普通烟草ATⅢ氨基转移酶家族序列鉴定与表达分析
|
摘要
氨基转移酶是5'-磷酸吡哆醛依赖酶,在植物的生长发育和非生物胁迫的反应中起重要作用。ATⅢ氨基转移酶家族(classⅢ aminotransferase family)是转氨酶家族中一个非常重要的亚家族。本研究利用普通烟草(Nicotiana tabacum)基因组序列信息,鉴定出26个ATⅢ家族成员,对烟草ATⅢ家族进行理化性质分析表明,普通烟草ATⅢ家族成员之间的理化性质差异较大;系统进化和结构域分析显示,烟草ATⅢ家族成员可形成4个分支,同一分支内ATⅢ家族成员的保守结构域的种类和组织形式高度一致;将19个家族成员定位在12条染色体上;分析普通烟草转录组数据,结果显示大多数家族成员在不同组织中都有表达,主要集中在叶脉、打顶后茎和叶、离体叶片等组织。对NtATⅢ1和NtATⅢ2基因的qRT-PCR分析显示,这两个基因主要在植物地上组织中表达。本研究为普通烟草ATⅢ基因的功能研究提供依据。
The aminotransferase is a 5'-phosphate pyridoxal-dependent enzyme, which plays an important role in plant growth and abiotic stress response. The ATⅢ aminotransferase family(class Ⅲ aminotransferase family) is a very important subfamily of the transaminase family. In this study, 26 ATⅢ family members were identified by using the genome sequence information of Nicotiana tabacum. The physical and chemical properties of tobacco AT Ⅲfamily were analyzed and it showed that the physicochemical properties of ATⅢ family members were significantly different. The phylogenetic and domain analysis showed that the ATⅢ family members of tobacco could form four branches, and the conserved domain types and organizational forms of AT Ⅲ family members in the same branch were highly consistent. The 19 family members were located on 12 chromosomes. The transcriptome data of Nicotiana tabacum were analyzed, and the results showed that most family members were expressed in different tissues, mainly in the veins, the stem and leaves after topping, vitro leaves and other tissues. The qRT-PCR analysis of NtATⅢ1 and NtATⅢ2 genes showed that the two genes were mainly expressed in the aboveground tissues of plants.This study would provide a basis for the functional study of ATⅢ gene of Nicotiana tabacum.
The aminotransferase is a 5'-phosphate pyridoxal-dependent enzyme, which plays an important role in plant growth and abiotic stress response. The ATⅢ aminotransferase family(class Ⅲ aminotransferase family) is a very important subfamily of the transaminase family. In this study, 26 ATⅢ family members were identified by using the genome sequence information of Nicotiana tabacum. The physical and chemical properties of tobacco AT Ⅲfamily were analyzed and it showed that the physicochemical properties of ATⅢ family members were significantly different. The phylogenetic and domain analysis showed that the ATⅢ family members of tobacco could form four branches, and the conserved domain types and organizational forms of AT Ⅲ family members in the same branch were highly consistent. The 19 family members were located on 12 chromosomes. The transcriptome data of Nicotiana tabacum were analyzed, and the results showed that most family members were expressed in different tissues, mainly in the veins, the stem and leaves after topping, vitro leaves and other tissues. The qRT-PCR analysis of NtATⅢ1 and NtATⅢ2 genes showed that the two genes were mainly expressed in the aboveground tissues of plants.This study would provide a basis for the functional study of ATⅢ gene of Nicotiana tabacum.
