毛竹萜类合成酶基因家族序列鉴定与表达分析
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摘要
通过生物信息学方法,对毛竹(Phyllostachys edulis(Carrière)J.Houzeau)TPS基因家族的成员进行鉴定,并对其编码蛋白的理化性质、基因结构、进化关系、蛋白结构、启动子元件及表达模式进行了分析。结果表明,毛竹全基因组含有14个TPS候选基因,大小为693~2439 bp。编码蛋白等电点为5.08~8.17。系统发育分析结果显示,毛竹含有TPS-a、TPS-b、TPS-e/f、和TPS-g 4个亚家族,成员数目分别为6、5、2、1个。TPS蛋白质二级结构中,α-螺旋和无规则卷曲所占比重较大;毛竹TPS基因家族各成员蛋白三维结构比较相似。基因启动子分析共获得50个调控元件,可分为6大类,其中光响应相关元件数量最多,共包含17个顺式调控元件。基于转录组测序数据构建的基因表达谱热图分析结果表明,Pe TPS在叶、花和笋等7个组织中的表达差异明显,表现出组织特异性,其中Pe TPS9仅在早花期花序中表达,Pe TPS8仅在叶中表达。
To explore the characteristics and evolutionary relationships of the TPS family in Phyllostachys edulis, we identified the TPS genes in P. edulis and analyzed their physicochemical properties,gene structure,evolutionary relationship,protein secondary and tertiary structure, promoter elements, and expression patterns based on bioinformatics methods. A total of 14 TPS genes were identified in P. edulis,which ranged in size from 693 to2439 bp. The encoding protein isoelectric points ranged from 5. 08 to 8. 17. Phylogenetic analysis suggested that the TPS family members from P. edulis could be divided into four subfamilies(a,b,e/f,g),with considerably different gene structures. The α-helix and random coil components in these proteins were dominant elements,and the predicted tertiary structure of the proteins in the Pe TPS gene family were similar. We identified 50 cis-acting regulatory elements through promotor analyses, which were classified into six categories according to their function. The heatmap of gene expression based on the RNA-seq datarevealed that the Pe TPS genes were expressed differently among seven different tissues,including leaves,flowers,and shoots,and thus exhibited tissue-specific expression patterns.Pe TPS9 was only expressed in the early panicle and Pe TPS8 was only expressed in the leaves.This research provides a theoretical foundation for deeper analysis of the function of the TPS genes in P. edulis.
To explore the characteristics and evolutionary relationships of the TPS family in Phyllostachys edulis, we identified the TPS genes in P. edulis and analyzed their physicochemical properties,gene structure,evolutionary relationship,protein secondary and tertiary structure, promoter elements, and expression patterns based on bioinformatics methods. A total of 14 TPS genes were identified in P. edulis,which ranged in size from 693 to2439 bp. The encoding protein isoelectric points ranged from 5. 08 to 8. 17. Phylogenetic analysis suggested that the TPS family members from P. edulis could be divided into four subfamilies(a,b,e/f,g),with considerably different gene structures. The α-helix and random coil components in these proteins were dominant elements,and the predicted tertiary structure of the proteins in the Pe TPS gene family were similar. We identified 50 cis-acting regulatory elements through promotor analyses, which were classified into six categories according to their function. The heatmap of gene expression based on the RNA-seq datarevealed that the Pe TPS genes were expressed differently among seven different tissues,including leaves,flowers,and shoots,and thus exhibited tissue-specific expression patterns.Pe TPS9 was only expressed in the early panicle and Pe TPS8 was only expressed in the leaves.This research provides a theoretical foundation for deeper analysis of the function of the TPS genes in P. edulis.
引文
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[13]Falara V,Akhtar TA,Nguyen TT,Spyropoulou EA,Bleeker PM,et al.The tomato terpene synthase gene family[J].Plant Physiol,2011,157(2):770-789.
[14]Peng Z,Lu Y,Li L,Zhao Q,Feng Q,et al.The draft genome of the fast-growing non-timber forest species moso bamboo(Phyllostachys heterocycla)[J].Nat Genet,2013,45(4):456.
