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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Available from: Guohua Chai
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    • " - rich region that contains a CHCH motif ( known as the RR region ) that is linked to a tandem zinc - finger ( TZF ) domain , which is unique to plants ( Wang et al . , 2008 ; Pomeranz et al . , 2010b ) . Members of the RR - TZF subfamily have been identified in several higher plants , including Arabidopsis ( AtTZF1 - 11 ) ( Wang et al . , 2008 ; Chai et al . , 2012 ; Peng et al . , 2012 ; Zhang et al . , 2013 ; Liu et al . , 2014 ; Xu , 2014 ) . The functions of some of the RR - TZF Arabidopsis proteins have been defined in relation to responses to a number of stress stimuli and developmental processes . PEI1 ( AtTZF6 ) is involved in embryogenesis ( Li and Thomas , 1998 ) , and AtTZF10 and AtTZF1"
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    ABSTRACT: Arginine-rich tandem zinc-finger proteins (RR-TZF) participate in a wide range of plant developmental processes and adaptive responses to abiotic stress, such as cold, salt and drought. This study investigates the conservation of the genes AtTZF1-5 at the level of their sequences and expression across plant species. The genomic sequences of the two RR-TZF genes TdTZF1-A and TdTZF1-B were isolated in durum wheat and assigned to chromosomes 3A and 3B, respectively. Sequence comparisons revealed that they encode proteins that are highly homologous to AtTZF1, AtTZF2 and AtTZF3. The expression profiles of these RR-TZF durum wheat and Arabidopsis proteins support a common function in the regulation of seed germination and responses to abiotic stress. In particular, analysis of plants with attenuated and overexpressed AtTZF3 indicate that AtTZF3 is a negative regulator of seed germination under conditions of salt stress. Finally, comparative sequence analyses establish that the RR-TZF genes are encoded by lower plants, including the bryophyte Physcomitrella patens and the alga Chlamydomonas reinhardtii. The regulation of the Physcomitrella AtTZF1-2-3-like genes by salt stress strongly suggests that a subgroup of the RR-TZF proteins has a function that has been conserved throughout evolution.
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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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    ABSTRACT: The CCCH-type zinc finger proteins comprise a large gene family of regulatory proteins and are widely distributed in eukaryotic organisms. The CCCH proteins have been implicated in multiple biological processes and environmental responses in plants. Little information is available, however, about CCCH genes in plants, especially in woody plants such as citrus. The release of the whole-genome sequence of citrus allowed us to perform a genome-wide analysis of CCCH genes and to compare the identified proteins with their orthologs in model plants. In this study, 62 CCCH genes and a total of 132 CCCH motifs were identified, and a comprehensive analysis including the chromosomal locations, phylogenetic relationships, functional annotations, gene structures and conserved motifs was performed. Distribution mapping revealed that 54 of the 62 CCCH genes are unevenly dispersed on the nine citrus chromosomes. Based on phylogenetic analysis and gene structural features, we constructed 5 subfamilies of 62 CCCH members and integrative subfamilies from citrus, Arabidopsis, and rice, respectively. Importantly, large numbers of SNPs and InDels in 26 CCCH genes were identified from Poncirus trifoliata and Fortunella japonica using whole-genome deep re-sequencing. Furthermore, citrus CCCH genes showed distinct temporal and spatial expression patterns in different developmental processes and in response to various stress conditions. Our comprehensive analysis of CleC3Hs is a valuable resource that further elucidates the roles of CCCH family members in plant growth and development. In addition, variants and comparative genomics analyses deepen our understanding of the evolution of the CCCH gene family and will contribute to further genetics and genomics studies of citrus and other plant species.
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    • "Using known R2R3-MYB protein sequences to query the recently updated Populus genome database, this work identified 194 full-length R2R3-MYB genes in Populus and manually verified their uniqueness (Supplementary Table S1), which covered 192 R2R3-MYB members reported by Wilkins et al. (2009). A neighbour-joining phylogenetic tree was constructed using the 194 full-length MYB protein sequences (Supplementary Fig. S1), which allowed this work to identify 81 pairs of paralogous genes at the terminal nodes (Table 1), with the percentage of paralogous genes (83.5%) similar to those of Populus Dof (78.1%) (Yang et al., 2006) and CCCH (74.7%) (Chai et al., 2012) gene families. "
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