引文
Bailey T.L.,Johnson J.,Grant C.E.,and Noble W.S.,2015,The MEME suite,Nucleic Acids Research,43:39-49
Chao J.T.,Kong Y.Z.,Wang Q.,Sun Y.H.,Gong D.P.,Lv J.,and Liu G.S.,2015,MapGene2Chrom,a tool to draw gene physical map based on Perl and SVG languages,Yi Chuan(Hereditas),37(1):91-97(晁江涛,孔英珍,王倩,孙玉合,龚达平,吕婧,刘贯山,2015,MapGene2Chrom基于Perl和SVG语言绘制基因物理图谱,遗传,37(1):91-97)
Finn R.D.,Clements J.,Arndt W.,Miller B.L.,Wheeler T.J.,Schreiber F.,Bateman A.,and Eddy S.R.,2015,HMMERweb server:2015 update,Nucleic Acids Research,43:30-38
Frémont N.,Riefler M.,Stolz A.,and Schmülling T.,2013,The Arabidopsis TUMOR PRONE5 gene encodes an acetylornithine aminotransferase required for arginine biosynthesis and root meristem maintenance in blue light,Plant Physiology,161(3):1127-1140
Han S.W.,Kim J.,Cho H.S.,and Shin J.S.,2017,Active site engineering ofω-transaminase guided by docking orientation analysis and virtual activity screening,ACS Catalysis,7(6):3752-3762
Hwang B.Y.,Cho B.K.,Yun H.,Koteshwar K.,and Kim B.G.,2005,Revisit of aminotransferase in the genomic era and its application to biocatalysis,Journal of Molecular Catalysis BEnzymatic,37(1-6):47-55
Letunic I.,Doerks T.,and Bork P.,2015,SMART:recent updates,new developments and status in 2015,Nucleic Acids Research,43:257-260
Li X.X.,Liu C.,Li W.,Zhang Z.L.,Gao X.M.,Zhou H.,and Guo Y.F.,2016,Genome-wide identification,phylogenetic analysis and expression profiling of the WOX family genes in solanum lycopersicum,Yichuan(Hereditas),38(5):444-460(李晓旭,刘成,李伟,张增林,高晓明,周慧,郭永峰,2016,番茄WOX转录因子家族的鉴定及其进化、表达分析,遗传,38(5):444-460)
Lv J.,Chen H.,Sun T.T.,and Sun Y.H.,2017,Genome-wide sequence identification and expression analysis of the tps gene family in Nicotiana tobacum,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(6):2518-2530(吕婧,陈浣,孙亭亭,孙玉合,2017,普通烟草TPS家族全基因组序列鉴定与表达分析,基因组学与应用生物学,36(6):2518-2530)
Olsen L.J.,2004,Genomic analysis of aminotransferases in Arabidopsis thaliana,Critical Reviews in Plant Sciences,23(1):73-89
Percudani R.,and Peracchi A.,2003,A genomic overview of pyridoxal-phosphate-dependent enzymes,Embo Reports,4(9):850-854
Phillips R.S.,2015,Chemistry and diversity of pyridoxal-5'-phosphate dependent enzymes,Biochimica Et Biophysica Acta,1854(9):1167-1174
Rajaram V.,Ratna P.P.,Savithri H.S.,and Murthy M.R.,2008,Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium:studies on substrate specificity and inhibitor binding,Proteins Structure Function and Bioinformatics,70(2):429-441
Roosens N.H.,Bitar F.A.,Loenders K.,Angenon G.,and Jacobs M.,2002,Overexpression of ornithine-δ-aminotransferase increases proline biosynthesis and confers osmotolerance in transgenic plants,Molecular Breeding,9(2):73-80
Roosens N.H.C.J.,Thu T.T.,Iskandar H.M.,and Jacobs M.,1998,Isolation of the ornithine-δ-aminotransferase cdna and effect of salt stress on its expression in Arabidopsis thaliana,Plant Physiology,117(1):263-271
Schmidt G.W.,and Delaney S.K.,2010,Stable internal reference genes for normalization of real-time RT-PCR in tobacco(Nicotiana tabacum)during development and abiotic stress,Molecular Genetics and Genomics,,283(3):233-241
