黄瓜全基因组SnRK2基因的鉴定和序列特征分析
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摘要
植物SnRK2基因在逆境应答和ABA信号转导及生长发育过程中具有重要功能。但是有关黄瓜(cucumis satovus L.)SnRK2全基因组水平的研究鲜见报道。本文利用生物信息学的方法从黄瓜基因组中鉴定出9个SnRK2基因,并对这些基因的染色体分布、内含子-外显子结构、系统进化、顺式调控元件等进行了系统分析。结果显示,黄瓜的SnRK2基因不均匀地的分布在基因组中,它们的外显子多数为9,编码区序列长度在909-1140bp之间。它们在遗传上分为3个不同的类群,预测编码的蛋白都具有激酶的典型结构。而且,在SnRK2基因上游调控序列中都含有多个不同激素和逆境应答顺式元件,预示它们在逆境应答和激素信号转导过程中具有一定功能。本文为进一步研究黄瓜SnRK2基因在逆境和激素应答中的功能奠定了基础。
Plant SnRK2 genes play important roles in environmental stress response,ABA signal transduction,plant growth and development. However,there is no investigation reported about cucumber( cucumis satovus L.) SnRK2s in whole genome level. In this text,9 SnRK2 genes in cucumber genome were identified through bioinformatic method. Their genome distribution,exon-intron structure,phylogeny,and cis-elements were systematically analyzed. The results showed that,cucumber SnRK2 genes are unevenly distributed in genome; their exon number mostly is nine,and their putative coding sequences range from 909bp to 1140bp; they are divided into 3 groups according to phylogeny analysis; and their putative encoding proteins all have typical kinase structure. What's more,there are multiple cis-elements responsive to different environmental stresses and hormones existed in upstream sequences of each of SnRK2 genes in cucumber,which suggests they may have some roles in stress response and hormone signaling. This study laid a foundation for further functional dissection of cucumber SnRK2 genes in stress and hormone response.
Plant SnRK2 genes play important roles in environmental stress response,ABA signal transduction,plant growth and development. However,there is no investigation reported about cucumber( cucumis satovus L.) SnRK2s in whole genome level. In this text,9 SnRK2 genes in cucumber genome were identified through bioinformatic method. Their genome distribution,exon-intron structure,phylogeny,and cis-elements were systematically analyzed. The results showed that,cucumber SnRK2 genes are unevenly distributed in genome; their exon number mostly is nine,and their putative coding sequences range from 909bp to 1140bp; they are divided into 3 groups according to phylogeny analysis; and their putative encoding proteins all have typical kinase structure. What's more,there are multiple cis-elements responsive to different environmental stresses and hormones existed in upstream sequences of each of SnRK2 genes in cucumber,which suggests they may have some roles in stress response and hormone signaling. This study laid a foundation for further functional dissection of cucumber SnRK2 genes in stress and hormone response.
