香蕉水通道蛋白基因家族的密码子偏好性分析
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摘要
[目的]研究香蕉水通道蛋白(AQP)基因家族密码子使用特点,为其基因编码规律及功能和分子进化研究提供依据。[方法]采用Codon W、SPSS、Origin等软件分析香蕉AQP基因家族密码子偏好性。[结果]从香蕉基因组中鉴定获得54条香蕉AQP基因,其中包括9条NIPs、21条PIPs、4条SIPs和20条TIPs。香蕉AQP基因家族A、T、C、G出现频率平均值分别为12.0%、15.9%、52.3%和37.4%,平均GC3s含量为75.8%,ENc值在31.0~60.7,平均值为42.9;SIPs、NIPs、PIPs和TIPs分别有2、5、7和6个最优密码子,且多以C结尾,少数以G结尾;ENc和CAI呈极显著负相关,说明密码子第3位碱基会影响基因表达能力。[结论]香蕉AQP家族基因密码子偏好性较弱,偏好使用G和C且以G/C结尾的密码子,PIPs和TIPs密码子偏好性受自然选择的影响较大,而NIPs和SIPs受碱基突变的影响较大。
[Objective] To explore the genetic encoding,function and evolution characteristics of banana aquaporin genes(AQPs),series of codon bias analysis was performed. [Method] Codon W,SPSS and Origin softwares were used to analyze the codon bias of the banana AQP gene family members. [Result]Totally,54 AQP sequences were identified from the banana genome,among which 9 NIPs,21 PIPs,4 SIPs and 20 TIPs were included. The average frequency of A,T,C and G in AQPs was 12.0%,15.9%,52.3%and 37.4%, respectively. The average GC3 s content was 75.8%,and the ENc value ranges from 31.0 to60.7,with an average value of 42.9. The SIPs,NIPs,PIPs and TIPs own 2,5,7 and 6 optimal codon respectively,and most of them end with C,and some of them end with G. Significant negative correlation was found between ENc and CAI,suggesting that the third base of codon would affect the genes' expression. [Conclusion] The codon bias of banana AQP gene family is weak,preferring to use G or C,and ending with G or C. The condon bias of PIPs and TIPs is strongly influenced by natural selection,while the condon bias of NIPs and SIPs is greatly influenced by the base mutations.
[Objective] To explore the genetic encoding,function and evolution characteristics of banana aquaporin genes(AQPs),series of codon bias analysis was performed. [Method] Codon W,SPSS and Origin softwares were used to analyze the codon bias of the banana AQP gene family members. [Result]Totally,54 AQP sequences were identified from the banana genome,among which 9 NIPs,21 PIPs,4 SIPs and 20 TIPs were included. The average frequency of A,T,C and G in AQPs was 12.0%,15.9%,52.3%and 37.4%, respectively. The average GC3 s content was 75.8%,and the ENc value ranges from 31.0 to60.7,with an average value of 42.9. The SIPs,NIPs,PIPs and TIPs own 2,5,7 and 6 optimal codon respectively,and most of them end with C,and some of them end with G. Significant negative correlation was found between ENc and CAI,suggesting that the third base of codon would affect the genes' expression. [Conclusion] The codon bias of banana AQP gene family is weak,preferring to use G or C,and ending with G or C. The condon bias of PIPs and TIPs is strongly influenced by natural selection,while the condon bias of NIPs and SIPs is greatly influenced by the base mutations.
引文
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[8]HECKWOLF M,PATER D,HANSON DT,et al.The Arabidopsis thaliana aquaporin At PIP1;2 is a physiologically relevant CO2transport facilitator[J].Plant Journal for Cell&Molecular Biology,2011,67(5):795-804.
[9]郑小亚.糯玉米(Zea Mays L.Ceretina Kulesh)逆境胁迫下AQP基因表达与水分利用效率及其种性品质分析研究[D].杨凌:西北农林科技大学,2011.
[10]WANG Y,LI R,LI D,et al.NIP1;2 is a Plasma membrane-localized transporter mediating aluminum uptake,translocation,and tolerance in arabidopsis.[J].Proceedings of the National Academy Ofences of the United States of America,2017,114(19):5047.
[11]吴向阳,程朝泽,吕高强,等.芝麻Aqp家族的全基因组序列鉴定及其特征分析[J].中国农业科学,2016,49(10):1844-1858.
[12]吴宪明,吴松锋,任大明,等.密码子偏性的分析方法及相关研究进展[J].遗传,2007(4):420-426.
[13]LIU Q,XUE Q.Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species[J].Journal of Genetics,2005,84(1):55-62.
[14]曲俊杰,黄羽,卢江,等.香蕉基因组密码子使用偏好性分析[J].南方农业学报,2017(1):14-19.
[15]唐晓芬,陈莉,马玉韬.密码子使用偏性量化方法研究综述[J].基因组学与应用生物学,2013(5):660-666.
[16]SHPAER EG.Constraints on codon context in escherichia coli genes their possible role in modulating the efficiency of translation[J].Journal of Molecular Biology,1986,188(4):555-564.
[17]ZHOU M,LI X.Analysis of synonymous codon usage patterns in different plant mitochondrial genomes[J].Molecular Biology Reports,2009,36(8):2039.
[18]WRIGHT F.The‘effective number of codons’used in a gene.[J].Gene,1990,87(1):23-29.
[19]SHI X,WANG X,LI Z,et al.Nucleotide substitution pattern in rice paralogues:implication for negative correlation between the synonymous substitution rate and codon isage bias.[J].Gene,2006,376(2):199.
