11 and shown as a percentage of expression in leaf. Numbers on the x-axis indicate various tissues: 1 (young leaf), 2 (root), 3 (stem), 4 (flower), and 5 (immature seed).

Mentions: To identify the tissue expression patterns of GmGATA genes in soybean, specific primers were designed for each of the GATA factor genes (S1 Table), and the expression profiles of the 64 GmGATA genes were investigated in various tissues, including root, stem, young leaf, flower, and immature seed, by real-time PCR. Results showed that the soybean GATA genes were expressed in distinct patterns (Fig 5). The GmGATA8, GmGATA45, and GmGATA49 genes showed less than twofold expression variation in different tissues, suggesting that they are not developmentally regulated at the transcription level. Some GmGATA genes were constitutively expressed in different tissues, but with preferential expression in certain tissues. For example, GmGATA33/34/42/46/58/62 were predominantly expressed in young leaf; GmGATA7/11/38/47/52 in root; GmGATA9, GmGATA20, and GmGATA23 in stem; and GmGATA10, GmGATA13, and GmGATA63 in immature seed. Moreover, GmGATA29, GmGATA32, GmGATA44, and GmGATA50 exhibited a highly tissue-specific expression pattern in flower, immature seed, young leaf, and root, respectively. Among these four genes, GmGATA44 having maximum similarity with the Arabidopsis GATA gene AtGATA22 based on GATA zinc finger sequences (Fig 4) shared a highly similar expression pattern to AtGATA22 [14], a regulator of chloroplast development and chlorophyll biosynthesis [7, 46]. The GATA genes highly expressed in specific organs of plants are crucial for the functioning or development of a specific organ.


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)

Relative expression profiles of soybean GATA genes in various organs.Data were obtained by real-time PCR normalized against the reference gene ACT11 and shown as a percentage of expression in leaf. Numbers on the x-axis indicate various tissues: 1 (young leaf), 2 (root), 3 (stem), 4 (flower), and 5 (immature seed).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0125174.g005: Relative expression profiles of soybean GATA genes in various organs.Data were obtained by real-time PCR normalized against the reference gene ACT11 and shown as a percentage of expression in leaf. Numbers on the x-axis indicate various tissues: 1 (young leaf), 2 (root), 3 (stem), 4 (flower), and 5 (immature seed).
Mentions: To identify the tissue expression patterns of GmGATA genes in soybean, specific primers were designed for each of the GATA factor genes (S1 Table), and the expression profiles of the 64 GmGATA genes were investigated in various tissues, including root, stem, young leaf, flower, and immature seed, by real-time PCR. Results showed that the soybean GATA genes were expressed in distinct patterns (Fig 5). The GmGATA8, GmGATA45, and GmGATA49 genes showed less than twofold expression variation in different tissues, suggesting that they are not developmentally regulated at the transcription level. Some GmGATA genes were constitutively expressed in different tissues, but with preferential expression in certain tissues. For example, GmGATA33/34/42/46/58/62 were predominantly expressed in young leaf; GmGATA7/11/38/47/52 in root; GmGATA9, GmGATA20, and GmGATA23 in stem; and GmGATA10, GmGATA13, and GmGATA63 in immature seed. Moreover, GmGATA29, GmGATA32, GmGATA44, and GmGATA50 exhibited a highly tissue-specific expression pattern in flower, immature seed, young leaf, and root, respectively. Among these four genes, GmGATA44 having maximum similarity with the Arabidopsis GATA gene AtGATA22 based on GATA zinc finger sequences (Fig 4) shared a highly similar expression pattern to AtGATA22 [14], a regulator of chloroplast development and chlorophyll biosynthesis [7, 46]. The GATA genes highly expressed in specific organs of plants are crucial for the functioning or development of a specific organ.

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