Biologia plantarum 2012, 56:667-674 | DOI: 10.1007/s10535-012-0247-3

Phylogenetic, structure and expression analysis of ABC1Ps gene family in rice

S. G. Yang1,2, T. Li1, M. Liu1, S. J. Gao3, S. Y. Yang1, L. Li1, C. W. Yang1,*
1 College of Life Science, South China Normal University, Guangzhou, P.R. China
2 South China Botanical Garden, Chinese Academy of Science, Guangzhou, P.R. China
3 Zhongkai University of Agiculture and Engineering, Guangzhou, P.R.China

The ABC1 protein family (ABC1P), a new family of putative kinases, widely existed in procaryote and eucaryote. A comprehensive genome-wide analysis was carried out in this study to find all ABC1Ps in rice (Oryza sativa subsp. japonica). We identified 15 ABC1P genes in rice. All the ABC1Ps contained an ABC1 domain of about 120 conserved amino acid residues and conserved kinase motifs-VAIK (VAVK, VAMK) and DFG (DEG). The phylogenetic analysis showed that all the ABC1Ps were grouped into three subgroups, and formed a total of 12 sister pairs. Conserved motifs analysed by MEME program indicated that almost all ABC1Ps contains motifs 1, 3, 7, 8 and 9. Predictably, the ABC1Ps were localized in mitochondria or chloroplasts, which implied that the ABC1Ps might be involved in energy metabolism in plants. RT-PCR assays demonstrated that all 15 ABC1P genes were active, and some of them were affected by abiotic stresses (NaCl, high temperature, methyl viologen, abscisic acid and cadmium).

Keywords: abiotic stress; kinases; Oryza sativa; phylogenetic analysis
Subjects: ABC1 proteins; gene expression; kinases; phylogenetic tree; chromosomes - gene localization; amino acid sequence; NaCl stress; temperature - high; abscisic acid; cadmium
Species: Oryza sativa

Received: May 3, 2011; Accepted: September 4, 2011; Published: December 1, 2012Show citation

ACS AIP APA ASA Harvard Chicago IEEE ISO690 MLA NLM Turabian Vancouver
Yang, S.G., Li, T., Liu, M., Gao, S.J., Yang, S.Y., Li, L., & Yang, C.W. (2012). Phylogenetic, structure and expression analysis of ABC1Ps gene family in rice. Biologia plantarum, 56(4), 667-674. doi: 10.1007/s10535-012-0247-3.
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)

