番茄GRAS转录因子家族的生物信息学分析
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摘要
笔者旨在进一步了解番茄GRAS基因家族的结构特征和进化信息,为GRAS转录因子的后续研究提供理论基础。利用HMMER 3.0软件,通过从Pfam蛋白数据库中下载的GRAS保守域(PF03514),来鉴定番茄GRAS基因。采用MEGA5.2、Web Logo 3、DNAMAN 5.0、Map Inspect和MEME等软件对其蛋白序列进行生物信息学分析。采用RT-PCR技术检测番茄GRAS基因在番茄根、茎、叶、花和果实中的表达情况。番茄基因组共挖掘出53条GRAS转录子基因,划分为I、II、III、IV、V、VI、VII、VIII 8个亚族。系统进化树结果显示V和VI组中GRAS家族成员最多,且拟南芥的GRAS基因家族中基因功能类似的基因聚类的在一起,则可能同组内番茄GRAS基因家族成员也具有类似功能;染色体定位分析显示GRAS基因在12条染色体中呈不均匀分布;根据Web Logo 3.0对GRAS基因家族的结构域蛋白分析,结果显示GRAS基因家族的蛋白序列并不都是高度保守的;保守元件分析表明番茄GRAS基因家族成员是部分高度保守的。番茄GRAS基因家族大部分成员结构是高度保守,可能参与调控番茄生长和发育等过程。
The paper aims to know the structural feature and evolutional information of GRAS gene family in tomato, and provide theoretical basis for further study on GRAS transcription factors. GRAS DNA- bindingdomain(PF03514) was downloaded from Pfam protein database, and was employed to identify GRAS genesfrom tomato genome using HMMER 3.0. The obtained amino acid sequences were analyzed with thebioinformatics software, including MEGA 5.2, Weblogo 3, DNAMAN 5.0, Map Inspect and MEME. RT-PCRwas used to detect GRAS genes expression in the tissue of roots, stems, leaves, flowers and fruit in tomato. Alltogether 53 tomato GRAS transcription factors were identified and classified into 8 groups, including I, II, III,IV, V, VI, VII, VIII. The phylogenetic tree of GRAS genes among tomato and Arabidopsis demonstrated thatthe group V and VI encompassed the largest number of GRAS genes, genes with similar function inArabidopsis thaliana clustered together, so the tomato GRAS genes had similar function within the same group.Chromosome mapping analysis showed that tomato GRAS genes were distributed with different densities on 12 chromosomes. According to the result of the GRAS domain sequence analysis with Web Logo3.0, not all GRASgenes were highly conserved in tomato. Conserved motifs analysis indicated that the part of GRAS genes familywas highly conserved. These results suggested that the most of GRAS genes were highly and structurally conserved, and might be involved in the regulation of growth and development processes in tomato.
The paper aims to know the structural feature and evolutional information of GRAS gene family in tomato, and provide theoretical basis for further study on GRAS transcription factors. GRAS DNA- bindingdomain(PF03514) was downloaded from Pfam protein database, and was employed to identify GRAS genesfrom tomato genome using HMMER 3.0. The obtained amino acid sequences were analyzed with thebioinformatics software, including MEGA 5.2, Weblogo 3, DNAMAN 5.0, Map Inspect and MEME. RT-PCRwas used to detect GRAS genes expression in the tissue of roots, stems, leaves, flowers and fruit in tomato. Alltogether 53 tomato GRAS transcription factors were identified and classified into 8 groups, including I, II, III,IV, V, VI, VII, VIII. The phylogenetic tree of GRAS genes among tomato and Arabidopsis demonstrated thatthe group V and VI encompassed the largest number of GRAS genes, genes with similar function inArabidopsis thaliana clustered together, so the tomato GRAS genes had similar function within the same group.Chromosome mapping analysis showed that tomato GRAS genes were distributed with different densities on 12 chromosomes. According to the result of the GRAS domain sequence analysis with Web Logo3.0, not all GRASgenes were highly conserved in tomato. Conserved motifs analysis indicated that the part of GRAS genes familywas highly conserved. These results suggested that the most of GRAS genes were highly and structurally conserved, and might be involved in the regulation of growth and development processes in tomato.
