河川沙塘鳢GH基因及侧翼的克隆与生物信息学分析
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摘要
利用长片段PCR、基因组步移法及T-A克隆技术,成功克隆出河川沙塘鳢(Odontobutis potamophila)GH基因全长序列,提交至GenBank获得登录号MH717101。河川沙塘鳢GH基因全序列长5 120 bp,5′端和3′端侧翼序列长度分别为920、682 bp,经预测,上游区域含有MF3、GAGA factor、HNF-3alpha、C/EBP、R2、GATA-1等多种转录调控元件;转录单元长3 518 bp,包含4个内含子和5个外显子,4个内含子大小分别为75、333、2 070和121 bp,5个外显子长度分别为150、131、117、138和373 bp,第3内含子长达2 070 bp,其长度是翘嘴鲌(Culter alburnus)第3内含子的4倍以上;开放阅读框区(open reading frame,ORF)为594 bp,编码由197个氨基酸残基组成的蛋白质多肽。河川沙塘鳢与鲈形目、鲉形目、鲤形目、鲇形目等13种鱼类的氨基酸序列同源性比较表明,其与彼氏冰鰕虎鱼(Leucopsarion petersii)同源性最高,为83.8%,与草鱼(Ctenopharyngodon idella)同源性最低,为49.1%,在180～197氨基酸序列处,河川沙塘鳢表现出高度不保守性,与所列鱼类氨基酸排列均完全不一致。该研究结果为进一步研究河川沙塘鳢GH基因的表达、功能及其转录调控特征奠定了分子基础。
The full-length sequence of the Odontobutis potamophila GH gene was successfully cloned by using long segment PCR, genome walking method and T-A cloning technology, which was submitted to GenBank to obtain the login number MH717101. The full-length of the GH gene of Odontobutis potamophila is 5 120 bp, the length of the 5′-end and 3′-end lateral sequence is 920 bp and 682 bp. It is predicted that the upstream region contains MF3, GAGA factor, hnf-3 alpha, C/EBP, R2, GATA-1 and other transcriptional regulatory elements, respectively. The transcription unit is 3 518 bp long and contains 4 introns and 5 exons. 4 introns are 75, 333, 2 070 and 121 bp; 5 exons are 150, 131, 117, 138 and 373 bp, respectively. The third intron is 2 070 bp, the length was more than 4 times of the culter third intron. The open reading frame area(ORF) is 594 bp, encoding a protein polypeptide composed of 197 amino acid residues. Comparison of amino acid sequence homology between Odontobutis potamophila and Perciformes, Scorpaeniformes, Cypriniformes, Siluriformes with 13 fishes showed that the homology was the highest to Leucopsarion petersii, at 83.8%, and the homology to Ctenopharyngodon idella was the lowest, at 49.1%, the Odontobutis potamophila to show highly nonconservative at 180-197 amino acid sequence and the amino acid arrangement was completely different with the listed fish. The results of this study laid a molecular foundation for further study on expression, function and transcriptional regulation of GH gene in Odontobutis potamophila.
The full-length sequence of the Odontobutis potamophila GH gene was successfully cloned by using long segment PCR, genome walking method and T-A cloning technology, which was submitted to GenBank to obtain the login number MH717101. The full-length of the GH gene of Odontobutis potamophila is 5 120 bp, the length of the 5′-end and 3′-end lateral sequence is 920 bp and 682 bp. It is predicted that the upstream region contains MF3, GAGA factor, hnf-3 alpha, C/EBP, R2, GATA-1 and other transcriptional regulatory elements, respectively. The transcription unit is 3 518 bp long and contains 4 introns and 5 exons. 4 introns are 75, 333, 2 070 and 121 bp; 5 exons are 150, 131, 117, 138 and 373 bp, respectively. The third intron is 2 070 bp, the length was more than 4 times of the culter third intron. The open reading frame area(ORF) is 594 bp, encoding a protein polypeptide composed of 197 amino acid residues. Comparison of amino acid sequence homology between Odontobutis potamophila and Perciformes, Scorpaeniformes, Cypriniformes, Siluriformes with 13 fishes showed that the homology was the highest to Leucopsarion petersii, at 83.8%, and the homology to Ctenopharyngodon idella was the lowest, at 49.1%, the Odontobutis potamophila to show highly nonconservative at 180-197 amino acid sequence and the amino acid arrangement was completely different with the listed fish. The results of this study laid a molecular foundation for further study on expression, function and transcriptional regulation of GH gene in Odontobutis potamophila.
