水稻赤霉素3β羟化酶基因(OsGA3ox1)同源基因的生物信息学分析
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摘要
赤霉素3β-双氧化酶(GA3ox)是赤霉素(GA)生物合成过程中的关键酶,它通过催化活性GA的形成来影响植物生长发育。为了了解水稻GA3ox家族成员的基本情况,本研究利用生物信息学方法对其家族成员进行了预测、蛋白结构及其聚类分析。结果表明:第一,以OsGA3ox1 (LOC_Os05g08540)作为靶序列,利用BlastP在gramene数据库中共查询到了24个同源基因,同源性为80%～90%;第二,经NCBI在线分析发现,各同源基因的蛋白产物都含有2OG-FeII_Oxy和DIOX_N两个保守结构域,其结构域中都具有与Fe~(2+)结合的2个组氨酸残基(H)和1个天冬氨酸残基(D)以及能结合α-酮戊二酸的1个精氨酸残基(R)和1个丝氨酸残基(S),并且还观察到这些蛋白间具有相同或相似的α-螺旋和β-转角等二级结构,因此,推测它们同属于GA3ox家族;第三,进一步地,利用MEGA7.0构建了该家族的系统进化树,并将该家族分成ClassⅠ和ClassⅡ两个亚族,各亚族分别包括了16个和8个成员。本研究结果为深入研究水稻OsGA3ox基因的生物学功能提供参考依据。
Gibberellin 3β-dioxygenase(GA3ox), a key enzyme involved in the biosynthesis of gibberellin(GAs),can affect the growth and development of plant by catalyzing the formation of active GAs. In order to understand the basic situation of rice GA3ox family members, we used bioinformatic methods to predict its family members,the protein structure and its cluster analysis of rice GA3ox family members were also carried out. The results showed that:(1) Using OsGA3ox1(LOC_Os05 g08540) as the target sequence, 24 homologous genes were found in the gramene database by BlastP, with homology of 80%～90%.(2) Through NCBI online analysis, it was found that the protein products of all homologous genes contained two conserved domains of 2 OG-FeII_Oxy and DIOX_N,each of which contained 2 histidine residues(H) and 1 aspartate residue(D) bound to Fe~(2+), and 1 arginine residue(R) and 1 serine residue(S) bound to α-oxoglutarate. Moreover, it was also observed that these proteins had the same or similar secondary structure, such as α-helix and β-angle. Therefore, it was presumed that they might belong to the GA3 ox family.(3) The phylogenetic tree of the family was constructed by using the MEGA7.0, and we divided the family into 2 subgroups, class Ⅰ and class Ⅱ, each of which included 16 and 8 members,respectively. The results would provided a reference for the further study of the biological functions of OsGA3ox in rice.
Gibberellin 3β-dioxygenase(GA3ox), a key enzyme involved in the biosynthesis of gibberellin(GAs),can affect the growth and development of plant by catalyzing the formation of active GAs. In order to understand the basic situation of rice GA3ox family members, we used bioinformatic methods to predict its family members,the protein structure and its cluster analysis of rice GA3ox family members were also carried out. The results showed that:(1) Using OsGA3ox1(LOC_Os05 g08540) as the target sequence, 24 homologous genes were found in the gramene database by BlastP, with homology of 80%～90%.(2) Through NCBI online analysis, it was found that the protein products of all homologous genes contained two conserved domains of 2 OG-FeII_Oxy and DIOX_N,each of which contained 2 histidine residues(H) and 1 aspartate residue(D) bound to Fe~(2+), and 1 arginine residue(R) and 1 serine residue(S) bound to α-oxoglutarate. Moreover, it was also observed that these proteins had the same or similar secondary structure, such as α-helix and β-angle. Therefore, it was presumed that they might belong to the GA3 ox family.(3) The phylogenetic tree of the family was constructed by using the MEGA7.0, and we divided the family into 2 subgroups, class Ⅰ and class Ⅱ, each of which included 16 and 8 members,respectively. The results would provided a reference for the further study of the biological functions of OsGA3ox in rice.