引文
[1]刘强,张贵友,陈受宜.植物转录因子的结构与调控作用[J].科学通报,2000,45(14):1465-1474.
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[11]高潜,刘玉瑛,费一楠,等.拟南芥根的辐射形态相关基因SHORTROOT研究进展[J].植物学通报,2008,25(3):363-372.
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[15]Torres-Galea P,Huang L F,Chua N H,et al.The GRAS pro-tein SCL13 is a positive regulator of phytochrome-dependent red light signaling,but can also modulate phytochrome A responses.Mol Genet Genomics,2006,276(1):13-30.
[16]石瑞,曹诣斌,陈文荣,等.佛手GRAS基因的克隆及表达分析[J].浙江师范大学学报,2011(4):446-451.
[17]郭华军,焦远年,邸超,等.拟南芥转录因子GRAS家族基因群响应渗透和干旱胁迫的初步探索[J].植物学报,2009,44(3):290-299.
[18]朱芸晔,薛冰,王安全,等.番茄b ZIP转录因子家族的生物信息学分析[J].应用与环境学报,2014,2(15):767-774
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[20]董庆龙,王海荣,安淼,等.苹果NADP依赖的苹果酸酶基因克隆、序列和表达分析[J].中国农业科学,2013,46(9):1857-1866.
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[22]董庆龙,冀志蕊,迟福梅,等.苹果MADS-box转录因子的生物信息学及其在不同组织中的表达[J].中国农业科学,2014 47(6):1151-1161.
[23]Hu L,Liu S.Genome-wide analysis of the MADS-box gene family in cucumber[J].Genome,2012,55(3):245-256.
[24]Velasco R,Zharkikh A,Affourtit J,et al.The genome of the domesticated apple(Malus×domestica Borkh.)[J].Nature Genetics,2010,42(10):833-839.
[25]Tian Y,Dong Q,Ji Z,et al.Genome-wide identification and analysis of the MADS-box gene family in apple[J].Gene,2015,555(2):277-290.
[26]刘翠芳,邹杰,陈信波.DREB转录因子与植物非生物胁迫抗性研究进展[J].生物技术通报,2010(10):26-30.
[27]庄静,彭日荷,高峰,等.沪油15中两个AP2/ERF-B1亚族转录因子的克降与分析[J].核农学报,2009,23(3):435-441.
[28]张珍珠,陈秀玲,王沛文,等.番茄b ZIP基因家族的系统进化分析[J].东北农业大学学报,2014,45(9):47-55.
[29]畅文军,刘习文,张治礼,等.植物GRAS蛋白结构和功能研究进展[J].生命科学,2013,(11):1004-0374.
[2]Peng J,Carol P,Richards D E,et al.The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses[J].Genes Development,1997,11(23):3194-3205.
[3]Silverstone A L,Ciampaglio C N,Sun T.The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway[J].Plant Cell,1998,10(2):155-169.
[4]Di Laurenzio L,Wysocka-Diller J,Malamy J E,et al.The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root[J].Cell,1996,86(3):423-433.
[5]Heery D M,Kalkhoven E.A signature motif in transcriptional coactivators mediates binding to nuclear receptor[J].Nature,1997,387(6634):733-736.
[6]Pyshl D,Wysocka-Diller J W,Camilleri C,et al.The GRAS gene family in Arabidopsis:sequence characterization and basic expression analysis of the SCARECROW-LIKE genes[J].The Plant Journal,1999,18(1):111-119.
[7]Bolle C.The role of GRAS proteins in plant signal transduction and development[J].Planta,2004,218(5):683-692.
[8]Sun X,Xue B,Jones W T,et al.A functionally required unfoldome from the plant kingdom:intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development[J].Plant Molecular Biology,2011,77:205-223.