引文
[1] 孙帼英,郭学彦.太湖河川沙塘鳢的生物学研究[J].水产学报,1996,20(3):2-11.SUN G Y,GUO X Y.Studies on the biology of Odontobutis potamophila in Taihu lake[J].Journal of Fisheries of China,1996,20(3):2-11.(in Chinese with English abstract)
[2] 刘士力,贾永义,迟美丽,等.浙江3个河川沙塘鳢群体线粒体16S rRNA基因序列的研究[J].基因组学与应用生物学,2018,37(11):4742-4748.LIU S L,JIA Y Y,CHI M L,et al.Research on mitochondrial 16S rRNA genetic sequence from three populations of Odontobutis potamophila in Zhejiang Province[J].Genomics and Applied Biology,2018,37(11):4742-4748.(in Chinese with English abstract)
[3] 杨学明,张立,黄光华,等.革胡子鲶生长激素基因克隆与序列同源分析[J].西南农业学报,2008,21(2):483-486.YANG X M,ZHANG L,HUANG G H,et al.Gene cloning and sequence homology of growth hormone from Clarias lazera[J].Southwest China Journal of Agricultural Sciences,2008,21(2):483-486.(in Chinese with English abstract)
[4] M?LLER N,COPELAND K C,NAIR K S.Growth hormone effects on protein metabolism[J].Endocrinology and Metabolism Clinics of North America,2007,36(1):89-100.
[5] SAKAMOTO T,SHEPHERD B S,MADSEN S S,et al.Osmoregulatory actions of growth hormone and prolactin in an advanced teleost[J].General and Comparative Endocrinology,1997,106(1):95-101.
[6] FORSYTH I A,WALLIS M.Growth hormone and prolactinmolecular and functional evolution[J].Journal of Mammary Gland Biology and Neoplasia,2002,7(3):291-312.
[7] 王文君,陈克飞,任军,等.中外不同猪品种生长激素基因遗传多态性检测[J].农业生物技术学报,2003,11(1):103-104.WANG W J,CHEN K F,REN J,et al.Detection of the polymorphisms of growth hormone gene in Chinese and European pig breeds[J].Journal of Agricultural Biotechnology,2003,11(1):103-104.(in Chinese with English abstract)
[8] 宋成义,经荣斌.畜禽GH基因多态性与生产性能相关研究进展[J].国外畜牧科技,2000,27(2):25-27.SONG C Y,JING R B.Research on the relation between polymorphims in the stock and poultry GH gene and production rerformance[J].Animal Science Abroad,2000,27(2):25-27.(in Chinese with English abstract)
[9] 郁二蒙,叶星,白俊杰,等.唐鱼生长激素基因的克隆及序列分析[J].安徽农业科学,2008,36(23):9914-9917.YU E M,YE X,BAI J J,et al.Cloning and sequence analysis of growth hormone gene from Tanichthys albonubes[J].Journal of Anhui Agricultural Sciences,2008,36(23):9914-9917.(in Chinese with English abstract)
[10] 刘滨,臧晓南,刘顺梅,等.7种鲽形目鱼类生长激素基因cDNA序列的克隆及系统分析[J].武汉大学学报(理学版),2008,54(4):485-491.LIU B,ZANG X N,LIU S M,et al.Molecular cloning and sequence analysis of the growth hormone cDNAs from seven Pleuronectiformes fishes[J].Journal of Wuhan University(Natural Science Edition),2008,54(4):485-491.(in Chinese with English abstract)
[11] 严美姣,吴旭,李钟杰.暗纹东方鲀生长激素基因克隆与同源性分析[J].江西农业大学学报,2010,32(2):236-242.YAN M J,WU X,LI Z J.Molecular cloning and sequence analysis of Takifugu fasciatus GH gene[J].Acta Agriculturae Universitatis Jiangxiensis(Natural Sciences Edition),2010,32(2):236-242.(in Chinese with English abstract)
[12] 贡成良,曹广力,薛仁宇,等.编码鳗鲡生长激素基因的序列与结构[J].水产学报,2002,26(4):295-300.GONG C L,CAO G L,XUE R Y,et al.Sequence and structure of encoding eel growth hormone gene[J].Journal of Fisheries of China,2002,26(4):295-300.(in Chinese with English abstract)
[13] ALLENDORF F W,THORGAARD G H.Tetraploidy and the evolution of salmonid fishes[M]//Evolutionary genetics of fishes.Boston,MA:Springer US,1984:1-53.