引文
Appleford N.E.,Evans D.J.,Lenton J.R.,Gaskin P.,Croker S.J.,Devos K.M.,Phillips A.L.,and Hedden P.,2006,Function and transcript analysis of gibberellin-biosynthetic enzymes in wheat,Planta,223(3):568-582
Aravind L.,and Koonin E.V.,2001,The DNA-repair protein AlkB,EGL-9,and leprecan define new families of 2-oxoglutarate-and iron-dependent dioxygenases,Genome Biology,2(3):1-8
Arnold K.,Bordoli L.,Kopp J.,and Schwede T.,2006,The Swiss-model workspace:a web-based environment for protein structure homology modelling,Bioinformatics,22(2):195-201
Born E.V.D.,Bekkelund A.,Moen M.N.,Omelchenko M.V.,Klungland A.,and Falnes P.,2009,Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria,Nucleic Acids Res.,37(21):7124-7136
Chiang H.H.,Hwang I.,and Goodman H.M.,1995,Isolation of the arabidopsis GA4 locus,Plant Cell,7(2):195-201
Dunwell J.M.,Purvis A.,and Khuri S.,2004,Cupins:the most functionally diverse protein superfamily?Phytochemistry,65(1):7-17
Eriksson S.,Bohlenius H.,Moritz T.,and Nilsson O.,2006,GA4is the active gibberellin in the regulation of LEAFY transcription and Arabidopsis floral initiation,Plant Cell,18(9):2172-2181
Grennan A.K.,2006,Gibberellin metabolism enzymes in rice,Plant Physiol.,141(2):524-526
Guex N.,and Peitsch M.C.,1997,Swiss-model and the swiss-pdb viewer:an environment for comparative protein modelling,Electrophoresis,18(15):2714-2723
Hedden P.,and Phillips A.L.,2000,Gibberellin metabolism:new insights revealed by the genes,Trends Plant Sci.,5(12):523-530
Hedden P.,and Proebsting W.M.,1999,Genetic analysis of gibberellin biosynthesis,Plant Physiol.,119(2):365-370
Hironori I.,Miyako U.T.,Naoki S.,Hidemi K.,Makoto M.,and Masatomo K.,2001,Cloning and functional analysis of two gibberellin 3β-hydroxylase genes that are differently expressed during the growth of rice,Proc.Natl.Acad.Sci.USA,98(15):8909-8914
MacMillan J.,2001,Occurrence of gibberellins in vascular plants,fungi and bacteria,J.Plant Growth Regul.,20(4):387-442
Martínez B.L.,Moritz T.,and López D.I.,2015,Silencing C19-GA 2-oxidases induces parthenocarpic development and inhibits lateral branching in tomato plants,J.Exp.Bot.,66(19):5897-5910
Mcdonough M.A.,Li V.,Flashman E.,Chowdhury R.,and Mohr C.,2006,Cellular oxygen sensing:crystal structure of hypoxia-inducible factor prolyl hydroxylase(PHD2),Proc.Natl.Acad.Sci.USA,103(26):9814-9819
Mitchum M.G.,Yamaguchi S.,Hanada A.,Kuwahara A.,Yoshioka Y.,Kato T.,Tabata S.,Kamiya Y.,and Sun T.P.,2006,Distinct and overlapping roles of two gibberellin 3-oxidases in arabidopsis development,Plant J.,45(5):804-818
Olszewski N.,Sun T.P.,and Gubler F.,2002,Gibberellin signaling:biosynthesis,catabolism,and response pathways,Plant Cell,14(90001):61-80
Pearce S.,Huttly A.K.,Prosser I.M.,Li Y.D.,Vaughan S.P.,Barbora G.,Archana P.,Coghill J.A.,Dubcovsky J.,Hedden P.,and Phillips A.L.,2015,Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family,BMCPlant Biol.,15(1):130
Richards D.E.,King K.E.,Ait-ali T.,and Harberd N.P.,2001,How gibberellin regulates plant growth and development:a molecular genetic analysis of gibberellin signaling,Annu.Rev.Plant Physiol.Plant Mol.Biol.,52:67-88
Sakamoto T.,Miura K.,Itoh H.,Tatsumi T.,Tanaka U.M.,Ishiyama K.,Kobayashi M.,Agrawal G.K.,Takeda S.,Kiyomi A.,Miyao A.,Hirochika H.,Kitano H.,Ashikari M.,and Matsuoka M.,2004,An overview of gibberellin metabolism enzyme genes and their related mutants in rice,Plant Physiol.,134(4):1642-1653
Schwede T.,Kopp J.,Guex N.,and Peitsch M.C.,2003,Swissmodel:an automated protein homology-modeling server,Nucleic Acids Res.,31(13):3381-3385
Toymasu T.,Kawaide H.,Sekimoto H.,Numers C.V.,Phillips A.L.,Hedden P.,and Kamiya Y.,2010,Cloning and characterization of a cDNA encoding gibberellin 20-oxidase from rice(Oryza sativa)seedings,Physiol.Plant,99(1):111-118