引文
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[27]Zhang H,Mao X,Jing R,Chang X,Xie H.Characterization of a common wheat(Triticum aestivum L.)TaSnRK2.7 gene involved in abiotic stress responses[J].Journal of Experimental Botany,2011,62(3):975-988
[28]Huai J,Wang M,He J,Zheng J,Dong Z,Lv H,Zhao J,Wang G.Cloning and characterization of the SnRK2 gene family from Zea mays[J].Plant Cell Report,2008,27:1861-1868
[29]Ying S,Zhang D F,Li H Y,Liu Y H,Shi Y S,Song Y C,Wang TY,Li Y.Cloning and characterization of a maize SnRK2 protein kinase gene confers enhanced salt tolerance in transgenic Arabidopsis[J].Plant Cell Report,2011,30(9):1683-1699
[30]LI Li-bin,ZHANG Yi-rong,LIU Kai-chang,NI Zhong-fu,FANG Zhi-jun,SUN Qi-xin,GAO Jianwei.Identification and Bioinformatics Analysis of SnRK2 and CIPK Family Genes in sorghum[J].Agricultural Sciences in China,2010,9(1):19-30
[31]Sun L,Wang Y P,Chen P,Ren J,Ji K,Li Q,Li P,Dai S J,Leng P.Transcriptional regulation of SlPYL,SlPP2C,and SlSnRK2gene families encoding ABA signal core components during tomato fruit development and drought stress[J].Journal of Experimental Botany.2011,62(15):5659-5669
[32]李斌,郭世荣,孙锦,陆晓民,李娟.外源Spd对盐胁迫下黄瓜SAMs基因表达的影响及SAMs蛋白的生物信息学分析[J].园艺学报,2011,38(12):2289-2296
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[36]宁宇,苗永美,李季,娄群峰,翁益群,陈劲枫.黄瓜转录因子CsCBF3的克隆及表达分析[J].中国蔬菜,2013(6):30-36
[37]冯卓,秦智伟,武涛,何红梅.黄瓜细胞质型谷氨酰胺合成酶基因(GS1)的克隆及其在低氮条件下的表达[J].中国农业科学,2012,45(15):3100-3107
[38]甘德芳,丁飞,庄丹,梁丹迪.黄瓜全基因组转录因子MADSbox家族基因的序列特征分析[J].核农学报,2012,26(9):1249-1256
[39]Wang Y,Wu Y,Duan C,Chen P,Li Q,Dai S,Sun L,Ji K,Sun Y,Xu W,Wang C,Luo H,Wang Y,Leng P.The expression profiling of the CsPYL,CsPP2C and CsSnRK2 gene families during fruit development and drought stress in cucumber[J].Journal of Plant Physiology,2012,169(18):1874-1882
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[2]Hirayama T,Umezawa T.The PP2C-SnRK2 complex.The central regulator of an abscisic acid signaling pathway[J].Plant Signaling&Behavior,2010,5(2):160-163
[3]Soon F F,Ng L M,Zhou X E,West G M,Kovach A,Tan M H,Suino-Powell KM,He Y,Xu Y,Chalmers MJ,Brunzelle JS,Zhang H,Yang H,Jiang H,Li J,Yong EL,Cutler S,Zhu JK,Griffin PR,Melcher K,Xu HE.Molecular Mimicry Regulates ABA Signaling by SnRK2 Kinases and PP2C Phosphatases[J].Science,2012,335(6064):85-88
[4]Boudsocq M,Barbier-Brygoo H,Laurière C.Identification of Nine Sucrose Nonfermenting 1-related Protein Kinases 2 Activated by Hyperosmotic and Saline Stresses in Arabidopsis thaliana[J].Journal of Biological Chemistry,2004,279:41758-41766
[5]Kobayashi Y,Yamamoto S,Minami H,Kagaya Y,Hattori T.Differential activation of rice sucrose nonfermenting 1-related protein kinase2 family by hyperosmotic stress and abscisic acid[J].Plant Cell,2004,16:163-117
[6]Kulik A,Wawer I,Krzywińska E,Bucholc M,Dobrowolska G.SnRK2 protein kinases-Key regulators of plant response to abiotic stresses[J].Omics:a journal of integrative biology,2011,15(12):859-872
[7]Fujii H,Verslues P E,Zhu J K.Arabidopsis decuple mutant reveals the importance of SnRK2 kinases in osmotic stress responses in vivo[J].Proceedings of the National Academy of Sciences,2011,108(4):717-722.