[14] 刘士力,张爱菊,练青平,等.泥鳅和大鳞副泥鳅细胞色素P450c17-Ⅰ(CYP17-Ⅰ)基因的克隆及组织表达分析[J].浙江农业学报,2016,28(11):1853-1861.LIU S L,ZHANG A J,LIAN Q P,et al.Cloning and tissue expression analysis of the cytochrome P450c17-Ⅰ(CYP17-Ⅰ) gene from mud loach(Misgurnus anguillicaudatus) and large-scale loach(Paramisgurnus dabryanus)[J].Acta Agriculturae Zhejiangensis,2016,28(11):1853-1861.(in Chinese with English abstract)
[15] 严美姣,吴旭,李钟杰.暗纹东方鲀生长激素基因克隆与同源性分析[J].江西农业大学学报,2010,32(2):236-242.YAN M J,WU X,LI Z J.Molecular cloning and sequence analysis of Takifugu fasciatus GH gene[J].Acta Agriculturae Universitatis Jiangxiensis,2010,32(2):236-242.(in Chinese with English abstract)
[16] SAKAMOTO T,MCCORMICK S D.Prolactin and growth hormone in fish osmoregulation[J].General and Comparative Endocrinology,2006,147(1):24-30.
[17] SCIARA A A,RUBIOLO J A,SOMOZA G M,et al.Molecular cloning,expression and immunological characterization of pejerrey (Odontesthes bonariensis) growth hormone[J].Comparative Biochemistry and Physiology Part C:Toxicology & Pharmacology,2006,142(3/4):284-292.
[18] 温海深,林浩然,肖东,等.野生鲇鱼生长激素分泌的季节变化及其神经内分泌调控[J].动物学报,2002,48(2):213-220.WEN H S,LIN H R,XIAO D,et al.Seasonal changes and neuroendocrine regulation of growth hormone secretion in feral catfish (Silurus asotus)[J].Acta Zoologica Sinica,2002,48(2):213-220.(in Chinese with English abstract)
[19] 刘士力,蒋文枰,程顺,等.翘嘴鲌生长激素基因侧翼2个微卫星位点与生长性状的关联分析[J].浙江农业学报,2019,31(1):62-68.LIU S L,JIANG W P,CHENG S,et al.Correlation analysis of growth traits and two microsatellite polymorphisms in flanking region of growth hormone gene in topmouth Culter(Culter alburnus Basilewsky)[J].Acta Agriculturae Zhejiangensis,2019,31(1):62-68.(in Chinese with English abstract)
[20] 刘士力,程顺,蒋文枰,等.翘嘴鲌胰岛素样生长因子-Ⅰ的克隆及序列分析[J].水生生物学报,2019,43(2):272-281.LIU S L,CHENG S,JIANG W P,et al.Cloning and sequence analysis of insulin-like growth factori gene in topmouth Culter(Culter alburnus Basilewsky)[J].Acta Hydrobiologica Sinica,2019,43(2):272-281.(in Chinese with English abstract)
[21] HO W K K,WONG M,CHAN A P Y.Cloning and sequencing of the grass carp (Ctenopharyngodon idellus) growth hormone gene[J].Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression,1991,1090(2):245-248.
[22] HONG Y H,SCHARTL M.Sequence of the growth hormone (GH) gene from the silver carp (Hypophthalmichthys molitrix) and evolution of GH genes in vertebrates[J].Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression,1993,1174(3):285-288.
