马铃薯StRFP2基因克隆及其生物信息学分析
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摘要
RING型泛素连接酶(RING finger protein,RFP)在植物响应非生物胁迫中有着重要作用。本研究在马铃薯干旱胁迫相关转录组测序的基础上,利用RT-PCR技术从马铃薯栽培品种"大西洋"和"青薯9号"中克隆得到StRFP2基因,并对该基因进行生物信息学分析。结果表明,该基因CDS为1 113 bp,且为连续基因,编码一个370个氨基酸的蛋白质。StRFP2蛋白不含信号肽序列,主要分布在线粒体;StRFP2蛋白含有典型的RING-H2保守结构域,并且"大西洋"和"青薯9号"的RING-H2保守结构域均未发生突变。栽培品种"大西洋"和"青薯9号"StRFP2 CDS序列高度同源,同源性达到98.20%;氨基酸序列进化分析表明StRFP2与野生番茄和番茄的亲缘关系最近。空间三维结构分析发现"大西洋"和"青薯9号"StRFP2均具有两个Zn~(2+),但其折叠方式存在一定差异。
RING finger protein(RFP) plays an important role in plant response to abiotic stress. In this study,StRFP2 gene was cloned from potato cultivars"Atlantic"and"Qingshu 9"by RT-PCR based on the sequencing of related transcriptional groups of potato droughts, and the bioinformatics analysis was carried out. The results showed that the gene CDS was 1 113 bp, which was a continuous gene encoding a 370 amino acid protein. StRFP2 protein did not contain signal peptide sequence, and it was mainly distributed in mitochondria. StRFP2 protein contained a typical RING-H2 conserved domain, and the RING-H2 conserved domains of "Atlantic"and"Qingshu 9"had not been mutated. The sequence of "Atlantic"and "Qingshu 9"StRFP2 CDS was highly homologous and the homology reached 98.20%. Amino acid sequence evolution analysis indicated that StRFP2 was closest to Solanum pennellii and Solanum lycopersicum. Spatial three-dimensional structure analysis found that StRFP2 of"Atlantic"and" Qingshu 9"had two Zn~(2+), but the folding methods of the two were different.
RING finger protein(RFP) plays an important role in plant response to abiotic stress. In this study,StRFP2 gene was cloned from potato cultivars"Atlantic"and"Qingshu 9"by RT-PCR based on the sequencing of related transcriptional groups of potato droughts, and the bioinformatics analysis was carried out. The results showed that the gene CDS was 1 113 bp, which was a continuous gene encoding a 370 amino acid protein. StRFP2 protein did not contain signal peptide sequence, and it was mainly distributed in mitochondria. StRFP2 protein contained a typical RING-H2 conserved domain, and the RING-H2 conserved domains of "Atlantic"and"Qingshu 9"had not been mutated. The sequence of "Atlantic"and "Qingshu 9"StRFP2 CDS was highly homologous and the homology reached 98.20%. Amino acid sequence evolution analysis indicated that StRFP2 was closest to Solanum pennellii and Solanum lycopersicum. Spatial three-dimensional structure analysis found that StRFP2 of"Atlantic"and" Qingshu 9"had two Zn~(2+), but the folding methods of the two were different.
引文
Du Z.,Zhou X.,Li L.,and Su Z.,2009,plants UPS:a database of plants'ubiquitin proteasome system,BMC Genomics,10(1):227-232
Gao W.,Liu W.W.,Zhao M.,and Li W.X.,2015,NERF encodes a RING E3 ligase important for drought resistance and enhances the expression of its antisense gene NFYA5 in Arabidopsis,Nucleic Acids Res.,43(1):607-617
Hershko A.,2005,The ubiquitin system for protein degradation and some of its roles in the control of the cell-division cycle(Nobel lecture),Angew.Chem.Int.Ed.Engl.,44(37)5932-5943
Hwang S.G.,Kim J.J.,Lim S.D.,Park Y.C.,Moon J.C.,and Jang C.S.,2016,Molecular dissection of Oryza sativa salt-induced RING finger protein 1(Os SIRP1):possible involvement in the sensitivity response to salinity stress,Physiol Plant,158(2):168-179
Kikuchi A.,Huynh H.D.,Endo T.,and Watanabe K.,2015,Review of recent transgenic studies on abiotic stress tolerance and future molecular breeding in potato,Breed Science,65(1):85-102
Lim C.W.,Baek W.,and Lee S.C.,2017a,The pepper RING-type E3 ligase Ca AIRF1 regulates ABA and drought signaling via Ca ADIP1 protein phosphatase degradation,Physiol.Plant173(4):2323-2339
Lim C.W.,Park C.,Kim J.H.,Joo H.,Hong E.,and Lee S.C.2017b,Pepper Ca REL1,a ubiquitin E3 ligase,regulates drought tolerance via the ABA-signalling pathway,Science Rep.,7(1):477
Liu J.P.,Zhang C.C.,Wei C.C.,Liu X.,Wang M.G.,Yu F.F.,Xie Q.,and Tu J.M.,2016,The RING finger ubiquitin E3 ligase Os HTAS enhances heat tolerance by promoting H2O2in duced stomatal closure in rice,Plant Physiol.,170(1):429-443
Morreale F.E.,and Walden H.,2016,Types of ubiquitin ligases Cell,165(1):248-249
Qi S.L.,Lin Q.F.,Zhu H.S.,Gao F.H.,Zhang W.H.,and Hua X.J.2016,The RING finger E3 ligase Sp Ring is a positive regulator of salt stress signaling in salt-tolerant wild tomato species,Plant Cell Physiol.,57(3):528-539
