梨萜类合成酶基因家族生物信息学与表达模式分析

doi:10.13560/j.cnki.biotech.bull.1985.2017-0804

摘要/Abstract

摘要： 萜类合成酶（Terpene synthases,TPS）是萜类化合物合成过程中的关键酶。基于梨（Pyrus bretschneideri）全基因组数据库,采用生物信息学和分子生物学方法,对梨TPS基因家族进行鉴定和亚家族分类,研究梨TPS基因的结构及编码蛋白质性质和表达模式。共鉴定获得33个萜类合成酶基因家族成员,聚类为5个亚家族,其中,TPS-a亚家族成员数量最多,包含4-7个外显子;主要定位于细胞质,少数分布在线粒体、叶绿体和内质网等;梨TPS蛋白均为亲水性蛋白,α-螺旋和无规卷曲是其二级结构主要组成元件,β-折叠和延伸链散布其中;TPS-a中保守基序个数相对较多,TPS-e/f相对较少;各亚族内蛋白质在三级结构上高度相似。除PbrTPS24外,其余9个TPS基因在根、茎、幼叶和幼芽中均有表达,并且不同的基因在不同部位高表达,PbrTPS存在组织特异性表达。

关键词: 梨, 萜类合成酶, TPS基因家族, 生物信息学, 表达分析

Abstract: Terpene synthases（TPS）are the key enzymes in the synthesis of terpenoids. The TPS gene family was identified and subfamilies were clustered based on the genome-wide database of Pyrus bretschneideri,then the structure of TPS genes,the characteristics of encoded proteins and expression patterns were analyzed by means of bioinformatics and molecular biology. The results showed that 33 TPS gene family members were identified and they were clustered into five subfamilies. Among them,TPS-a subfamily had the largest number of members and owned 4-7 exons;most of TPS proteins were located in cytoplasm,and a few of them were distributed in mitochondria,chloroplasts and endoplasmic reticulum. All pear TPS proteins were hydrophilic proteins,the secondary structure of most TPS proteins was α-helix and random coil,and the folded and extended strands scattered in it. TPS-a subfamily had the largest number of conserved motifs and less in TPS-e/f. Proteins in each subfamily were highly similar in tertiary structure. The qRT-PCR analysis of 10 TPS genes showed that 9 PbrTPS genes except PbrTPS24 expressed in roots,stems,young leaves and sprouts,each gene expressed highly in different part,indicating that the expression of PbrTPS gene was tissue-specific.

Key words: pear, terpene synthases, TPS gene family, bioinformatics, expression analysis

赵荣荣,刘斌,郭超,刘恒,张元湖. 梨萜类合成酶基因家族生物信息学与表达模式分析[J]. 生物技术通报, 2018, 34(5): 131-141.

ZHAO Rong-rong, LIU Bin, GUO Chao, LIU Heng, ZHANG Yuan-hu. Genome-wide Identification and Expression Analysis of TPS Gene Family in Pear[J]. Biotechnology Bulletin, 2018, 34(5): 131-141.

