Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa).
Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa).
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杨树CCCH锌指家族的综合分析
DOI：
10.1186/1471-2164-13-253
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发表时间：
2012-06-18
期刊：
影响因子：
4.4
通讯作者：
Zhou G
中科院分区：
文献类型：
--
作者：
Chai G;Hu R;Zhang D;Qi G;Zuo R;Cao Y;Chen P;Kong Y;Zhou G
背景CCCH锌指蛋白是由三个半胱氨酸和一个组氨酸残基组成的典型结构，在mRNA代谢的各个阶段发挥调控作用。在植物中，CCCH型锌指蛋白包括一个大的基因家族，在拟南芥中有68个成员，在水稻中有67个成员。这些CCCH蛋白已被证明在植物发育过程和环境响应中发挥不同的作用。然而，这个家庭还没有被研究的模式树物种Populustodat.ResultsIn本研究中，编码CCCH锌指家族在Populus的基因进行了全面的分析。通过对杨属植物CCCH基因序列的全面注释，共鉴定出91个杨属植物CCCH基因的全长序列，其中大多数含有一个以上的CCCH基序，并且有一种非常规的C-X11-C-X6-C-X3-H基序是杨属植物所特有的。所有的杨CCCH基因在遗传学上可聚为13个不同的亚科。各亚家族的基因结构和基序组成相对保守。这些基因的染色体定位显示，大多数CCCH（81/90，90%）的物理分布在重复块。共鉴定出34对杨属植物的旁系同源对，其中22对（64.7%）可能是由全基因组片段重复产生的，4对可能是由串联重复产生的。在91个CCCH蛋白中，我们还鉴定了63个核质穿梭蛋白和3个典型的RNA结合蛋白。所有PopulusCCCH基因的表达谱已在6个组织中的不同发育阶段，并在各种干旱胁迫条件下进行了数字化分析。CCCH基因在杨树生长发育过程中的表达具有多样性，其中34个基因在根中高表达，22个基因在木质部分化过程中表达量最高。通过实时荧光定量RT-PCR（RT-qPCR）进一步验证了12个杨树CCCH基因的组织特异性表达及其对干旱胁迫的响应。综合基因组分析表明，片段重复对杨CCCH基因家族的扩展起重要作用。转录组谱分析首次揭示了杨树CCCH基因家族成员间的功能差异。特别地，一些CCCH基因可能参与木材发育，而另一些则参与耐旱性调节。我们的研究结果可能提供了一个起点，这个家庭的潜在RNA结合蛋白的功能解剖。
BackgroundCCCH 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 inArabidopsisand 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 speciesPopulusto date.ResultsIn the present study, a comprehensive analysis of the genes encoding CCCH zinc finger family inPopuluswas performed. Using a thorough annotation approach, a total of 91 full-length CCCH genes were identified inPopulus, of which most contained more than one CCCH motif and a type of non-conventional C-X11-C-X6-C-X3-H motif was unique forPopulus. All of thePopulusCCCH 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 inPopulus, 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 allPopulusCCCH 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 duringPopulusdevelopment, 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 selectedPopulusCCCH genes.ConclusionsThis study provides the first systematic analysis of thePopulusCCCH proteins. Comprehensive genomic analyses suggested that segmental duplications contribute significantly to the expansion ofPopulusCCCH gene family. Transcriptome profiling provides first insights into the functional divergences among members ofPopulusCCCH 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.