[23] TANG Y,LIN C M,CHEN T T,et al.Structure of the channel catfish(Ictalurus punctatus)growth hormone gene and its evolutionary implications[J].Molecular Marine Biology and Biotechnology,1993,2(4):198-206.
[24] ALMULY R,CAVARI B,FERSTMAN H,et al.Genomic structure and sequence of the gilthead seabream (Sparus aurata) growth hormone-encoding gene:identification of minisatellite polymorphism in intron I[J].Genome,2000,43(5):836-845.
[25] 鲁双庆,刘峰,刘臻,等.三种鳜鱼(Siniperca)生长激素基因的克隆及序列比较[J].海洋与湖沼,2008,39(4):354-361.LU S Q,LIU F,LIU Z,et al.Comparison in cloning and sequence of growth hormone gene in three species of genus Siniperca[J].Oceanologia et Limnologia Sinica,2008,39(4):354-361.(in Chinese with English abstract)
[26] MA Q,LIU S F,ZHUANG Z M,et al.Genomic structure,polymorphism and expression analysis of the growth hormone (GH) gene in female and male Half-smooth tongue sole (Cynoglossus semilaevis)[J].Gene,2012,493(1):92-104.
[27] 王发新,连总强,吴旭东,等.兰州鲇生长激素(GH)基因的克隆及序列分析[J].淡水渔业,2015,45(4):20-25.WANG F X,LIAN Z Q,WU X D,et al.Cloning and sequence analysis of growth hormone(GH) gene in Silurus lanzhouensis[J].Freshwater Fisheries,2015,45(4):20-25.(in Chinese with English abstract)
[28] 刘士力,贾永义,蒋文枰,等.翘嘴鲌生长激素(GH)基因与侧翼区的克隆及分析[J].浙江农业学报,2017,29(8):1281-1289.LIU S L,JIA Y Y,JIANG W P,et al.Cloning and sequence analysis of growth hormone gene and its flanking region in topmouth Culter(Culter alburnus Basilewsky)[J].Acta Agriculturae Zhejiangensis,2017,29(8):1281-1289.(in Chinese with English abstract)
[29] 杨学明,张立,黄光华,等.革胡子鲶生长激素基因克隆与序列同源分析[J].西南农业学报,2008,21(2):483-486.YANG X M,ZHANG L,HUANG G H,et al.Gene cloning and sequence homology of growth hormone from Clarias lazera[J].Southwest China Journal of Agricultural Sciences,2008,21(2):483-486.(in Chinese with English abstract)
[2] 刘士力,贾永义,迟美丽,等.浙江3个河川沙塘鳢群体线粒体16S rRNA基因序列的研究[J].基因组学与应用生物学,2018,37(11):4742-4748.LIU S L,JIA Y Y,CHI M L,et al.Research on mitochondrial 16S rRNA genetic sequence from three populations of Odontobutis potamophila in Zhejiang Province[J].Genomics and Applied Biology,2018,37(11):4742-4748.(in Chinese with English abstract)
[3] 杨学明,张立,黄光华,等.革胡子鲶生长激素基因克隆与序列同源分析[J].西南农业学报,2008,21(2):483-486.YANG X M,ZHANG L,HUANG G H,et al.Gene cloning and sequence homology of growth hormone from Clarias lazera[J].Southwest China Journal of Agricultural Sciences,2008,21(2):483-486.(in Chinese with English abstract)
[4] M?LLER N,COPELAND K C,NAIR K S.Growth hormone effects on protein metabolism[J].Endocrinology and Metabolism Clinics of North America,2007,36(1):89-100.
[5] SAKAMOTO T,SHEPHERD B S,MADSEN S S,et al.Osmoregulatory actions of growth hormone and prolactin in an advanced teleost[J].General and Comparative Endocrinology,1997,106(1):95-101.
[6] FORSYTH I A,WALLIS M.Growth hormone and prolactinmolecular and functional evolution[J].Journal of Mammary Gland Biology and Neoplasia,2002,7(3):291-312.