[15]张英,汤坚,袁身淑,刘扬岷,王林祥.竹叶精油和头香的CGC-MS-DS研究[J].天然产物研究与开发,1998,10(4):38-44.Zhang Y,Tang J,Yuan SS,Liu YM,Wang LX.Analysis on the chemical components in the essential oil and headspace volatile of bamboo leaves[J].Natural Product Research and Development,1998,10(4):38-44.
[16]Toub O,Michel S,Laurent D,Schouwey MB,Sébastien A,et al.Genome size and sequence composition of moso bamboo:A comparative study[J].Sci China Ser C,2007,50(5):700-705.
[17]郭起荣,周建梅,孙立方,廉超,冯云,等.毛竹的花序发育研究[J].植物科学学报,2015,33(1):19-24.Guo QR,Zhou JM,Sun LF,Lian C,Feng Y,et al.Development of Phyllostachs edulis inflorescences[J].Plant Science Journal,2015,33(1):19-24.
[18]Toub O,Michel S,Laurent D,Schouwey MB,Sébastien A,et al.Genome-wide analysis of the AP2/ERF transcription factors family and the expression patterns of DREB genes in moso bamboo(Phyllostachys edulis)[J].PLo S One,2015,10(5):e0126657.
[19]Sun HY,Li LC,Lou YF,Zhao HS,Gao ZM.Genomewide identification and characterization of aquaporin gene family in moso bamboo(Phyllostachys edulis)[J].Mol Biol Rep,2016,43(5):437-450.
[20]Wu M,Li Y,Chen DM,Liu HL,Zhu DY,Xiang Y.Genome-wide identification and expression analysis of the IQD gene family in moso bamboo(Phyllostachys edulis)[J].Sci Rep,2016,6:24520.
[21]Bai Q,Hou D,Li L,Cheng Z,Ge W,et al.Genomewide analysis and expression characteristics of small auxin-up RNA(SAUR)genes in moso bamboo(Phyllostachys edulis)[J].Genome,2016,60(4):325.
[22]Chen DM,Chen Z,Wu M,Wang Y,Wang YJ,et al.Genome-wide identification and expression analysis of the HD-Zip gene family in moso bamboo(Phyllostachys edulis)[J].J Plant Growth Regul,2017,36(2):323-337.
[23]Pan F,Wang Y,Liu H,Wu M,Chu W,et al.Genomewide identification and expression analysis of SBP-like transcription factor genes in moso bamboo(Phyllostachys edulis)[J].BMC Genomics,2017,18(1):486.
[24]Pan F,Wang Y,Liu H,Wu M,Chu W,et al.Genomewide analysis of the AAAP gene family in moso bamboo(Phyllostachys edulis)[J].BMC Plant Biol,2017,17(1):29.
[25]Eddy SR.Profile hidden Markov models[J].Bioinformatics,1998,14(9):755-763.
[26]Gasteiger E,Hoogland C,Gattiker A,Duvaud S,Wilkins MR,et al.Protein identification and analysis tools on the Ex PASy Server[M]//Walker JM,ed.The Proteomics Protocols Handbook:Vol 1.Totowa:Humana Press,2005:571-607.
[27]Lee GW,Lee S,Chung MS,Jeong YS,Chung BY.Rice terpene synthase 20(Os TPS 20)plays an important role in producing terpene volatiles in response to abiotic stresses[J].Protoplasma,2015,252:997-1007.
[28]叶文武,王源超,窦道龙.Seq Hunter:序列搜索与分析的生物信息学软件包[J].生物信息学,2010,8(4):364-367.Ye WW,Wang YC,Dou DL.Seq Hunter:a bioinformatics toolbox for local Blast and sequence analysis[J].China Journal of Bioinformatics,2010,8(4):364-367.
[29]Lescot M,Dehais P,Thijs G,Marchal K,Moreau Y.Plant CARE,a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J].Nucleic Acids Res,2002,30(1):325-327.
[30]Higo K,Ugawa Y,Iwamoto M,Korenaga T.Plant cisacting regulatory DNA elements(PLACE)database[J].Nucleic Acids Res,1999,27(1):297-300.