[9]Tian C,Wan P,Sun S,et al.Genome-wide analysis of the GRAS gene family in rice and Arabidopsis[J].Plant Molecular Biology,2004,54(4):519-532.
[10]周莲洁,张富春,王艳.GRAS家族基因在植物生长、代谢及逆境胁迫中的功能研究进展[J].植物生理学报,2013(9):855-860.
[11]高潜,刘玉瑛,费一楠,等.拟南芥根的辐射形态相关基因SHORTROOT研究进展[J].植物学通报,2008,25(3):363-372.
[12]Smit P,Raedts J,Portyanko V,et al.NSP1 of the GRAS protein family is essential for rhizobial Nod factor-induced transcription[J].Science,2005,308(5729):1789-1791.
[13]Kalo P,Gleason C,Edwards A,et al.Nodulation signaling in legumes requires NSP2,a member of the GRAS family of transcriptional regulators[J].Science,2005,308(5729):1786-1789.
[14]Schumacher K,Schmitt T,Rossberg M,et al.The lateral suppressor(LS)gene of tomato encodes a new member of the VHIID protein family[J].Proceedings of the National Academy of Science of the United States of America,1999,96(1):290-295.
[15]Torres-Galea P,Huang L F,Chua N H,et al.The GRAS pro-tein SCL13 is a positive regulator of phytochrome-dependent red light signaling,but can also modulate phytochrome A responses.Mol Genet Genomics,2006,276(1):13-30.
[16]石瑞,曹诣斌,陈文荣,等.佛手GRAS基因的克隆及表达分析[J].浙江师范大学学报,2011(4):446-451.
[17]郭华军,焦远年,邸超,等.拟南芥转录因子GRAS家族基因群响应渗透和干旱胁迫的初步探索[J].植物学报,2009,44(3):290-299.
[18]朱芸晔,薛冰,王安全,等.番茄b ZIP转录因子家族的生物信息学分析[J].应用与环境学报,2014,2(15):767-774
[19]Arnaud F,Elisabeth G,Aurélien G,et al.Ex PASy:SIB bioinformatics resource portal[J].Nucleic Acids Research,2012,40(1):597-603
[20]董庆龙,王海荣,安淼,等.苹果NADP依赖的苹果酸酶基因克隆、序列和表达分析[J].中国农业科学,2013,46(9):1857-1866.
[21]Tamura K,Peterson D,Peterson N,et al.MEGA5:Molecular evolutionary genetics analysis using Maximum Likelihood,Evolutionary Distance,and Maximum Parsimony Methods.Molecular Biology and Evolution[J],2011,28(10):2731-2739.
[22]董庆龙,冀志蕊,迟福梅,等.苹果MADS-box转录因子的生物信息学及其在不同组织中的表达[J].中国农业科学,2014 47(6):1151-1161.
[23]Hu L,Liu S.Genome-wide analysis of the MADS-box gene family in cucumber[J].Genome,2012,55(3):245-256.
[24]Velasco R,Zharkikh A,Affourtit J,et al.The genome of the domesticated apple(Malus×domestica Borkh.)[J].Nature Genetics,2010,42(10):833-839.
[25]Tian Y,Dong Q,Ji Z,et al.Genome-wide identification and analysis of the MADS-box gene family in apple[J].Gene,2015,555(2):277-290.
[26]刘翠芳,邹杰,陈信波.DREB转录因子与植物非生物胁迫抗性研究进展[J].生物技术通报,2010(10):26-30.
[27]庄静,彭日荷,高峰,等.沪油15中两个AP2/ERF-B1亚族转录因子的克降与分析[J].核农学报,2009,23(3):435-441.
[28]张珍珠,陈秀玲,王沛文,等.番茄b ZIP基因家族的系统进化分析[J].东北农业大学学报,2014,45(9):47-55.
[29]畅文军,刘习文,张治礼,等.植物GRAS蛋白结构和功能研究进展[J].生命科学,2013,(11):1004-0374.