Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2008 Jan 27:9:44.
doi: 10.1186/1471-2164-9-44.

Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice

Dong Wang  1 , Yinghui Guo, Changai Wu, Guodong Yang, Yingying Li, Chengchao Zheng
Affiliations
Comparative Study

Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice

Dong Wang et al. BMC Genomics. .

Abstract

Background: 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. To date, few plant CCCH proteins have been studied functionally.

Results: In 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.

Conclusion: Our 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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Alignment of the CCCH zinc finger motifs from selected CCCH proteins. Black and light grey shading indicate identical and conserved amino acid residues, respectively. The three cysteine and one histidine residues putatively responsible for the zinc-finger structure are indicated.
Figure 2
Figure 2
The program for detecting the CCCH motifs by regular expression. The code was used to detect the proteins containing CCCH motifs from local MySQL database. The whole program is available in additional file (see Additional file 5 and 7).
Figure 3
Figure 3
An analytical view of the Arabidopsis CCCH gene family. The following parts are shown from left to right. Protein neighbor-joining tree: The unrooted tree, constructed using ClustalX (1.83), summarizes the evolutionary relationship among the 68 members of CCCH families. The neighbor-joining tree was constructed using aligned full-length amino acid sequences. The proteins are named according to their gene name (see Table 2) with the CCCH zinc finger number of each protein. The tree shows the 11 major phylogenetic subfamilies (left column, numbered I to XI and marked with different alternating tones of a gray background to make subfamily identification easier) with high predictive value. The numbers beside the branches represent bootstrap values (≥500) based on 1000 replications that were used to class the major 11 subfamilies. Gene structure: The gene structure is presented by black exon(s) and spaces between the black boxes correspond to introns. The sizes of exons and introns can be estimated using the horizontal lines. Protein structure: Each black box represents the motif in the protein, as indicated in the table on the left side. The conserved motifs outside CCCH motif are highlighted with an arranged number, and the same number referred to the same motif. The length of the motif can be estimated using the scale at top. aa, amino acids.
Figure 4
Figure 4
Chromosomal distribution and segmental duplication events for Arabidopsis CCCH genes. The chromosome number is indicated at the top of each chromosome. The green boxes indicate the duplicated segmental regions resulting from the most recent polyploidy. Only the duplicated regions containing CCCH genes are shown. Blue lines connect corresponding sister gene pairs in duplicated blocks. AtC3H1 and AtC3H51, AtC3H8 and AtC3H60, AtC3H12 and AtC3H28, AtC3H14 and AtC3H15, AtC3H30 and AtC3H56, AtC3H46 and AtC3H55, AtC3H59 and AtC3H62 are potential duplicated gene pairs which are marked with the same color rectangle, as described in the text.
Figure 5
Figure 5
Schematic structures of Arabidopsis CCCH proteins. The figure is schematic protein structures of all CCCH-type zinc-finger proteins identified in Arabidopsis. The CCCH zinc fingers are shown by black boxes. Types of zinc fingers are indicated by A to W, which are cross-indexed in the table on the right side. Numbers of amino acids in the spacers are indicated on each spacer region for several-fingered proteins. The lengths of each protein are shown on the right of the schematic structures. Numbers of different types of CCCH zinc finger proteins are presented in the brackets.
Figure 6
Figure 6
Sequence logos for the CCCH zinc finger motifs of Arabidopsis and rice. Numbers on the x-axis represent the sequence positions in zinc finger motifs. The y-axis represents the information content measured in bits. The sequence logos were derived using WebLogo [4].
Figure 7
Figure 7
The expression patterns for Arabidopsis and rice CCCH genes from MPSS and EST data. The expression patterns for Arabidopsis (the part of left side) and rice (the part of right side) CCCH genes are shown. The letter R above the column of expression data refers to root, I refers to inflorescence, L refers to leaf, and S refers to seed (silique). A positive signal is indicated by a colored box for the following tissues: grey for roots (R), red for inflorescences (I), green for rosette leaves (L), and yellow for siliques (S). The white box indicates that no expression could be detected. The number on the left indicates the subfamily and the black points on the right show the origin of expression data for each gene. CCCH proteins are aligned in the same order as they appear in the phylogenetic trees. Subfamilies of CCCH proteins are highlighted by vertical bars next to the gene identifiers. The expression profile of AtC3H37 (HUA1) was got from RNA filter hybridization [19].
