Systematic Identification of Rice ABC1 Genes and Their Expression Analysis under Abiotic Stresses
GAO Qing-song;ZHANG Dan; XU Liang; XU Chen-wu*
Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; *Corresponding author, E-mail: email@example.com
摘要ABC1（Activity of bc1 complex）家族属于蛋白质激酶家族，其成员普遍存在于原核和真核生物中。已有研究表明，几个植物ABC1基因参与非生物胁迫应答。为了解ABC1基因在水稻中的结构和功能，采用生物信息学方法分别在水稻和拟南芥上鉴定出15个和17个ABC1基因，并进行了系统发育和表达分析。结果表明，该家族在单、双子叶植物分离之前就已经发生了分化，其基本特征已经形成；单、双子叶植物分离之后，该家族在水稻和拟南芥中均以物种特异的方式进行了扩增。内含子/外显子结构分析显示多数直系同源基因之间外显子大小接近，而内含子差别较大，水稻含有更多大的内含子；内含子获得是近期伴随水稻ABC1家族进化的重要事件。多序列比对显示，ABC1结构域具有1个保守的氨基酸片段和4个保守的氨基酸残基。在线亚细胞定位预测9个水稻ABC1蛋白定位在叶绿体上。实时定量RT-PCR分析表明，水稻ABC1基因主要在叶片中表达，并且受多种非生物胁迫因素包括H2O2、脱落酸、低温、干旱、黑暗和高盐的调控。说明水稻ABC1家族不仅在逆境胁迫应答中发挥重要作用，可能还与水稻特定的生理过程有关。
ABC1 (Activity of bc1 complex) family belongs to protein kinase families, whose members widely exist in prokaryotes and eukaryotes. It has been reported that several plant ABC1 genes participate in abiotic stress response. To understand the structure and function of ABC1 genes in rice, the systematic characterization of rice and Arabidopsis ABC1 genes and the expression analysis of rice ABC1 genes were performed. A total of 15 and 17 members of rice and Arabidopsis ABC1 families were identified by the bioinformatics method. The phylogenetic analysis of these proteins suggested that divergence of this family had occurred and the main characteristics had established before the dicotmonocot split; speciesspecific expansion contributed to the evolution of this family in rice and Arabidopsis after the split of monocots and dicots. Intron/exon stucture analysis indicated that most of the orthologous genes had similar exon sizes but diverse intron sizes and the rice genes contained more large introns; intron gain was an important event accompanying the recent evolution of rice ABC1 family. Multiple sequence alignment revealed one conserved amino acid segment and four conserved amino acids of the ABC1 domain. Online subcellular localization predicted that nine rice ABC1 proteins were localized in the chloroplast. Realtime RTPCR assay established that rice ABC1 genes expressed primarily in leaves and could be modulated by a broad range of abiotic factors such as H2O2, abscisic acid, low temperature, drought, darkness and high salinity. These results illustrate that rice ABC1 family played roles not only in the environmental stress response but also likely in the specific biological process of rice.
GAO Qing-song,ZHANG Dan,XU Liang et al. Systematic Identification of Rice ABC1 Genes and Their Expression Analysis under Abiotic Stresses [J]. , 2011, 25(1): 1-10 .
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, 1991, 10(8): 2023-2031.
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, 1998, 8(10): 1038-1047.
Macinga D R, Cook G M, Poole R K, et al. Identification and characterization of aarF, a locus required for production of ubiquinone in Providencia stuartii and Escherichia coli and for expression of 2′-N-acetyltransferase in P. stuartii. J Bacteriol, 1998, 180(1): 128-135.
Do T Q, Hsu A Y, Jonassen T, et al. A defect in coenzyme Q biosynthesis is responsible for the respiratory deficiency in Saccharomyces cerevisiae ABC1 mutants. J Biol Chem, 2001, 276(21): 18161-18168.
Hsieh E J, Dinoso J B, Clarke C F. A tRNATRP gene mediates the suppression of cbs2-223 previously attributed to ABC1/COQ8. Biochem Biophys Res Commun, 2004, 317(2): 648-653.
Mollet J, Delahodde A, Serre V, et al. CABC1 gene mutations cause ubiquinone deficiency with cerebellar ataxia and seizures. Am J Hum Genet, 2008, 82(3): 623-630.
Tauche A, Krause-Buchholz U, Rodel G. Ubiquinone biosynthesis in Saccharomyces cerevisiae: The molecular organization of O-methylase Coq3p depends on Abc1p/Coq8p. FEMS Yeast Res, 2008, 8(8): 1263-1275.
Trumpower B L. New concepts on the role of ubiquinone in the mitochondrial respiratory chain. J Bioenerg Biomembr, 1981, 13(1/2): 1-24.
Ernster L, Forsmark-Andree P. Ubiquinol: An endogenous antioxidant in aerobic organisms. Clin Investig, 1993, 71(8 Suppl): S60-S65.
Villalba J M, Navas P. Plasma membrane redox system in the control of stress-induced apoptosis. Antioxid Redox Signal, 2000, 2(2): 213-230.
Jasinski M, Sudre D, Schansker G, et al. AtOSA1, a member of the Abc1-like family, as a new factor in cadmium and oxidative stress response. Plant Physiol, 2008, 147(2): 719-731.
International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature, 2005, 436(7052): 793-800.
Goff S A, Ricke D, Lan T H, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 2002, 296(5565): 92-100.
Yu J, Hu S, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 2002, 296(5565): 79-92.
Kaul S, Koo H L, Jenkins J, et al. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 2000, 408(6814): 796-815.
Haas B J, Wortman J R, Ronning C M, et al. Complete reannotation of the Arabidopsis genome: Methods, tools, protocols and the final release. BMC Biol, 2005, 3: 7.
Yu J, Wang J, Lin W, et al. The Genomes of Oryza sativa: A history of duplications. PLoS Biol, 2005, 3(2): e38.
Kong H, Landherr L L, Frohlich M W, et al. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: Evidence for multiple mechanisms of rapid gene birth. Plant J, 2007, 50(5): 873-885.
Vandepoele K, Simillion C, van de Peer Y. Evidence that rice and other cereals are ancient aneuploids. Plant Cell, 2003, 15(9): 2192-2202.
Wang X, Shi X, Hao B, et al. Duplication and DNA segmental loss in the rice genome: Implications for diploidization. New Phytol, 2005, 165(3): 937-946.
He X, Zhang J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics, 2005, 169(2): 1157-1164.
Fang Y, Xie K, Hou X, et al. Systematic analysis of GT factor family of rice reveals a novel subfamily involved in stress responses. Mol Genet Genom, 2010, 283(2): 157-169.
Ye H, Du H, Tang N, et al. Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol Biol, 2009, 71(3): 291-305.
Ding X, Hou X, Xie K, et al. Genome-wide identification of BURP domain-containing genes in rice reveals a gene family with diverse structures and responses to abiotic stresses. Planta, 2009, 230(1): 149-163.
Liu J, Liang D, Song Y, et al. Systematic identification and expression analysis of BREVIS RADIX-like homologous genes in rice. Plant Sci, 2009, 178(2): 183-191.