Sierro N.,Battey J.N.D.,Ouadi S.,Bakaher N.,Bovet L.,Willig A.,Goepfert S.,Peitsch M.C.,and Ivanov N.V.,2014,The tobacco genome sequence and its comparison with those of tomato and potato,Nature Communications,5(5):1-9
Sun J.,Xie D.W.,Zhao H.W.,and Zou D.T.,2013,Genome-wide identification of the classⅢaminotransferase gene family in rice and expression analysis under abiotic stress,Genes and Genomics,35(5):597-608
Tamura K.,Stecher G.,Peterson D.,Filipski A.,and Kumar S.,2013,MEGA6:molecular evolutionary genetics analysis version 6.0,Molecular Biology and Evolution,30(12):2725-2729
Toyokura K.,Yamaguchi K.,Shigenobu S.,Fukaki H.,Tatematsu K.,and Okada K.,2015,Mutations in Plastidial 5-aminolevulinic acid biosynthesis genes suppress a pleiotropic defect in shoot development of a mitochondrial gaba shunt mutant in arabidopsis,Plant and Cell Physiology,56(6):1229-1238
Wu L.,Fan Z.,Guo L.,Li Y.,Chen Z.L.,and Qu L.J.,2005,Over-expression of the bacterial nhaA gene in rice enhances salt and drought tolerance,Plant Science,168(2):297-302
Yuan Q.,Zhang C.L.,Zhao T.T.,and Xu X.Y.,2017,Bioinformatics analysis of GRF transcription factor family in tomato,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(8):2949-2956(袁岐,张春利,赵婷婷,许向阳,2017,番茄GRF转录因子家族的生物信息学分析,分子植物育种,15(8):2949-2956)
Zhang H.,Jiang J.B.,Xu X.Y.,and Li J.F.,2016,Bioinformatics analysis of WRKY gene family in tomato,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(8):1965-1976(张红,姜景彬,许向阳,李景富,2016,番茄WRKY基因家族的生物信息学分析,分子植物育种,14(8):1965-1976)
Chao J.T.,Kong Y.Z.,Wang Q.,Sun Y.H.,Gong D.P.,Lv J.,and Liu G.S.,2015,MapGene2Chrom,a tool to draw gene physical map based on Perl and SVG languages,Yi Chuan(Hereditas),37(1):91-97(晁江涛,孔英珍,王倩,孙玉合,龚达平,吕婧,刘贯山,2015,MapGene2Chrom基于Perl和SVG语言绘制基因物理图谱,遗传,37(1):91-97)
Finn R.D.,Clements J.,Arndt W.,Miller B.L.,Wheeler T.J.,Schreiber F.,Bateman A.,and Eddy S.R.,2015,HMMERweb server:2015 update,Nucleic Acids Research,43:30-38
Frémont N.,Riefler M.,Stolz A.,and Schmülling T.,2013,The Arabidopsis TUMOR PRONE5 gene encodes an acetylornithine aminotransferase required for arginine biosynthesis and root meristem maintenance in blue light,Plant Physiology,161(3):1127-1140
Han S.W.,Kim J.,Cho H.S.,and Shin J.S.,2017,Active site engineering ofω-transaminase guided by docking orientation analysis and virtual activity screening,ACS Catalysis,7(6):3752-3762
Hwang B.Y.,Cho B.K.,Yun H.,Koteshwar K.,and Kim B.G.,2005,Revisit of aminotransferase in the genomic era and its application to biocatalysis,Journal of Molecular Catalysis BEnzymatic,37(1-6):47-55
Letunic I.,Doerks T.,and Bork P.,2015,SMART:recent updates,new developments and status in 2015,Nucleic Acids Research,43:257-260
Li X.X.,Liu C.,Li W.,Zhang Z.L.,Gao X.M.,Zhou H.,and Guo Y.F.,2016,Genome-wide identification,phylogenetic analysis and expression profiling of the WOX family genes in solanum lycopersicum,Yichuan(Hereditas),38(5):444-460(李晓旭,刘成,李伟,张增林,高晓明,周慧,郭永峰,2016,番茄WOX转录因子家族的鉴定及其进化、表达分析,遗传,38(5):444-460)
