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

Dong Wang; Yinghui Guo; Changai Wu; Guodong Yang; Yingying Li; Chengchao Zheng
January 2008
BMC Genomics;2008, Vol. 9, Special section p1
Academic Journal
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.


Related Articles

  • A Zinc Finger-Containing Glycine-Rich RNA-Binding Protein, atRZ-1a, Has a Negative Impact on Seed Germination and Seedling Growth of Arabidopsis thaliana Under Salt or Drought Stress Conditions. Yeon-Ok Kim; SangO Pan; Che-Hun Jung; Hunseung Kang // Plant & Cell Physiology;Aug2007, Vol. 48 Issue 8, p1170 

    Despite the fact that glycine-rich RNA-binding proteins (GRPs) have been implicated in the responses of plants to changing environmental conditions, the reports demonstrating their biological roles are severely limited. Here, we examined the functional roles of a zinc finger-containing GRP,...

  • Expression of a RING-HC protein from rice improves resistance to Pseudomonas syringae pv. tomato DC3000 in transgenic Arabidopsis thaliana. Ming-Yan Cheung; Nai-Yan Zeng; Suk-Wah Tong; Francisca Wing-Yen Li; Kai-Jun Zhao; Qi Zhang; Samuel Sai-Ming Sun; Hon-Ming Lam // Journal of Experimental Botany;Dec2007, Vol. 58 Issue 15/16, p4147 

    A cDNA clone (OsRHC1) was obtained, which encodes a novel RING zinc finger protein sharing similar structural features (multiple transmembrane domains at the N-half; a unique RING zinc finger consensus Cys-X2-Cys-X11-Cys-X-His-X3-Cys-X2-Cys-X6-Cys-X2-Cys at the C terminus) to a group of closely...

  • Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. Conte, Matthieu G.; Gaillard, Sylvain; Droc, Gaetan; Perin, Christophe // BMC Genomics;2008, Vol. 9, Special section p1 

    Background: Gene ortholog identification is now a major objective for mining the increasing amount of sequence data generated by complete or partial genome sequencing projects. Comparative and functional genomics urgently need a method for ortholog detection to reduce gene function inference and...

  • Genomic Organization, Phylogenetic and Expression Analysis of the B-BOX Gene Family in Tomato. Zhuannan Chu; Xin Wang; Ying Li; Huiyang Yu; Jinhua Li; Yongen Lu; Hanxia Li; Bo Ouyang; Han Xiao; Gang Lu // Frontiers in Plant Science;10/19/2016, Vol. 7, p1 

    The B-BOX (BBX) proteins encode a class of zinc-finger transcription factors possessing one or two B-BOX domains and in some cases an additional CCT (CO, CO-like and TOC1) motif, which play important roles in regulating plant growth, development and stress response. Nevertheless, no systematic...

  • Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants. Mi-Jeong Yoo; Albert, Victor A.; Soltis, Pamela S.; Soltis, Douglas E. // BMC Plant Biology;2006, Vol. 6, p1 

    Background: The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases (GSKs) are non-receptor serine/threonine protein kinases that are involved in a variety of biological processes. In contrast to the two members of the GSK3 family in mammals, plants appear to have a much larger set of...

  • Identification and functional characterization of silicon transporters in soybean using comparative genomics of major intrinsic proteins in Arabidopsis and rice. Deshmukh, Rupesh; Vivancos, Julien; Guérin, Valérie; Sonah, Humira; Labbé, Caroline; Belzile, François; Bélanger, Richard // Plant Molecular Biology;Nov2013, Vol. 83 Issue 4-5, p303 

    Silicon (Si) confers several benefits to many plant species when absorbed as silicic acid through nodulin 26-like intrinsic proteins (NIPs). The NIPs belong to major intrinsic protein (MIP) family, members of which form channels with high selectivity to control transport of water and different...

  • The first karyogram of a Bromeliaceae species: an allopolyploid genome. Nunes, Andrei; Nogueira, Ester; Gontijo, Andreia; Carvalho, Carlos; Clarindo, Wellington // Plant Systematics & Evolution;Jun2013, Vol. 299 Issue 6, p1135 

    The Bromeliaceae family has been traditionally distributed in the subfamilies Bromelioideae, Tillandsioideae and Pitcairnioideae. However, phylogenetic studies have provided other classifications, highlighting the need for analyses in order to characterize the genome of different species from...

  • Crystal structure of Cwc2 reveals a novel architecture of a multipartite RNA-binding protein. Schmitzová, Jana; Rasche, Nicolas; Dybkov, Olexander; Kramer, Katharina; Fabrizio, Patrizia; Urlaub, Henning; Lührmann, Reinhard; Pena, Vladimir // EMBO Journal;5/2/2012, Vol. 31 Issue 9, p2222 

    The yeast splicing factor Cwc2 contacts several catalytically important RNA elements in the active spliceosome, suggesting that Cwc2 is involved in determining their spatial arrangement at the spliceosome's catalytic centre. We have determined the crystal structure of the Cwc2 functional core,...

  • Fingering nucleic acids: the RNA did it. Berg, Jeremy M. // Nature Structural Biology;Dec2003, Vol. 10 Issue 12, p986 

    Discusses research being done on the structure of zinc fingers. Reference to study by Lu, Searles and Klug, published in the journal "Nature"; Role of RNA in zinc fingers-TFIIIA protein interaction; Biological significance of zinc finger proteins; Interaction of zinc fingers with RNA;...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics