Abstract
BackgroundGenes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. They have been known to play important roles in RNA processing as RNA-binding proteins in animals. To date, few plant CCCH proteins have been studied functionally.ResultsIn this study, a comprehensive computational analysis identified 68 and 67 CCCH family genes in Arabidopsis and rice, respectively. A complete overview of this gene family in Arabidopsis was presented, including the gene structures, phylogeny, protein motifs, and chromosome locations. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. These results revealed that the CCCH families in Arabidopsis and rice were divided into 11 and 8 subfamilies, respectively. The gene duplication contributed to the expansion of the CCCH gene family in Arabidopsis genome. Expression studies indicated that CCCH proteins exhibit a variety of expression patterns, suggesting diverse functions. Finally, evolutionary analysis showed that one subfamily is higher plant specific. The expression profile indicated that most members of this subfamily are regulated by abiotic or biotic stresses, suggesting that they could have an effective role in stress tolerance.ConclusionOur comparative genomics analysis of CCCH genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of potential RNA-binding proteins.
Highlights
Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues
Identification of genes coding for CCCH zinc finger protein in Arabidopsis The previous research revealed that CCCH zinc finger protein contained 1–6 copies of C3H-type zinc-finger motifs characterized by three Cys and one His (Figure 1)
Berg et al defined that the CCCH family is a group of zinc-finger protein consisting of canonical C-X-C-X-C-X-H motif (CX6–14-C-X4–5-C-X3-H) [21]
Summary
Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. They have been known to play important roles in RNA processing as RNA-binding proteins in animals. The CCCH proteins are a large family of zinc finger containing C3H-type motifs and many evidences proved that they may be RNA-binding proteins functioning in RNA processing [19,20,21]. PEI1 is an embryo-specific CCCH zinc finger protein that plays an important role during Arabidopsis embryogenesis, functioning primarily in the apical domain of the embryo [28]. It was proposed to play a role in posttranscriptional level by interacting with target RNA
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