Lv J.,Chen H.,Sun T.T.,and Sun Y.H.,2017,Genome-wide sequence identification and expression analysis of the tps gene family in Nicotiana tobacum,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(6):2518-2530(吕婧,陈浣,孙亭亭,孙玉合,2017,普通烟草TPS家族全基因组序列鉴定与表达分析,基因组学与应用生物学,36(6):2518-2530)
Olsen L.J.,2004,Genomic analysis of aminotransferases in Arabidopsis thaliana,Critical Reviews in Plant Sciences,23(1):73-89
Percudani R.,and Peracchi A.,2003,A genomic overview of pyridoxal-phosphate-dependent enzymes,Embo Reports,4(9):850-854
Phillips R.S.,2015,Chemistry and diversity of pyridoxal-5'-phosphate dependent enzymes,Biochimica Et Biophysica Acta,1854(9):1167-1174
Rajaram V.,Ratna P.P.,Savithri H.S.,and Murthy M.R.,2008,Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium:studies on substrate specificity and inhibitor binding,Proteins Structure Function and Bioinformatics,70(2):429-441
Roosens N.H.,Bitar F.A.,Loenders K.,Angenon G.,and Jacobs M.,2002,Overexpression of ornithine-δ-aminotransferase increases proline biosynthesis and confers osmotolerance in transgenic plants,Molecular Breeding,9(2):73-80
Roosens N.H.C.J.,Thu T.T.,Iskandar H.M.,and Jacobs M.,1998,Isolation of the ornithine-δ-aminotransferase cdna and effect of salt stress on its expression in Arabidopsis thaliana,Plant Physiology,117(1):263-271
Schmidt G.W.,and Delaney S.K.,2010,Stable internal reference genes for normalization of real-time RT-PCR in tobacco(Nicotiana tabacum)during development and abiotic stress,Molecular Genetics and Genomics,,283(3):233-241
Sierro N.,Battey J.N.D.,Ouadi S.,Bakaher N.,Bovet L.,Willig A.,Goepfert S.,Peitsch M.C.,and Ivanov N.V.,2014,The tobacco genome sequence and its comparison with those of tomato and potato,Nature Communications,5(5):1-9
Sun J.,Xie D.W.,Zhao H.W.,and Zou D.T.,2013,Genome-wide identification of the classⅢaminotransferase gene family in rice and expression analysis under abiotic stress,Genes and Genomics,35(5):597-608
Tamura K.,Stecher G.,Peterson D.,Filipski A.,and Kumar S.,2013,MEGA6:molecular evolutionary genetics analysis version 6.0,Molecular Biology and Evolution,30(12):2725-2729
Toyokura K.,Yamaguchi K.,Shigenobu S.,Fukaki H.,Tatematsu K.,and Okada K.,2015,Mutations in Plastidial 5-aminolevulinic acid biosynthesis genes suppress a pleiotropic defect in shoot development of a mitochondrial gaba shunt mutant in arabidopsis,Plant and Cell Physiology,56(6):1229-1238
Wu L.,Fan Z.,Guo L.,Li Y.,Chen Z.L.,and Qu L.J.,2005,Over-expression of the bacterial nhaA gene in rice enhances salt and drought tolerance,Plant Science,168(2):297-302
Yuan Q.,Zhang C.L.,Zhao T.T.,and Xu X.Y.,2017,Bioinformatics analysis of GRF transcription factor family in tomato,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(8):2949-2956(袁岐,张春利,赵婷婷,许向阳,2017,番茄GRF转录因子家族的生物信息学分析,分子植物育种,15(8):2949-2956)
Zhang H.,Jiang J.B.,Xu X.Y.,and Li J.F.,2016,Bioinformatics analysis of WRKY gene family in tomato,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(8):1965-1976(张红,姜景彬,许向阳,李景富,2016,番茄WRKY基因家族的生物信息学分析,分子植物育种,14(8):1965-1976)