[31]Menkens AE,Al E.The G-box:a ubiquitous regulatory DNA element in plants bound by the GBF family of b ZIP proteins[J].Trends Biochem Sci,1995,20(12):506-510.
[32]Argüello-Astorga GR,Herrera-Estrella LR.Ancestral multipartite units in light-responsive plant promoters have structural features correlating with specific phototransduction pathways[J].Plant Physiol,1996,112(3):1151-1166.
[33]Calvert J,Baten A,Butler J,Bronwyn B,Mervyn S.Terpene synthase genes in Melaleuca alternifolia:comparative analysis of lineage-specific subfamily variation within Myrtaceae[J].Plant Syst Evol,2017,304(3):1-11.
[34]Yamaguchi S.Gibberellin metabolism and its regulation[J].Annu Rev Plant Biol,2008,59(4):225-251.
[35]Nieuwenhuizen NJ,Green SA,Chen X,Bailleul EJ,Matich AJ,et al.Functional genomics reveals that a compact terpene synthase gene family can account for terpene volatile production in apple[J].Plant Physiol,2013,161(2):787-804.
[36]Lin YL,Lee YR,Huang WK,Chang ST,Chu FH.Characterization of S-(+)-linalool synthase from several provenances of Cinnamomum osmophloeum[J].Tree Genet Genomes,2014,10(1):75-86.
[37]Lu S,Xu R,Chen XY.Cloning and functional characterization of a beta-pinene synthase from Artemisia annua that shows a circadian pattern of expression[J].Plant Physiol,2002,130(1):477.
[38]Winzer T,Gazda V,He Z,Kaminski F,Kern M,et al.A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine[J].Science,2012,336(6089):1704-1708.
[39]Kumar S,Kempinski C,Zhuang X,Norrris A,Mafu S,Zi J.Molecular diversity of terpene synthases in the liverwort Marchantia polymorpha[J].Plant Cell,2016,28(10):2632.
[40]Yuan JS,K9llner TG,Wiggins G,Grant J,Degenhardt J,Chen F.Molecular and genomic basis of volatile-mediated indirect defense against insects in rice[J].Plant Mol Biol,2010,55(3):491-503.
[41]Chen X,Wang Y,Sun J,Wang J,Xun H,Tang F.Cloning,expression and functional characterization of two sesquiterpene synthase genes from moso bamboo(Phyllostachys edulis)[J].Protein Expres Purif,2016,120:1-6.
[2]Loreto F,Forster A,Durr M,Seufert G.On the monoterpene emission under heat stress and on the increased thermotolerance of leaves of Quercusi lex L.fumigated with selected monoterpenes[J].Plant Cell Environ,1998,21(1):101-107.
[3]Attaran E,Rostás M,Zeier J.Pseudomonas syringae elicits emission of the terpenoid(E,E)-4,8,12-trimethyl-1,3,7,11-tridecatetraene in Arabidopsis leaves via jasmonate signaling and expression of the terpene synthase TPS4[J].Mol Plant Microbe,2008,21(11):1482-1497.
[4]Gil M,Pontin M,Berli F,Bottini R,Piccoli P.Metabolism of terpenes in the response of grape(Vitis vinifera L.)leaf tissues to UV-B radiation[J].Phytochemistry,2012,77(15-16):89-98.
[5]Chen F,Tholl D,Bohlmann J,Pichersky E.The family of terpene synthases in plants:a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom[J].Plant Mol Biol,2011,66(1):212-229.
[6]Aubourg S,Lecharny A,Bohlmann J.Genomic analysis of the terpenoid synthase(At TPS)gene family of Arabidopsis thaliana[J].Mol Genet Genomics,2002,267(6):730-745.
[7]Toub O,Michel S,Laurent D,Schouwey MB,Sébastien A,et al.Functional annotation,genome organization and phylogeny of the Grapevine(Vitis vinifera)terpene synthase gene family based on genome assembly,FLc DNA cloning,and enzyme assays[J].BMC Plant Biol,2010,10(1):1-22.
