Comprehensive analysis of CCCH zinc finger family in poplar (

Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, PR China.
BMC Genomics (Impact Factor: 3.99). 06/2012; 13(1):253. DOI: 10.1186/1471-2164-13-253
Source: PubMed


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 Arabidopsis 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 Populus to date.
In the present study, a comprehensive analysis of the genes encoding CCCH zinc finger family in Populus was performed. Using a thorough annotation approach, a total of 91 full-length CCCH genes were identified in Populus, of which most contained more than one CCCH motif and a type of non-conventional C-X(11)-C-X(6)-C-X(3)-H motif was unique for Populus. All of the Populus 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 Populus, 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 Populus 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 Populus 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 Populus CCCH genes.
This study provides the first systematic analysis of the Populus CCCH proteins. Comprehensive genomic analyses suggested that segmental duplications contribute significantly to the expansion of Populus CCCH gene family. Transcriptome profiling provides first insights into the functional divergences among members of Populus 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.

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    • "A number of RR - TZF genes have been identified previously in higher plants , and their products have been shown to have important roles in the regulation of some developmental processes and adaptive responses to abiotic stress , such as to cold , salt and drought ( Wang et al . , 2008 ; Chai et al . , 2012 ; Lee et al . , 2012 ) . In the present study , we characterized two durum wheat RR - TZF genes , TdTZF1 - A , and TdTZF1 - B , which are highly homologous to AtTZF2 and AtTZF3 . Using a short conserved peptide sequence derived from the RR - region , we identified 461 putative RR - TZF plant proteins that share the unique signature of K"
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    • "a integrative phylogenetic tree using the three representative species (citrus, Arabidopsis and rice) could not be constructed due to some genes have low bootstrap values. Therefore, we divided the genes into five subfamilies based on a previous study (Chai et al. 2012). The citrus CCCHa subfamily contains the largest number of genes among the five subfamilies (18), which is more than Arabidopsis and rice (15 and 14, respectively). "
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