Genome-wide Analysis Of CCCH Zinc Finger Family In Arabidopsis And Rice

CCCH-type zinc finger proteins are a large group among the zinc finger proteins. Genes of CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. Compared to animals, only a few of plant CCCH proteins have been characterized functionally. To date, there are not any reaseach present the information of this zinc finger family from genome level.In this study, we used two methods to search the CCCH genes from the genome of the model plant, Arabidopsis and rice. Firstly, we performed multiple BLAST algorithms to search against the corresponding data set using the known CCCH proteins got from several database as our query. Then, we analyzed the proteome data with a program written by Perl in which a regular expression was used to search for the CCCH motifs from the genome data of the local Mysql database. We eliminated the proteins that did not contain the CCCH motif after detecting by SMART and Pfam. Finally, we found 68 and 67 genes which encode the proteins containing the CCCH motif from Arabidopsis and rice, respectively. A complete overview of this gene family was presented, including the classification of subfamily, chromosome locations, the analysis of the tissue expression, the prediction of the structure of CCCH motifs. The main results are as follows:1. We used BLAST and the program written by Perl to identify 68 and 67 CCCH family genes in Arabidopsis and rice, respectively.2. The phylogenetic trees of CCCH gene family were generated with the neighbor-joining method. Based on the statistical support of each branch, we divided the Arabidopsis CCCH family into 11 subfamilies, designated I to XI. In rice, the CCCH family was divided into 8 subfamilies, designated I to VIII. Form the phylogenetic tree, we found that CCCH gene family is a large group of zinc finger proteins and the subfamily might be the real gene family shared the same feature.3. Based on the chromosomal location information on Internet, we localized Arabidopsis and rice CCCH genes in chromosomes. After analyzing the CCCH genes in duplicated segmental regions, we found the large-scale segmental duplication events appear to have exclusively contributed to the current complexes of the CCCH gene family.4. CCCH genes in moss, gymnosperm and angiosperm are also identified.5. We performed sequence alignments of 302 CCCH motifs in 135 CCCH proteins. The resulut showed that, in Arabidopsis, 42 members contain C-X7-C-X5-C-X3-H motif and 44 members contain C-X8-C-X5-C-X3-H motif, while the number is 35 and 36 in rice, respectively. More than 75% of the CCCH motifs contain glycine and phenylalanine. Given these characteristic of verified protein sequences, we developed a new criteria to objectively define those sequences to be considered as CCCH motif. The CCCH proteins are characterized by one to six C-X4–15-C-X4–6-C-X3-H motifs which are glycine-rich and phenylalanine-rich sequences.6. We examined the expression of Arabidopsis and rice CCCH genes using massively parallel signature sequencing (MPSS) and EST data. According to expression profiles, CCCH genes can be classified into three groups. The largest group is the genes that expressed in all tissues, including 33 genes in Arabidopsis and 36 genes in rice, and the second group contains 18 Arabidopsis CCCH genes and 12 rice CCCH genes whose expression were detected in the majority, but not all, of the tissues. The third group includes 17 genes with tissue specific expression.7. Twenty genes of Arabidopsis subfamily IX and rice subfamily I were investigated in details. Sequences analyses show that these genes contain the C-X5-C-X4-C-X3-H motif and CHCH (C-X5-H-X4-C-X3-H) motif. DBSubLoc indicate that these genes are localized in the cell nucleus. NES sequences were identified in all these genes by pergram written by Perl. The result suggests that all these proteins may be nucleocytoplasmic shuttle proteins involved in signal transduction events.8. The microarray date from Genevestigator site and the result of RT- PCR showed that the expression of the Arabidopsis genes of subfamily IX changed under stresses stimuli.9. We modelled the structure of the interaction of CCCH domain peptide with the RNA nonamer using the Swiss-Model programs.