[20]赖瑞联,林玉玲,钟春水,等.龙眼生长素受体基因Tir1密码子偏好性分析[J].园艺学报,2016(4):771-780.
[21]周子维,常笑君,游芳宁,等.茶树脂肪氧合酶(Lox)基因家族成员的分子进化及密码子偏好性分析[J].中国农业科技导报,2017(12):43-51.
[22]FOTIADIS D,JEN P,MINI T,et al.Structural characterization of two aquaporins isolated from native spinach leaf plasma membranes[J].Journal of Biological Chemistry,2001,276(3):1707-1714.
[23]许奕,侯晓婉,徐碧玉,等.香蕉水通道蛋白Sip2-1基因的克隆和表达分析[J].生物技术通报,2016,32(7):81-86.
[24]HU W,HOU X,HUANG C,et al.Genome-Wide identification and expression analyses of aquaporin gene family during development and abiotic stress in banana[J].International Journal of Molecular Sciences,2015,16(8):19728-19751.
[25]WSPALZ T,FUJIYOSHI Y,ENGEL A.The AQP structure and functional implications[J].Springer Berlin Heidelberg,2009,31-56.
[2]CHRISPEELS M J.The major Intrinsic protein family of Arabidopsis has 23 members that form three distinct groups with functional aquaporinsineachgroup[J].Plant Physiology,1997,114(4):1347-1357.
[3]CHAUMONT F,MOSHELION M,Daniels M J.Regulation of plant aquaporin activity[J].Biology of the Cell,2005,97(10):749-764.
[4]QUIGLEY F,ROSENBERG J M,SHACHARHILL Y,et al.From genome to function:the arabidopsis aquaporins.[J].Genome Biology,2001,3(1):1-17.
[5]PRESTON G M,AGRE P.Isolation of the c DNA for erythrocyte integral membrane protein of 28 kilodaltons:member of an ancient channel family[J].Proceeding of the National Academy of Sciences of the United States of America,1991,88(24):11110-11114.
[6]杨淑慎,山仑,郭蔼光,等.水通道蛋白与植物的抗旱性[J].干旱地区农业研究,2005,23(6):214-218.
[7]KIRCH H H,VERAESTRELLA R,GOLLDACK D,et al.Expression of water channel proteins in mesembryanthemum crystallinum[J].Plant Physio-logy,2000,123(1):111-124.
[8]HECKWOLF M,PATER D,HANSON DT,et al.The Arabidopsis thaliana aquaporin At PIP1;2 is a physiologically relevant CO2transport facilitator[J].Plant Journal for Cell&Molecular Biology,2011,67(5):795-804.
[9]郑小亚.糯玉米(Zea Mays L.Ceretina Kulesh)逆境胁迫下AQP基因表达与水分利用效率及其种性品质分析研究[D].杨凌:西北农林科技大学,2011.
[10]WANG Y,LI R,LI D,et al.NIP1;2 is a Plasma membrane-localized transporter mediating aluminum uptake,translocation,and tolerance in arabidopsis.[J].Proceedings of the National Academy Ofences of the United States of America,2017,114(19):5047.
[11]吴向阳,程朝泽,吕高强,等.芝麻Aqp家族的全基因组序列鉴定及其特征分析[J].中国农业科学,2016,49(10):1844-1858.
[12]吴宪明,吴松锋,任大明,等.密码子偏性的分析方法及相关研究进展[J].遗传,2007(4):420-426.
[13]LIU Q,XUE Q.Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species[J].Journal of Genetics,2005,84(1):55-62.
[14]曲俊杰,黄羽,卢江,等.香蕉基因组密码子使用偏好性分析[J].南方农业学报,2017(1):14-19.
[15]唐晓芬,陈莉,马玉韬.密码子使用偏性量化方法研究综述[J].基因组学与应用生物学,2013(5):660-666.
[16]SHPAER EG.Constraints on codon context in escherichia coli genes their possible role in modulating the efficiency of translation[J].Journal of Molecular Biology,1986,188(4):555-564.
[17]ZHOU M,LI X.Analysis of synonymous codon usage patterns in different plant mitochondrial genomes[J].Molecular Biology Reports,2009,36(8):2039.
[18]WRIGHT F.The‘effective number of codons’used in a gene.[J].Gene,1990,87(1):23-29.
[19]SHI X,WANG X,LI Z,et al.Nucleotide substitution pattern in rice paralogues:implication for negative correlation between the synonymous substitution rate and codon isage bias.[J].Gene,2006,376(2):199.
[20]赖瑞联,林玉玲,钟春水,等.龙眼生长素受体基因Tir1密码子偏好性分析[J].园艺学报,2016(4):771-780.
[21]周子维,常笑君,游芳宁,等.茶树脂肪氧合酶(Lox)基因家族成员的分子进化及密码子偏好性分析[J].中国农业科技导报,2017(12):43-51.
[22]FOTIADIS D,JEN P,MINI T,et al.Structural characterization of two aquaporins isolated from native spinach leaf plasma membranes[J].Journal of Biological Chemistry,2001,276(3):1707-1714.
[23]许奕,侯晓婉,徐碧玉,等.香蕉水通道蛋白Sip2-1基因的克隆和表达分析[J].生物技术通报,2016,32(7):81-86.
[24]HU W,HOU X,HUANG C,et al.Genome-Wide identification and expression analyses of aquaporin gene family during development and abiotic stress in banana[J].International Journal of Molecular Sciences,2015,16(8):19728-19751.
[25]WSPALZ T,FUJIYOSHI Y,ENGEL A.The AQP structure and functional implications[J].Springer Berlin Heidelberg,2009,31-56.