Comprehensive analysis of CCCH zinc finger family in poplar (<it>Populus trichocarpa</it>)
<p>Abstract</p> <p>Background</p> <p>CCCH zinc finger proteins contain a typical motif of three cysteines and one histidine residues and serve regulatory functions at all stages of mRNA metabolism. In plants, CCCH type zinc finger proteins comprise a large gene family r...
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| Format: | Article |
| Language: | English |
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BMC
2012-06-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/13/253 |
| _version_ | 1811294317529006080 |
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| author | Chai Guohua Hu Ruibo Zhang Dongyuan Qi Guang Zuo Ran Cao Yingping Chen Peng Kong Yingzhen Zhou Gongke |
| author_facet | Chai Guohua Hu Ruibo Zhang Dongyuan Qi Guang Zuo Ran Cao Yingping Chen Peng Kong Yingzhen Zhou Gongke |
| author_sort | Chai Guohua |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>CCCH zinc finger proteins contain a typical motif of three cysteines and one histidine residues and serve regulatory functions at all stages of mRNA metabolism. In plants, CCCH type zinc finger proteins comprise a large gene family represented by 68 members in <it>Arabidopsis</it> and 67 in rice. These CCCH proteins have been shown to play diverse roles in plant developmental processes and environmental responses. However, this family has not been studied in the model tree species <it>Populus</it> to date.</p> <p>Results</p> <p>In the present study, a comprehensive analysis of the genes encoding CCCH zinc finger family in <it>Populus</it> was performed. Using a thorough annotation approach, a total of 91 full-length CCCH genes were identified in <it>Populus</it>, of which most contained more than one CCCH motif and a type of non-conventional C-X<sub>11</sub>-C-X<sub>6</sub>-C-X<sub>3</sub>-H motif was unique for <it>Populus</it>. All of the <it>Populus</it> CCCH genes were phylogeneticly clustered into 13 distinct subfamilies. In each subfamily, the gene structure and motif composition were relatively conserved. Chromosomal localization of these genes revealed that most of the CCCHs (81 of 90, 90 %) are physically distributed on the duplicated blocks. Thirty-four paralogous pairs were identified in <it>Populus</it>, of which 22 pairs (64.7 %) might be created by the whole genome segment duplication, whereas 4 pairs seem to be resulted from tandem duplications. In 91 CCCH proteins, we also identified 63 putative nucleon-cytoplasm shuttling proteins and 3 typical RNA-binding proteins. The expression profiles of all <it>Populus</it> CCCH genes have been digitally analyzed in six tissues across different developmental stages, and under various drought stress conditions. A variety of expression patterns of CCCH genes were observed during <it>Populus</it> development, of which 34 genes highly express in root and 22 genes show the highest level of transcript abundance in differentiating xylem. Quantitative real-time RT-PCR (RT-qPCR) was further performed to confirm the tissue-specific expression and responses to drought stress treatment of 12 selected <it>Populus</it> CCCH genes.</p> <p>Conclusions</p> <p>This study provides the first systematic analysis of the <it>Populus</it> CCCH proteins. Comprehensive genomic analyses suggested that segmental duplications contribute significantly to the expansion of <it>Populus</it> CCCH gene family. Transcriptome profiling provides first insights into the functional divergences among members of <it>Populus</it> CCCH gene family. Particularly, some CCCH genes may be involved in wood development while others in drought tolerance regulation. Our results presented here may provide a starting point for the functional dissection of this family of potential RNA-binding proteins.</p> |
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| spelling | doaj.art-6e8af8844f174b7a9584d09413361a532022-12-22T03:00:55ZengBMCBMC Genomics1471-21642012-06-0113125310.1186/1471-2164-13-253Comprehensive analysis of CCCH zinc finger family in poplar (<it>Populus trichocarpa</it>)Chai GuohuaHu RuiboZhang DongyuanQi GuangZuo RanCao YingpingChen PengKong YingzhenZhou Gongke<p>Abstract</p> <p>Background</p> <p>CCCH zinc finger proteins contain a typical motif of three cysteines and one histidine residues and serve regulatory functions at all stages of mRNA metabolism. In plants, CCCH type zinc finger proteins comprise a large gene family represented by 68 members in <it>Arabidopsis</it> and 67 in rice. These CCCH proteins have been shown to play diverse roles in plant developmental processes and environmental responses. However, this family has not been studied in the model tree species <it>Populus</it> to date.</p> <p>Results</p> <p>In the present study, a comprehensive analysis of the genes encoding CCCH zinc finger family in <it>Populus</it> was performed. Using a thorough annotation approach, a total of 91 full-length CCCH genes were identified in <it>Populus</it>, of which most contained more than one CCCH motif and a type of non-conventional C-X<sub>11</sub>-C-X<sub>6</sub>-C-X<sub>3</sub>-H motif was unique for <it>Populus</it>. All of the <it>Populus</it> CCCH genes were phylogeneticly clustered into 13 distinct subfamilies. In each subfamily, the gene structure and motif composition were relatively conserved. Chromosomal localization of these genes revealed that most of the CCCHs (81 of 90, 90 %) are physically distributed on the duplicated blocks. Thirty-four paralogous pairs were identified in <it>Populus</it>, of which 22 pairs (64.7 %) might be created by the whole genome segment duplication, whereas 4 pairs seem to be resulted from tandem duplications. In 91 CCCH proteins, we also identified 63 putative nucleon-cytoplasm shuttling proteins and 3 typical RNA-binding proteins. The expression profiles of all <it>Populus</it> CCCH genes have been digitally analyzed in six tissues across different developmental stages, and under various drought stress conditions. A variety of expression patterns of CCCH genes were observed during <it>Populus</it> development, of which 34 genes highly express in root and 22 genes show the highest level of transcript abundance in differentiating xylem. Quantitative real-time RT-PCR (RT-qPCR) was further performed to confirm the tissue-specific expression and responses to drought stress treatment of 12 selected <it>Populus</it> CCCH genes.</p> <p>Conclusions</p> <p>This study provides the first systematic analysis of the <it>Populus</it> CCCH proteins. Comprehensive genomic analyses suggested that segmental duplications contribute significantly to the expansion of <it>Populus</it> CCCH gene family. Transcriptome profiling provides first insights into the functional divergences among members of <it>Populus</it> CCCH gene family. Particularly, some CCCH genes may be involved in wood development while others in drought tolerance regulation. Our results presented here may provide a starting point for the functional dissection of this family of potential RNA-binding proteins.</p>http://www.biomedcentral.com/1471-2164/13/253 |
| spellingShingle | Chai Guohua Hu Ruibo Zhang Dongyuan Qi Guang Zuo Ran Cao Yingping Chen Peng Kong Yingzhen Zhou Gongke Comprehensive analysis of CCCH zinc finger family in poplar (<it>Populus trichocarpa</it>) BMC Genomics |
| title | Comprehensive analysis of CCCH zinc finger family in poplar (<it>Populus trichocarpa</it>) |
| title_full | Comprehensive analysis of CCCH zinc finger family in poplar (<it>Populus trichocarpa</it>) |
| title_fullStr | Comprehensive analysis of CCCH zinc finger family in poplar (<it>Populus trichocarpa</it>) |
| title_full_unstemmed | Comprehensive analysis of CCCH zinc finger family in poplar (<it>Populus trichocarpa</it>) |
| title_short | Comprehensive analysis of CCCH zinc finger family in poplar (<it>Populus trichocarpa</it>) |
| title_sort | comprehensive analysis of ccch zinc finger family in poplar it populus trichocarpa it |
| url | http://www.biomedcentral.com/1471-2164/13/253 |
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