Sadhukhan A.,Panda S.K.,and Sahoo L.,2014,The cowpea RING ubiquitin ligase Vu DRIP interacts with transcription factor Vu DREB2A for regulating abiotic stress responses,Plant Physiol.Biochem.,83:51-56
Shu K.,and Yang W.Y.,2017,E3 ubiquitin ligases:ubiquitous actors in plant development and abiotic stress responses,Plant Cell Physiol.,58(9):1461-1476
Stone S.L.,2014,The role of ubiquitin and the 26S proteasome in plant abiotic stress signaling,Front.Plant Sci.,5(5):135-144
Suh J.Y.,Kim S.J.,Oh T.R.,Cho S.K.,Yang S.W.,and Kim W.T.,2016,Arabidopsis toxicos en Levadura 78(At ATL78)mediates ABA-dependent ROS signaling in response to drought stress,Biochem.Biophys.Res.Commun.,469:8-14
Xia Z.L.,Liu Q.J.,Wu J.Y.,and Ding J.Q.,2012,Zm RFP1,the putative ortholog of SDIR1,encodes a RING-H2 E3 ubiquitin ligase and responds to drought stress in an ABA-dependent manner in maize,Gene,495(2):146-153
Xia Z.L.,Su X.H.,Liu J.J.,and Wang M.P.,2013,The RING-H2finger gene 1(RHF1)encodes an E3 ubiquitin ligase and participates in drought stress response in Nicotiana tabacum,Genetica,141(1-3):11-21
Zhang N.,Liu B.L.,Ma C.Y.,Zhang G.D.,Chang J.,Si H.J.,and Wang D.,2014,Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato,Mol.Biol.Rep.,41(1):505-517
Zheng N.,and Shabek N.,2017,Ubiquitin ligases:structure,function,and regulation,Annu.Rev.Biochem.,86:129-157
Gao W.,Liu W.W.,Zhao M.,and Li W.X.,2015,NERF encodes a RING E3 ligase important for drought resistance and enhances the expression of its antisense gene NFYA5 in Arabidopsis,Nucleic Acids Res.,43(1):607-617
Hershko A.,2005,The ubiquitin system for protein degradation and some of its roles in the control of the cell-division cycle(Nobel lecture),Angew.Chem.Int.Ed.Engl.,44(37)5932-5943
Hwang S.G.,Kim J.J.,Lim S.D.,Park Y.C.,Moon J.C.,and Jang C.S.,2016,Molecular dissection of Oryza sativa salt-induced RING finger protein 1(Os SIRP1):possible involvement in the sensitivity response to salinity stress,Physiol Plant,158(2):168-179
Kikuchi A.,Huynh H.D.,Endo T.,and Watanabe K.,2015,Review of recent transgenic studies on abiotic stress tolerance and future molecular breeding in potato,Breed Science,65(1):85-102
Lim C.W.,Baek W.,and Lee S.C.,2017a,The pepper RING-type E3 ligase Ca AIRF1 regulates ABA and drought signaling via Ca ADIP1 protein phosphatase degradation,Physiol.Plant173(4):2323-2339
Lim C.W.,Park C.,Kim J.H.,Joo H.,Hong E.,and Lee S.C.2017b,Pepper Ca REL1,a ubiquitin E3 ligase,regulates drought tolerance via the ABA-signalling pathway,Science Rep.,7(1):477
Liu J.P.,Zhang C.C.,Wei C.C.,Liu X.,Wang M.G.,Yu F.F.,Xie Q.,and Tu J.M.,2016,The RING finger ubiquitin E3 ligase Os HTAS enhances heat tolerance by promoting H2O2in duced stomatal closure in rice,Plant Physiol.,170(1):429-443
Morreale F.E.,and Walden H.,2016,Types of ubiquitin ligases Cell,165(1):248-249
Qi S.L.,Lin Q.F.,Zhu H.S.,Gao F.H.,Zhang W.H.,and Hua X.J.2016,The RING finger E3 ligase Sp Ring is a positive regulator of salt stress signaling in salt-tolerant wild tomato species,Plant Cell Physiol.,57(3):528-539
Sadhukhan A.,Panda S.K.,and Sahoo L.,2014,The cowpea RING ubiquitin ligase Vu DRIP interacts with transcription factor Vu DREB2A for regulating abiotic stress responses,Plant Physiol.Biochem.,83:51-56
Shu K.,and Yang W.Y.,2017,E3 ubiquitin ligases:ubiquitous actors in plant development and abiotic stress responses,Plant Cell Physiol.,58(9):1461-1476
Stone S.L.,2014,The role of ubiquitin and the 26S proteasome in plant abiotic stress signaling,Front.Plant Sci.,5(5):135-144
Suh J.Y.,Kim S.J.,Oh T.R.,Cho S.K.,Yang S.W.,and Kim W.T.,2016,Arabidopsis toxicos en Levadura 78(At ATL78)mediates ABA-dependent ROS signaling in response to drought stress,Biochem.Biophys.Res.Commun.,469:8-14
Xia Z.L.,Liu Q.J.,Wu J.Y.,and Ding J.Q.,2012,Zm RFP1,the putative ortholog of SDIR1,encodes a RING-H2 E3 ubiquitin ligase and responds to drought stress in an ABA-dependent manner in maize,Gene,495(2):146-153
Xia Z.L.,Su X.H.,Liu J.J.,and Wang M.P.,2013,The RING-H2finger gene 1(RHF1)encodes an E3 ubiquitin ligase and participates in drought stress response in Nicotiana tabacum,Genetica,141(1-3):11-21
Zhang N.,Liu B.L.,Ma C.Y.,Zhang G.D.,Chang J.,Si H.J.,and Wang D.,2014,Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato,Mol.Biol.Rep.,41(1):505-517
Zheng N.,and Shabek N.,2017,Ubiquitin ligases:structure,function,and regulation,Annu.Rev.Biochem.,86:129-157