参考文献

[1] Brown GD.The biosynthesis of artemisinin(Qinghaosu)and the phytochemistry of Artemisia annua L. (Qinghao)[J]. Molecules, 2010, 15(11):7603-7698.
[2] Cragg GM.Paclitaxel(Taxol):a success story with valuable lessons for natural product drug discovery and development[J]. Medicinal Research Reviews, 1998, 29(49):315-331.
[3] Rohmer M.The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants[J]. Natural Product Reports, 1999, 16(5):565-574.
[4] Schwender J, Zeidler J, Gröner R, et al.Incorporation of 1-deoxy-D-xylulose into isoprene and phytol by higher plants and algae[J]. FEBS letters, 1997, 414(1):129-134.
[5] Rohmer M, Knani M, Simonin P, et al.Isoprenoid biosynthesis in bacteria:a novel pathway for the early steps leading to isopentenyl diphosphate[J]. Biochemical Journal, 1993, 295(2):517-524.
[6] Aubourg S, Lecharny A, Bohlmann LJ.Genomic analysis of the terpenoid synthase(AtTPS)gene family of Arabidopsis thaliana[J]. Molecular Genetics and Genomics, 2002, 267(6):730-745.
[7] Chen H, Li G, Köllner TG, et al.Positive Darwinian selection is a driving force for the diversification of terpenoid biosynthesis in the genus Oryza[J]. BMC Plant Biology, 2014, 14(1):239.
[8] Falara V, Akhtar TA, Nguyen TT, et al.The tomato terpene synthase gene family[J]. Plant Physiology, 2011, 157(2):770-789.
[9] Irmisch S, Jiang Y, Chen F, et al.Terpene synthases and their contribution to herbivore-induced volatile emission in western balsam poplar(Populus trichocarpa)[J]. BMC Plant Biology, 2014, 14(1):270.
[10] Zavarin E, Snajberk K, Critchfield WB.Terpenoid chemosystematic studies of Abies grandis[J]. Biochemical Systematics & Ecology, 1977, 5(2):81-93.
[11] Matarese F, Scalabrelli G, D’Onofrio C. Analysis of the expression of terpene synthase genes in relation to aroma content in two aromatic Vitis vinifera varieties[J]. Functional Plant Biology, 2013, 40(6):552-565.
[12] Nieuwenhuizen NJ, Green SA, Chen X, et al.Functional genomics reveals that a compact terpene synthase gene family can account for terpene volatile production in apple.[J]. Plant Physiology, 2013, 161(2):787-804.
[13] Wu J, Wang Z, Shi Z, et al.The genome of the pear(Pyrus bretschneideri Rehd.)[J]. Genome Res, 2013, 23(2):396-408.
[14] Bohlmann J, Meyer-Gauen G, Croteau R.Plant terpenoid synthases:Molecular biology and phylogenetic analysis[J]. Proc Natl Acad Sci USA, 1998, 95(8):4126-4133.
[15] Trapp SC, Croteau RB.Genomic organization of plant terpene synthases and molecular evolutionary implications[J]. Genetics, 2001, 158(2):811-832.
[16] Altschul SF, Gish W, Miller W, et al.Basic local alignment search tool[J]. Journal of Molecular Biology, 1990, 215(3):403-410.
[17] Schultz J, Milpetz F, Bork P, et al.SMART, a simple modular architecture research tool:identification of signaling domains[J]. Proc Natl Acad Sci USA, 1998, 95(11):5857-5864.
[18] Tamura K, Peterson D, Peterson N, et al.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods[J]. Molecular Biology & Evolution, 2014, 28(10):2731-2739.
[19] Bailey TL, Boden M, Buske F A, et al.MEME suite:tools for motif discovery and searching[J]. Nucleic acids research, 2009, 37
(Web Server issue):202-208.
[20] Kiefer F, Arnold K, Künzli M, et al.The SWISS-MODEL repository and associated resources[J]. Nucleic Acids Research, 2009, 37(Database issue):387-392.
[21] Martin DM, Fäldt J, Bohlmann J.Functional characterization of nine Norway Spruce TPS genes and evolution of gymnosperm terpene synthases of the TPS-d subfamily[J]. Plant Physiology, 2004, 135(4):1908-1927.
[22] Martin DM, Aubourg S, Schouwey MB, et al.Functional annotation, genome organization and phylogeny of the grapevine(Vitis vinifera)terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays[J]. BMC Plant Biology, 2010, 10(1):1-22.
[23] 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.
[24] 王淋, 乌云塔娜, 叶生晶. 杜仲EuHMGRS基因家族的鉴定及生物信息学分析[J]. 经济林研究, 2013, 31(4):16-24.
[25] Yoshikuni Y, Keasling JD.Pathway engineering by designed divergent evolution[J]. Current Opinion in Chemical Biology, 2007, 11(2):233-239.
[26] Chen F, Tholl D, Bohlmann J, et al.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 Journal for Cell & Molecular Biology, 2011, 66(1):212-229.
[27] Liu J, Huang F, Wang X, et al.Genome-wide analysis of terpene synthases in soybean:functional characterization of GmTPS3[J]. Gene, 2014, 544(1):83-92.
[28] Parker MT, Zhong Y, Dai X, et al.Comparative genomic and transcriptomic analysis of terpene synthases in Arabidopsis and Medicago[J]. Systems Biology Iet, 2014, 8(4):146-153.