    • Open full article

    References

    1. Bailey, T.L., Williams, N., Misleh, C., Li, W.W.: MEME: discovering and analyzing DNA and protein sequence motifs. - Nucl. Acids Res. 34: W369-W373, 2006. Go to original source...
    2. Bairoch, A.: PROSITE: a dictionary of sites and patterns in proteins. - Nucl. Acids Res. 20: 2013-2018, 1992.
    3. Bonnefoy, N., Kermorgant, M., Brivet, C.P., Dujardin, G.: Cloning by functional complementation, and inactivation, of the Schizosaccharomyces pombe homologue of the Saccharomyces cerevisiae gene ABC1. - Mol. gen. Genet. 251: 204-210, 1996.
    4. Bousquet, I., Dujardin, G., Slonimski, P.P.: ABC1, a novel yeast nuclear gene has a dual function in mitochondria: it suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex. - EMBO J. 10: 2023-2031, 1991. Go to original source...
    5. Brasseur, G., Tron, G., Dujardin, G., Slonimski, P.P., Brivet-Chevillotte, P.: The nuclear ABC1 gene is essential for the correct conformation and functioning of the cytochrome bc1 complex and the neighbouring complexes II and IV in the mitochondrial respiratory chain. - Eur. J. Biochem. 246: 103-111, 1997. Go to original source...
    6. Cardazzo, B., Hamel, P., Sakamoto, W., Wintz, H., Dujardin, G.: Isolation of an Arabidopsis thaliana cDNA by complementation of a yeast abc1 deletion mutant deficient in complex III respiratory activity. - Gene 221: 117-125, 1998. Go to original source...
    7. Gao, Q.S., Yong, Z.F., Zhou, Y., Zhang, D., Yan, C.H., Liang, G.H., Xu, C.W.: Cloning of an ABC1-like gene ZmABC1-10 and its responses to cadmium and other abiotic stresses in maize (Zea mays L.). - Acta agron. sin. 36: 2073-2083, 2010. Go to original source...
    8. Haas, B.J., Wortman, J.R., Ronning, C.M., Hannick, L.I., Smith, R.K., Jr., Maiti, R., Chan, A.P., Yu, C., Farzad, M., Wu, D., White, O., Town, C.D.: Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. - BMC Biol. 3: 1-7, 2005. Go to original source...
    9. Hirochika, H.: Contribution of the Tos17 retrotransposon to rice functional genomics. - Curr. Opin. Plant Biol. 4: 118-122, 2001. Go to original source...
    10. Horton, P., Park, K.J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C.J., Nakai, K.: WoLF PSORT: protein localization predictor. - Nucl. Acids Res. 35: 585-587, 2007. Go to original source...
    11. Hsieh, E.J., Dinoso, J.B., Clarke, C.F.: A tRNA(TRP) gene mediates the suppression of cbs2-223 previously attributed to ABC1/COQ8. - Biochem. biophys. Res. Commun. 317: 648-653, 2004. Go to original source...
    12. Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B.A., De Castro, E., Lachaize, C., Langendijk-Genevaux, P.S., Sigrist, C.J.: The 20 years of PROSITE. - Nucl. Acids Res. 36: 245-249, 2008.
    13. IRGSP: The map-based sequence of the rice genome. - Nature 436: 793-800, 2005.
    14. Jasinski, M., Sudre, D., Schansker, G., Schellenberg, M., Constant, S., Martinoia, E., Bovet, L. AtOSA1, a member of the Abc1-like family, as a new factor in cadmium and oxidative stress response. - Plant Physiol. 147: 719-731, 2008. Go to original source...
    15. Kikuchi, S., Satoh, K., Nagata, T., Kawagashira, N., Doi, K., Kishimoto, N., Yazaki, J., Ishikawa, M., Yamada, H., Ooka, H.: Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. - Science 301: 376-379, 2003. Go to original source...
    16. Kumar, S., Tamura, K., Nei, M.: MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. - Brief Bioinform. 5: 150-163, 2004. Go to original source...
    17. Leonard, C.J., Aravind, L., Koonin, E.V.: Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily. - Genome Res. 8: 1038-1047, 1998. Go to original source...
    18. Marchler-Bauer, A., Panchenko, A.R., Shoemaker, B.A., Thiessen, P.A., Geer, L.Y., Bryant, S.H.: CDD: a database of conserved domain alignments with links to domain threedimensional structure. - Nucl. Acids Res. 30: 281-283, 2002. Go to original source...
    19. Gao, Q.S., Yong, Z.F., Zhou, Y., Zhang, D., Yan, C.H., Liang, G.H., Xu, C.W.: Cloning of an ABC1-like gene ZmABC1-10 and its responses to cadmium and other abiotic stresses in maize (Zea mays L.). - Acta agron. sin. 36: 2073-2083, 2010. Go to original source...
    20. Sanchez-Fernandez, R., Davies, T.G., Coleman, J.O., Rea, P.A.: The Arabidopsis thaliana ABC protein superfamily, a complete inventory. - J. biol. Chem. 276: 30231-30244, 2001. Go to original source...
    21. Sigrist, C.J., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., Bairoch, A., Bucher, P.: PROSITE: a documented database using patterns and profiles as motif descriptors. - Brief Bioinform. 3: 265-274, 2002. Go to original source...
    22. Terol, J., Domingo, C., Talon, M.: The GH3 family in plants: genome wide analysis in rice and evolutionary history based on EST analysis. - Gene 371: 279-290, 2006. Go to original source...
    23. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G.: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. - Nucl. Acids Res. 25: 4876-4882, 1997. Go to original source...
    24. Wang, C.X., Jing, R.L., Mao, X.G., Chang, X.P., Li, A.: TaABC1, a member of the activity of bc1 complex protein kinase family from common wheat, confers enhanced tolerance to abiotic stresses in Arabidopsis. - J. exp. Bot. 62: 1299-1311, 2011. Go to original source...
    25. Yuan, Q., Ouyang, S., Liu, J., Suh, B., Cheung, F., Sultana, R., Lee, D., Quackenbush, J., Buell, C.R.: The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. - Nucl. Acids Res. 31: 229-233, 2003. Go to original source...
    26. Yuen, C.Y.L., Leelapon, O., Chanvivattana, Y., Warakanot, J., Narangajavana, J.: Molecular characterization of two genes encoding plastidic ATP/ADP transport proteins in cassava. - Biol. Plant. 53: 37-44, 2009. Go to original source...
    27. Zhou, L., Zhou, Y.T., Wang, M.L., Wang, H.Y. Zhao, Y.: Expressions and dimerization affinities of three highly identical APETALA3 gene in Brassica napus. - Biol. Plant. 54: 33-40, 2010. Go to original source...

    Return to the content