[7] 王文君,陈克飞,任军,等.中外不同猪品种生长激素基因遗传多态性检测[J].农业生物技术学报,2003,11(1):103-104.WANG W J,CHEN K F,REN J,et al.Detection of the polymorphisms of growth hormone gene in Chinese and European pig breeds[J].Journal of Agricultural Biotechnology,2003,11(1):103-104.(in Chinese with English abstract)
[8] 宋成义,经荣斌.畜禽GH基因多态性与生产性能相关研究进展[J].国外畜牧科技,2000,27(2):25-27.SONG C Y,JING R B.Research on the relation between polymorphims in the stock and poultry GH gene and production rerformance[J].Animal Science Abroad,2000,27(2):25-27.(in Chinese with English abstract)
[9] 郁二蒙,叶星,白俊杰,等.唐鱼生长激素基因的克隆及序列分析[J].安徽农业科学,2008,36(23):9914-9917.YU E M,YE X,BAI J J,et al.Cloning and sequence analysis of growth hormone gene from Tanichthys albonubes[J].Journal of Anhui Agricultural Sciences,2008,36(23):9914-9917.(in Chinese with English abstract)
[10] 刘滨,臧晓南,刘顺梅,等.7种鲽形目鱼类生长激素基因cDNA序列的克隆及系统分析[J].武汉大学学报(理学版),2008,54(4):485-491.LIU B,ZANG X N,LIU S M,et al.Molecular cloning and sequence analysis of the growth hormone cDNAs from seven Pleuronectiformes fishes[J].Journal of Wuhan University(Natural Science Edition),2008,54(4):485-491.(in Chinese with English abstract)
[11] 严美姣,吴旭,李钟杰.暗纹东方鲀生长激素基因克隆与同源性分析[J].江西农业大学学报,2010,32(2):236-242.YAN M J,WU X,LI Z J.Molecular cloning and sequence analysis of Takifugu fasciatus GH gene[J].Acta Agriculturae Universitatis Jiangxiensis(Natural Sciences Edition),2010,32(2):236-242.(in Chinese with English abstract)
[12] 贡成良,曹广力,薛仁宇,等.编码鳗鲡生长激素基因的序列与结构[J].水产学报,2002,26(4):295-300.GONG C L,CAO G L,XUE R Y,et al.Sequence and structure of encoding eel growth hormone gene[J].Journal of Fisheries of China,2002,26(4):295-300.(in Chinese with English abstract)
[13] ALLENDORF F W,THORGAARD G H.Tetraploidy and the evolution of salmonid fishes[M]//Evolutionary genetics of fishes.Boston,MA:Springer US,1984:1-53.
[14] 刘士力,张爱菊,练青平,等.泥鳅和大鳞副泥鳅细胞色素P450c17-Ⅰ(CYP17-Ⅰ)基因的克隆及组织表达分析[J].浙江农业学报,2016,28(11):1853-1861.LIU S L,ZHANG A J,LIAN Q P,et al.Cloning and tissue expression analysis of the cytochrome P450c17-Ⅰ(CYP17-Ⅰ) gene from mud loach(Misgurnus anguillicaudatus) and large-scale loach(Paramisgurnus dabryanus)[J].Acta Agriculturae Zhejiangensis,2016,28(11):1853-1861.(in Chinese with English abstract)
[15] 严美姣,吴旭,李钟杰.暗纹东方鲀生长激素基因克隆与同源性分析[J].江西农业大学学报,2010,32(2):236-242.YAN M J,WU X,LI Z J.Molecular cloning and sequence analysis of Takifugu fasciatus GH gene[J].Acta Agriculturae Universitatis Jiangxiensis,2010,32(2):236-242.(in Chinese with English abstract)
[16] SAKAMOTO T,MCCORMICK S D.Prolactin and growth hormone in fish osmoregulation[J].General and Comparative Endocrinology,2006,147(1):24-30.
[17] SCIARA A A,RUBIOLO J A,SOMOZA G M,et al.Molecular cloning,expression and immunological characterization of pejerrey (Odontesthes bonariensis) growth hormone[J].Comparative Biochemistry and Physiology Part C:Toxicology & Pharmacology,2006,142(3/4):284-292.