[8]Mustilli A C,Merlot S,Vavasseur A,Fenzi F,Giraudat J.Arabidopsis OST1 protein kinase mediates the regulation of stomatal aperture by abscisic acid and acts upstream of reactive oxygen species production[J].Plant Cell,2002,14(12):3089-3099
[9]Yoshida R,Umezawa T,Mizoguchi T,Takahashi S,Takahashi F,Shinozaki K.The regulatory domain of SRK2E/OST1/SnRK2.6interacts with ABI1 and integrates abscisic acid(ABA)and osmotic stress signals controlling stomatal closure in Arabidopsis[J].Journal of Biological Chemistry,2006,281:5310-5318
[10]Kimura T,Shibagaki N,Ohkama-Ohtsu N,Hayashi H,Yoneyama T,Davies JP,Fujiwara T.Arabidopsis SNRK2.3 protein kinase is involved in the regulation of sulfur-responsive gene expression and Oacetyl-l-serine accumulation under limited sulfur supply[J].Soil Science&Plant Nutrition,2006,52(2):211-220
[11]Fujii H,Verslues P.E,and Zhu JK.Identification of Two Protein Kinases Required for Abscisic Acid Regulation of Seed Germination,Root Growth,and Gene Expression in Arabidopsis[J].The Plant Cell,2007,19:485-494
[12]Zheng Z,Xu X,Crosley R A,Greenwalt S A,Sun Y,Blakeslee B,Wang L,Ni W,Sopko M S,Yao C,Yau K,Burton S,Zhuang M,McCaskill D G,Gachotte D,Thompson M,Greene T W.The protein kinase SnRK2.6 mediates the regulation of sucrose metabolism and plant growth in Arabidopsis[J].Plant Physiology,2010,153(1):99-113
[13]Kulik A,Anielska-Mazur A,Bucholc M,Koen E,Szymańska K,Zmieńko A,Krzywinska E,Wawer I,Mcloughlin F,Ruszkowski D,Figlerowicz M,Testerink C,Sklodowska A,Wendehenne D,Dobrowolska G.SNF1-related protein kinases type 2 are involved in plant responses to cadmium stresses[J].Plant Physiology,2012:160(2),868-883
[14]Munnik T,Haring M A,Testerink C.The Snf1-related protein kinases SnRK2.4 and SnRK2.10 are involved in maintenance of rootsystem architecture during salt stress[J].Plant Journal.2012,2(3):436-449
[15]Imes D,Mumm P,Bhm J,Al-Rasheid KA,Marten I,Geiger D,Hedrich R.Open stomata 1(OST1)kinase controls R-type anion channel QUAC1 in Arabidopsis guard cells[J].Plant Journal,2013,74(3):372-382
[16]Geiger D,Scherzer S,Mumm P,Stange A,Marten I,Bauer H,&Hedrich R.(2009).Activity of guard cell anion channel SLAC1 is controlled by drought-stress signaling kinase-phosphatase pair[J].Proceedings of the National Academy of Sciences,106(50),21425-21430.
[17]Melotto M,Underwood W,Koczan J,Nomura K,He S Y.Plant Stomata Function in Innate Immunity against Bacterial Invasion[J].Cell,2006,126(5):969-980
[18]Xu M R,Huang L Y,Zhang F,Zhu L H,Zhou Y L,Li Z K.Genome-Wide Phylogenetic Analysis of Stress-Activated Protein Kinase Genes in Rice(OsSAPKs)and Expression Profiling in Response to Xanthomonas oryzae pv.oryzicola Infection[J].Plant Molecular Biology Reporter,2013:1-9
[19]Umezawa T,Yoshida R,Maruyama M,Yamaguchi-Shinozaki K,Shinozaki K.SRK2C,a SNF1-related protein kinase 2,improves drought tolerance by controlling stress-responsive gene expression in Arabidopsis thaliana[J].Proceedings of the National Academy of Sciences,2004,101(49):17306-17311
[20]Shin R,Alvarez S,Burch A Y,Jez J M,Schachtman D P.Phosphoproteomic identification of targets of the Arabidopsis sucrose nonfermenting-like kinase SnRK2.8 reveals a connection to metabolic processe[J].Proceedings of the National Academy of Sciences,2007,104(15):6460-6465