[8]Irmisch S,Jiang Y,Chen F,Gershenzon J,Kollner TG.Terpene synthases and their contribution to herbivore-induced volatile emission in western balsam poplar(Populus trichocarpa)[J].BMC Plant Biol,2014,14(1):270.
[9]Chen H,Li G,Kollner TG,Jia Q,Gershenzon J,Chen F.Positive Darwinian selection is a driving force for the diversification of terpenoid biosynthesis in the genus Oryza[J].BMC Plant Biol,2014,14(1):239.
[10]Liu J,Huang F,Wang X,Zhang M,Zheng R,et al.Genome-wide analysis of terpene synthases in soybean:functional characterization of Gm TPS3[J].Gene,2014,544(1):83-92.
[11]Yang CQ,Wu XM,Ruan JX,Wang JL.Isolation and characterization of terpene synthases in cotton(Gossypium hirsutum)[J].Phytochemistry,2013,96(12):46-56.
[12]程甜,魏强,李广林.中粒咖啡萜类合成酶基因家族的生物信息学分析[J].植物学报,2016,51(2):235-250.Tian C,Qiang W,Li GL.Bioinformatics analysis of the TPS gene family in Coffee canephora[J].Chinese Bulletin of Botany,2016,51(2):235-250.
[13]Falara V,Akhtar TA,Nguyen TT,Spyropoulou EA,Bleeker PM,et al.The tomato terpene synthase gene family[J].Plant Physiol,2011,157(2):770-789.
[14]Peng Z,Lu Y,Li L,Zhao Q,Feng Q,et al.The draft genome of the fast-growing non-timber forest species moso bamboo(Phyllostachys heterocycla)[J].Nat Genet,2013,45(4):456.
[15]张英,汤坚,袁身淑,刘扬岷,王林祥.竹叶精油和头香的CGC-MS-DS研究[J].天然产物研究与开发,1998,10(4):38-44.Zhang Y,Tang J,Yuan SS,Liu YM,Wang LX.Analysis on the chemical components in the essential oil and headspace volatile of bamboo leaves[J].Natural Product Research and Development,1998,10(4):38-44.
[16]Toub O,Michel S,Laurent D,Schouwey MB,Sébastien A,et al.Genome size and sequence composition of moso bamboo:A comparative study[J].Sci China Ser C,2007,50(5):700-705.
[17]郭起荣,周建梅,孙立方,廉超,冯云,等.毛竹的花序发育研究[J].植物科学学报,2015,33(1):19-24.Guo QR,Zhou JM,Sun LF,Lian C,Feng Y,et al.Development of Phyllostachs edulis inflorescences[J].Plant Science Journal,2015,33(1):19-24.
[18]Toub O,Michel S,Laurent D,Schouwey MB,Sébastien A,et al.Genome-wide analysis of the AP2/ERF transcription factors family and the expression patterns of DREB genes in moso bamboo(Phyllostachys edulis)[J].PLo S One,2015,10(5):e0126657.
[19]Sun HY,Li LC,Lou YF,Zhao HS,Gao ZM.Genomewide identification and characterization of aquaporin gene family in moso bamboo(Phyllostachys edulis)[J].Mol Biol Rep,2016,43(5):437-450.
[20]Wu M,Li Y,Chen DM,Liu HL,Zhu DY,Xiang Y.Genome-wide identification and expression analysis of the IQD gene family in moso bamboo(Phyllostachys edulis)[J].Sci Rep,2016,6:24520.
[21]Bai Q,Hou D,Li L,Cheng Z,Ge W,et al.Genomewide analysis and expression characteristics of small auxin-up RNA(SAUR)genes in moso bamboo(Phyllostachys edulis)[J].Genome,2016,60(4):325.
[22]Chen DM,Chen Z,Wu M,Wang Y,Wang YJ,et al.Genome-wide identification and expression analysis of the HD-Zip gene family in moso bamboo(Phyllostachys edulis)[J].J Plant Growth Regul,2017,36(2):323-337.
[23]Pan F,Wang Y,Liu H,Wu M,Chu W,et al.Genomewide identification and expression analysis of SBP-like transcription factor genes in moso bamboo(Phyllostachys edulis)[J].BMC Genomics,2017,18(1):486.
