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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

GmGATA44 modulates chlorophyll content.(a) Expression levels of GmGATA44 and AtGNC in the wild-type Arabidopsis (wt), the gnc mutant and two GmGATA44 overexpressing transgenic lines (OX31 and OX43) using semi-quantitative RT-PCR from 3 week old rosette leaf tissue.(b) Images of the wild-type plant, the gnc mutant and GmGATA44 overexpressing transgenic plants at one week (upper panel), 3 weeks (middle panel) and 5 weeks (bottom panel) post germination. Bars = 1 cm.(c) Chlorophyll content of the wild-type plants, the gnc mutant and two GmGATA44 overexpressing transgenic lines at 3 weeks post germination. Data are presented as mean ± SD (N = 10) from triplicate independent measurements. Data analysis was performed using SAS software, and significant differences were calculated using the Student’s t-test at 95% confidence limit. Asterisk indicates significant differences from the wild-type plant.(d) Relative expression levels of AtPORA, AtPORB and AtPORC in the wild-type plant, the gnc mutant and two GmGATA44 overexpressing transgenic lines by real-time PCR from 3 week old rosette leaf tissue. Data were obtained by real-time PCR normalized against the reference gene GAPDH and shown as a percentage of expression in the wild-type plant.
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pone.0125174.g009: GmGATA44 modulates chlorophyll content.(a) Expression levels of GmGATA44 and AtGNC in the wild-type Arabidopsis (wt), the gnc mutant and two GmGATA44 overexpressing transgenic lines (OX31 and OX43) using semi-quantitative RT-PCR from 3 week old rosette leaf tissue.(b) Images of the wild-type plant, the gnc mutant and GmGATA44 overexpressing transgenic plants at one week (upper panel), 3 weeks (middle panel) and 5 weeks (bottom panel) post germination. Bars = 1 cm.(c) Chlorophyll content of the wild-type plants, the gnc mutant and two GmGATA44 overexpressing transgenic lines at 3 weeks post germination. Data are presented as mean ± SD (N = 10) from triplicate independent measurements. Data analysis was performed using SAS software, and significant differences were calculated using the Student’s t-test at 95% confidence limit. Asterisk indicates significant differences from the wild-type plant.(d) Relative expression levels of AtPORA, AtPORB and AtPORC in the wild-type plant, the gnc mutant and two GmGATA44 overexpressing transgenic lines by real-time PCR from 3 week old rosette leaf tissue. Data were obtained by real-time PCR normalized against the reference gene GAPDH and shown as a percentage of expression in the wild-type plant.

Mentions: The Arabidopsis gnc mutant has a T-DNA insertion in the exon of AtGATA21 gene, leading to the reduced chlorophyll phenotype. To confirm whether GmGATA44 had similar biological functions of the orthologous gene AtGATA21, overexpression of GmGATA44 under the control of CaMV 35S promoter was carried out in the gnc mutant background to complement this mutant. A total of 50 GmGATA44 overexpressing (OX) transgenic plants were obtained, and two lines (OX31 and OX43) were chose for further analysis. Semi-quantitative RT-PCR results showed that the exogenous GmGATA44 was abundantly expressed in both OX31 and OX43 lines, and the endogenous AtGNC was expressed in wild-type Arabidopsis rather not in the gnc mutant and two transgenic lines (Fig 9A). Both OX31 and OX43 lines restored pale green leaves of the gnc mutant to green and even greener leaves than that of wild-type plants (Fig 9B). The results of chlorophyll content in leaves also corresponded to this complementation. The chlorophyll accumulation was improved significantly in both OX31 and OX43 lines, compared to the gnc mutant, even more than that of wild-type plants (Fig 9C). In addition, strong accumulation of chlorophyll was also obviously observed in the seedling hypocotyls of both OX31 and OX43 lines (Fig 9B).


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)

GmGATA44 modulates chlorophyll content.(a) Expression levels of GmGATA44 and AtGNC in the wild-type Arabidopsis (wt), the gnc mutant and two GmGATA44 overexpressing transgenic lines (OX31 and OX43) using semi-quantitative RT-PCR from 3 week old rosette leaf tissue.(b) Images of the wild-type plant, the gnc mutant and GmGATA44 overexpressing transgenic plants at one week (upper panel), 3 weeks (middle panel) and 5 weeks (bottom panel) post germination. Bars = 1 cm.(c) Chlorophyll content of the wild-type plants, the gnc mutant and two GmGATA44 overexpressing transgenic lines at 3 weeks post germination. Data are presented as mean ± SD (N = 10) from triplicate independent measurements. Data analysis was performed using SAS software, and significant differences were calculated using the Student’s t-test at 95% confidence limit. Asterisk indicates significant differences from the wild-type plant.(d) Relative expression levels of AtPORA, AtPORB and AtPORC in the wild-type plant, the gnc mutant and two GmGATA44 overexpressing transgenic lines by real-time PCR from 3 week old rosette leaf tissue. Data were obtained by real-time PCR normalized against the reference gene GAPDH and shown as a percentage of expression in the wild-type plant.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4401516&req=5

pone.0125174.g009: GmGATA44 modulates chlorophyll content.(a) Expression levels of GmGATA44 and AtGNC in the wild-type Arabidopsis (wt), the gnc mutant and two GmGATA44 overexpressing transgenic lines (OX31 and OX43) using semi-quantitative RT-PCR from 3 week old rosette leaf tissue.(b) Images of the wild-type plant, the gnc mutant and GmGATA44 overexpressing transgenic plants at one week (upper panel), 3 weeks (middle panel) and 5 weeks (bottom panel) post germination. Bars = 1 cm.(c) Chlorophyll content of the wild-type plants, the gnc mutant and two GmGATA44 overexpressing transgenic lines at 3 weeks post germination. Data are presented as mean ± SD (N = 10) from triplicate independent measurements. Data analysis was performed using SAS software, and significant differences were calculated using the Student’s t-test at 95% confidence limit. Asterisk indicates significant differences from the wild-type plant.(d) Relative expression levels of AtPORA, AtPORB and AtPORC in the wild-type plant, the gnc mutant and two GmGATA44 overexpressing transgenic lines by real-time PCR from 3 week old rosette leaf tissue. Data were obtained by real-time PCR normalized against the reference gene GAPDH and shown as a percentage of expression in the wild-type plant.
Mentions: The Arabidopsis gnc mutant has a T-DNA insertion in the exon of AtGATA21 gene, leading to the reduced chlorophyll phenotype. To confirm whether GmGATA44 had similar biological functions of the orthologous gene AtGATA21, overexpression of GmGATA44 under the control of CaMV 35S promoter was carried out in the gnc mutant background to complement this mutant. A total of 50 GmGATA44 overexpressing (OX) transgenic plants were obtained, and two lines (OX31 and OX43) were chose for further analysis. Semi-quantitative RT-PCR results showed that the exogenous GmGATA44 was abundantly expressed in both OX31 and OX43 lines, and the endogenous AtGNC was expressed in wild-type Arabidopsis rather not in the gnc mutant and two transgenic lines (Fig 9A). Both OX31 and OX43 lines restored pale green leaves of the gnc mutant to green and even greener leaves than that of wild-type plants (Fig 9B). The results of chlorophyll content in leaves also corresponded to this complementation. The chlorophyll accumulation was improved significantly in both OX31 and OX43 lines, compared to the gnc mutant, even more than that of wild-type plants (Fig 9C). In addition, strong accumulation of chlorophyll was also obviously observed in the seedling hypocotyls of both OX31 and OX43 lines (Fig 9B).

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