[18] 温海深,林浩然,肖东,等.野生鲇鱼生长激素分泌的季节变化及其神经内分泌调控[J].动物学报,2002,48(2):213-220.WEN H S,LIN H R,XIAO D,et al.Seasonal changes and neuroendocrine regulation of growth hormone secretion in feral catfish (Silurus asotus)[J].Acta Zoologica Sinica,2002,48(2):213-220.(in Chinese with English abstract)
[19] 刘士力,蒋文枰,程顺,等.翘嘴鲌生长激素基因侧翼2个微卫星位点与生长性状的关联分析[J].浙江农业学报,2019,31(1):62-68.LIU S L,JIANG W P,CHENG S,et al.Correlation analysis of growth traits and two microsatellite polymorphisms in flanking region of growth hormone gene in topmouth Culter(Culter alburnus Basilewsky)[J].Acta Agriculturae Zhejiangensis,2019,31(1):62-68.(in Chinese with English abstract)
[20] 刘士力,程顺,蒋文枰,等.翘嘴鲌胰岛素样生长因子-Ⅰ的克隆及序列分析[J].水生生物学报,2019,43(2):272-281.LIU S L,CHENG S,JIANG W P,et al.Cloning and sequence analysis of insulin-like growth factori gene in topmouth Culter(Culter alburnus Basilewsky)[J].Acta Hydrobiologica Sinica,2019,43(2):272-281.(in Chinese with English abstract)
[21] HO W K K,WONG M,CHAN A P Y.Cloning and sequencing of the grass carp (Ctenopharyngodon idellus) growth hormone gene[J].Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression,1991,1090(2):245-248.
[22] HONG Y H,SCHARTL M.Sequence of the growth hormone (GH) gene from the silver carp (Hypophthalmichthys molitrix) and evolution of GH genes in vertebrates[J].Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression,1993,1174(3):285-288.
[23] TANG Y,LIN C M,CHEN T T,et al.Structure of the channel catfish(Ictalurus punctatus)growth hormone gene and its evolutionary implications[J].Molecular Marine Biology and Biotechnology,1993,2(4):198-206.
[24] ALMULY R,CAVARI B,FERSTMAN H,et al.Genomic structure and sequence of the gilthead seabream (Sparus aurata) growth hormone-encoding gene:identification of minisatellite polymorphism in intron I[J].Genome,2000,43(5):836-845.
[25] 鲁双庆,刘峰,刘臻,等.三种鳜鱼(Siniperca)生长激素基因的克隆及序列比较[J].海洋与湖沼,2008,39(4):354-361.LU S Q,LIU F,LIU Z,et al.Comparison in cloning and sequence of growth hormone gene in three species of genus Siniperca[J].Oceanologia et Limnologia Sinica,2008,39(4):354-361.(in Chinese with English abstract)
[26] MA Q,LIU S F,ZHUANG Z M,et al.Genomic structure,polymorphism and expression analysis of the growth hormone (GH) gene in female and male Half-smooth tongue sole (Cynoglossus semilaevis)[J].Gene,2012,493(1):92-104.
[27] 王发新,连总强,吴旭东,等.兰州鲇生长激素(GH)基因的克隆及序列分析[J].淡水渔业,2015,45(4):20-25.WANG F X,LIAN Z Q,WU X D,et al.Cloning and sequence analysis of growth hormone(GH) gene in Silurus lanzhouensis[J].Freshwater Fisheries,2015,45(4):20-25.(in Chinese with English abstract)
[28] 刘士力,贾永义,蒋文枰,等.翘嘴鲌生长激素(GH)基因与侧翼区的克隆及分析[J].浙江农业学报,2017,29(8):1281-1289.LIU S L,JIA Y Y,JIANG W P,et al.Cloning and sequence analysis of growth hormone gene and its flanking region in topmouth Culter(Culter alburnus Basilewsky)[J].Acta Agriculturae Zhejiangensis,2017,29(8):1281-1289.(in Chinese with English abstract)
[29] 杨学明,张立,黄光华,等.革胡子鲶生长激素基因克隆与序列同源分析[J].西南农业学报,2008,21(2):483-486.YANG X M,ZHANG L,HUANG G H,et al.Gene cloning and sequence homology of growth hormone from Clarias lazera[J].Southwest China Journal of Agricultural Sciences,2008,21(2):483-486.(in Chinese with English abstract)
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