[24]Pan F,Wang Y,Liu H,Wu M,Chu W,et al.Genomewide analysis of the AAAP gene family in moso bamboo(Phyllostachys edulis)[J].BMC Plant Biol,2017,17(1):29.
[25]Eddy SR.Profile hidden Markov models[J].Bioinformatics,1998,14(9):755-763.
[26]Gasteiger E,Hoogland C,Gattiker A,Duvaud S,Wilkins MR,et al.Protein identification and analysis tools on the Ex PASy Server[M]//Walker JM,ed.The Proteomics Protocols Handbook:Vol 1.Totowa:Humana Press,2005:571-607.
[27]Lee GW,Lee S,Chung MS,Jeong YS,Chung BY.Rice terpene synthase 20(Os TPS 20)plays an important role in producing terpene volatiles in response to abiotic stresses[J].Protoplasma,2015,252:997-1007.
[28]叶文武,王源超,窦道龙.Seq Hunter:序列搜索与分析的生物信息学软件包[J].生物信息学,2010,8(4):364-367.Ye WW,Wang YC,Dou DL.Seq Hunter:a bioinformatics toolbox for local Blast and sequence analysis[J].China Journal of Bioinformatics,2010,8(4):364-367.
[29]Lescot M,Dehais P,Thijs G,Marchal K,Moreau Y.Plant CARE,a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J].Nucleic Acids Res,2002,30(1):325-327.
[30]Higo K,Ugawa Y,Iwamoto M,Korenaga T.Plant cisacting regulatory DNA elements(PLACE)database[J].Nucleic Acids Res,1999,27(1):297-300.
[31]Menkens AE,Al E.The G-box:a ubiquitous regulatory DNA element in plants bound by the GBF family of b ZIP proteins[J].Trends Biochem Sci,1995,20(12):506-510.
[32]Argüello-Astorga GR,Herrera-Estrella LR.Ancestral multipartite units in light-responsive plant promoters have structural features correlating with specific phototransduction pathways[J].Plant Physiol,1996,112(3):1151-1166.
[33]Calvert J,Baten A,Butler J,Bronwyn B,Mervyn S.Terpene synthase genes in Melaleuca alternifolia:comparative analysis of lineage-specific subfamily variation within Myrtaceae[J].Plant Syst Evol,2017,304(3):1-11.
[34]Yamaguchi S.Gibberellin metabolism and its regulation[J].Annu Rev Plant Biol,2008,59(4):225-251.
[35]Nieuwenhuizen NJ,Green SA,Chen X,Bailleul EJ,Matich AJ,et al.Functional genomics reveals that a compact terpene synthase gene family can account for terpene volatile production in apple[J].Plant Physiol,2013,161(2):787-804.
[36]Lin YL,Lee YR,Huang WK,Chang ST,Chu FH.Characterization of S-(+)-linalool synthase from several provenances of Cinnamomum osmophloeum[J].Tree Genet Genomes,2014,10(1):75-86.
[37]Lu S,Xu R,Chen XY.Cloning and functional characterization of a beta-pinene synthase from Artemisia annua that shows a circadian pattern of expression[J].Plant Physiol,2002,130(1):477.
[38]Winzer T,Gazda V,He Z,Kaminski F,Kern M,et al.A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine[J].Science,2012,336(6089):1704-1708.
[39]Kumar S,Kempinski C,Zhuang X,Norrris A,Mafu S,Zi J.Molecular diversity of terpene synthases in the liverwort Marchantia polymorpha[J].Plant Cell,2016,28(10):2632.
[40]Yuan JS,K9llner TG,Wiggins G,Grant J,Degenhardt J,Chen F.Molecular and genomic basis of volatile-mediated indirect defense against insects in rice[J].Plant Mol Biol,2010,55(3):491-503.
[41]Chen X,Wang Y,Sun J,Wang J,Xun H,Tang F.Cloning,expression and functional characterization of two sesquiterpene synthase genes from moso bamboo(Phyllostachys edulis)[J].Protein Expres Purif,2016,120:1-6.