Figure 8
Figure 8
Amino acid sequence analysis of the members in subfamily IX of Arabidopsis. A, Multiple sequence alignment of the three zinc finger motifs of the members in the subfamily IX. The black and dashed bars represent CCCH motifs and putative CHCH zinc finger, respectively. Black and gray shading indicate identical and conserved amino acid residues present in more than 50% of the aligned sequences, respectively. B, Amino acid sequence alignment of ankyrin repeats in CCCH family. C, Amino acid sequence alignment of putative NES sequences in subfamily IX.
Figure 9
Figure 9
Phylogenetic trees of genes in subfamily IX of Arabidopsis and subfamily I of rice. A, Phylogenetic tree of Arabidopsis CCCH genes in subfamily IX. The unrooted tree was inferred by MEGA 3.1 and the neighbor-joining method after the alignment of the full-length amino acid sequences of the 11 Arabidopsis genes in subfamily IX. The numbers beside the branches represent bootstrap values based on 1000 replications. Subgroups of CCCH proteins are highlighted by vertical bars next to the gene identifiers. The scale bar corresponds to 0.1 estimated amino acid substitutions per site. B, Joined phylogenetic tree of rice subfamily I and Arabidopsis subfamily IX CCCH genes. The unrooted tree was constructed using MEGA 3.1 and the neighbor-joining method after the alignment of the full-length amino acid sequences of 20 Arabidopsis and rice genes. Numbers on branches indicate the percentage of 1000 bootstrap replicates that support the adjacent node. Black braces and numerals at right indicate the three subgroups. The scale bar corresponds to 0.05 estimated amino acid substitutions per site.
Figure 10
Figure 10
The expression patterns of subfamily IX genes in response to abiotic stress and ABA treatments. A, Microarray data for the CCCH genes of subfamily IX of Arabidopsis were extracted using Genevestigator. Up- and down-expression patterns of eleven genes under six different treatments are indicated by black and grey arrowhead, respectively. B, Expression pattern for genes in subfamily IX of Arabidopsis following stress and ABA treatments detected by RT-PCR. Plants were grown on Murashige and Skoog (1962) (MS) agar medium for 3 weeks and were treated with NaCl (300 mM), mannitol (300 mM), cold (4°C), ABA (100 μM) or water (as a control). The EF1-α gene was used as an internal control.
Figure 11
Figure 11
Sequence alignments and the structure of AtC3H14 tandem domains in complex with the RNA. A, Alignment of AtC3H14, AtC3H15, OsC3H9, OsC3H39, hTTP and hTIS11d. Conserved motifs are highlighted in light blue, gold and red (cysteines and histidines involved in zinc binding, respectively), and green (aromatic residues involved in base-stacking interactions with RNA). h, Homo sapiens. B, Structure of the RNA complex of AtC3H14. This proposed structure was modelled on the original nuclear magnetic resonance structure describe by Hudson et al. [69], using their pdb coordinates and the Swiss-Model program. The RNA oligonucleotide is shown in magenta (A3 and A7 are shown in yellow) with the 5' and 3' ends indicated. The protein backbone are shown to represent the structure, with alpha helices are coloured royal blue, beta sheets are coloured yellow, the zinc-coordinating ligands are colored green and the zinc residues are coloured red. C, Molecular contact surface of AtC3H14 structure showing surface topology. Blue denotes convex surfaces. The location of the motifs that form the U6 and U2 binding pockets and the aromatic residues which are essential for high-affinity binding are indicated.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Takatsuji H. Zinc-finger transcription factors in plants. Cell Mol Life Sci. 1998;54:582–596. doi: 10.1007/s000180050186. - DOI - PMC - PubMed
    1. Moore M, Ullman C. Recent developments in the engineering of zinc finger proteins. Brief Funct Genomic Proteomic. 2003;1:342–355. doi: 10.1093/bfgp/1.4.342. - DOI - PubMed
    1. Freemont PS. The RING finger. A novel protein sequence motif related to the zinc finger. Ann N Y Acad Sci. 1993;684:174–192. doi: 10.1111/j.1749-6632.1993.tb32280.x. - DOI - PubMed
    1. Arnaud D, Dejardin A, Leple JC, Lesage-Descauses MC, Pilate G. Genome-wide analysis of LIM gene family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa. DNA Res. 2007;14:103–116. doi: 10.1093/dnares/dsm013. - DOI - PMC - PubMed
    1. Kosarev P, Mayer KF, Hardtke CS. Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome. Genome Biol. 2002;3:RESEARCH0016. doi: 10.1186/gb-2002-3-4-research0016. - DOI - PMC - PubMed

Publication types

MeSH terms

LinkOut - more resources