[21]Mizoguchi M,Umezawa T,Nakashima K,Kidokoro S,Takasaki H,Fujita Y,Yamaguchi-Shinozaki K,Shinozaki K.Two closely related subclass II SnRK2 protein kinases cooperatively regulate droughtinducible gene expression[J].Plant Cell Physiology.2010,51(5):842-7
[22]Hétu M F.Effect of nutritional status on phenotypic characteristics of Arabidopsis and alfalfa in relation to the expression of AtSnRK2.9[D].Canada:Queen’s University,2007,http://hdl.handle.net/1974/746
[23]Vlad F,Turk B,Peynot P,Leung J,Merlot S.A versatile strategy to define the phosphorylation preferences of plant protein kinases and screen for putative substrates[J].Plant Journal,2008,55(1):104-117
[24]Boudsocq M,Droillard M J,Barbier-Brygoo H,Laurière C.Different phosphorylation mechanisms are involved in the activation of sucrose non-fermenting 1 related protein kinases 2 by osmotic stresses and abscisic acid[J].Plant Molecular Biology,2007,63(4):491-503
[25]Vlad F,Droillard MJ,Valot B,Khafif M,Rodrigues A,Brault M,Zivy M,Rodriguez PL,Merlot S,Laurière C.Phospho-site mapping,genetic and in planta activation studies reveal key aspects of the different phosphorylation mechanisms involved in activation of SnRK2s[J].Plant Journal,2010,63(5):778-790
[26]Mao X,Zhang H,Tian S,Chang X,Jing R.TaSnRK2.4,an SNF1-type serine/threonine protein kinase of wheat(Triticum aestivum L.),confers enhanced multistress tolerance in Arabidopsis[J].Journal of Experimental Botany,2010,61(3):683-696
[27]Zhang H,Mao X,Jing R,Chang X,Xie H.Characterization of a common wheat(Triticum aestivum L.)TaSnRK2.7 gene involved in abiotic stress responses[J].Journal of Experimental Botany,2011,62(3):975-988
[28]Huai J,Wang M,He J,Zheng J,Dong Z,Lv H,Zhao J,Wang G.Cloning and characterization of the SnRK2 gene family from Zea mays[J].Plant Cell Report,2008,27:1861-1868
[29]Ying S,Zhang D F,Li H Y,Liu Y H,Shi Y S,Song Y C,Wang TY,Li Y.Cloning and characterization of a maize SnRK2 protein kinase gene confers enhanced salt tolerance in transgenic Arabidopsis[J].Plant Cell Report,2011,30(9):1683-1699
[30]LI Li-bin,ZHANG Yi-rong,LIU Kai-chang,NI Zhong-fu,FANG Zhi-jun,SUN Qi-xin,GAO Jianwei.Identification and Bioinformatics Analysis of SnRK2 and CIPK Family Genes in sorghum[J].Agricultural Sciences in China,2010,9(1):19-30
[31]Sun L,Wang Y P,Chen P,Ren J,Ji K,Li Q,Li P,Dai S J,Leng P.Transcriptional regulation of SlPYL,SlPP2C,and SlSnRK2gene families encoding ABA signal core components during tomato fruit development and drought stress[J].Journal of Experimental Botany.2011,62(15):5659-5669
[32]李斌,郭世荣,孙锦,陆晓民,李娟.外源Spd对盐胁迫下黄瓜SAMs基因表达的影响及SAMs蛋白的生物信息学分析[J].园艺学报,2011,38(12):2289-2296
[33]王磊,刘兴旺,金宝燕,陈明远,张雷,任华中.水杨酸提高黄瓜低温耐受性的生理及CATmRNA基因响应机制[J].华北农学报,2010,25(3):92-96
[34]秦爱国,于贤昌.低温胁迫下嫁接对黄瓜叶片SOD和CAT基因表达与活性变化的影响[J].应用生态学报,2009,20(1):213-217
[35]齐晓花,许学文,罗晶晶,高海洁,徐强,林肖剑,朱碧云,陈学好.黄瓜3-磷酸甘油醛脱氢酶基因CsGAPDH的克隆及其涝胁迫响应分析[J].园艺学报2011,38(9):1693-1698
[36]宁宇,苗永美,李季,娄群峰,翁益群,陈劲枫.黄瓜转录因子CsCBF3的克隆及表达分析[J].中国蔬菜,2013(6):30-36
[37]冯卓,秦智伟,武涛,何红梅.黄瓜细胞质型谷氨酰胺合成酶基因(GS1)的克隆及其在低氮条件下的表达[J].中国农业科学,2012,45(15):3100-3107
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