Xu J.,Lange T.,and Altpeter T.,2002,Cloning and characterization of a cDNA encoding a multifunctional gibberellin 20-oxidase from perennial Ryegrass(Lolium perenne L.),Plant Sci.,163(1):147-155
Aravind L.,and Koonin E.V.,2001,The DNA-repair protein AlkB,EGL-9,and leprecan define new families of 2-oxoglutarate-and iron-dependent dioxygenases,Genome Biology,2(3):1-8
Arnold K.,Bordoli L.,Kopp J.,and Schwede T.,2006,The Swiss-model workspace:a web-based environment for protein structure homology modelling,Bioinformatics,22(2):195-201
Born E.V.D.,Bekkelund A.,Moen M.N.,Omelchenko M.V.,Klungland A.,and Falnes P.,2009,Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria,Nucleic Acids Res.,37(21):7124-7136
Chiang H.H.,Hwang I.,and Goodman H.M.,1995,Isolation of the arabidopsis GA4 locus,Plant Cell,7(2):195-201
Dunwell J.M.,Purvis A.,and Khuri S.,2004,Cupins:the most functionally diverse protein superfamily?Phytochemistry,65(1):7-17
Eriksson S.,Bohlenius H.,Moritz T.,and Nilsson O.,2006,GA4is the active gibberellin in the regulation of LEAFY transcription and Arabidopsis floral initiation,Plant Cell,18(9):2172-2181
Grennan A.K.,2006,Gibberellin metabolism enzymes in rice,Plant Physiol.,141(2):524-526
Guex N.,and Peitsch M.C.,1997,Swiss-model and the swiss-pdb viewer:an environment for comparative protein modelling,Electrophoresis,18(15):2714-2723
Hedden P.,and Phillips A.L.,2000,Gibberellin metabolism:new insights revealed by the genes,Trends Plant Sci.,5(12):523-530
Hedden P.,and Proebsting W.M.,1999,Genetic analysis of gibberellin biosynthesis,Plant Physiol.,119(2):365-370
Hironori I.,Miyako U.T.,Naoki S.,Hidemi K.,Makoto M.,and Masatomo K.,2001,Cloning and functional analysis of two gibberellin 3β-hydroxylase genes that are differently expressed during the growth of rice,Proc.Natl.Acad.Sci.USA,98(15):8909-8914
MacMillan J.,2001,Occurrence of gibberellins in vascular plants,fungi and bacteria,J.Plant Growth Regul.,20(4):387-442
Martínez B.L.,Moritz T.,and López D.I.,2015,Silencing C19-GA 2-oxidases induces parthenocarpic development and inhibits lateral branching in tomato plants,J.Exp.Bot.,66(19):5897-5910
Mcdonough M.A.,Li V.,Flashman E.,Chowdhury R.,and Mohr C.,2006,Cellular oxygen sensing:crystal structure of hypoxia-inducible factor prolyl hydroxylase(PHD2),Proc.Natl.Acad.Sci.USA,103(26):9814-9819
Mitchum M.G.,Yamaguchi S.,Hanada A.,Kuwahara A.,Yoshioka Y.,Kato T.,Tabata S.,Kamiya Y.,and Sun T.P.,2006,Distinct and overlapping roles of two gibberellin 3-oxidases in arabidopsis development,Plant J.,45(5):804-818
Olszewski N.,Sun T.P.,and Gubler F.,2002,Gibberellin signaling:biosynthesis,catabolism,and response pathways,Plant Cell,14(90001):61-80
Pearce S.,Huttly A.K.,Prosser I.M.,Li Y.D.,Vaughan S.P.,Barbora G.,Archana P.,Coghill J.A.,Dubcovsky J.,Hedden P.,and Phillips A.L.,2015,Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family,BMCPlant Biol.,15(1):130
Richards D.E.,King K.E.,Ait-ali T.,and Harberd N.P.,2001,How gibberellin regulates plant growth and development:a molecular genetic analysis of gibberellin signaling,Annu.Rev.Plant Physiol.Plant Mol.Biol.,52:67-88
Sakamoto T.,Miura K.,Itoh H.,Tatsumi T.,Tanaka U.M.,Ishiyama K.,Kobayashi M.,Agrawal G.K.,Takeda S.,Kiyomi A.,Miyao A.,Hirochika H.,Kitano H.,Ashikari M.,and Matsuoka M.,2004,An overview of gibberellin metabolism enzyme genes and their related mutants in rice,Plant Physiol.,134(4):1642-1653
Schwede T.,Kopp J.,Guex N.,and Peitsch M.C.,2003,Swissmodel:an automated protein homology-modeling server,Nucleic Acids Res.,31(13):3381-3385
Toymasu T.,Kawaide H.,Sekimoto H.,Numers C.V.,Phillips A.L.,Hedden P.,and Kamiya Y.,2010,Cloning and characterization of a cDNA encoding gibberellin 20-oxidase from rice(Oryza sativa)seedings,Physiol.Plant,99(1):111-118
Xu J.,Lange T.,and Altpeter T.,2002,Cloning and characterization of a cDNA encoding a multifunctional gibberellin 20-oxidase from perennial Ryegrass(Lolium perenne L.),Plant Sci.,163(1):147-155