中粒咖啡萜类合成酶基因家族的生物信息学分析
收稿日期: 2015-02-12
录用日期: 2015-06-23
网络出版日期: 2016-03-31
基金资助
国家自然科学基金(31370329);中央高校基本科研业务费(GK201403004)
Bioinformatics Analysis of the TPS Gene Family in Coffee canephora
Received date: 2015-02-12
Accepted date: 2015-06-23
Online published: 2016-03-31
萜类化合物具有重要的生理、生态作用和药用价值, 萜类合成酶(TPS)是合成萜类化合物的关键酶。通过整合中粒咖啡(Coffee canephora)的基因组和转录组数据, 利用生物信息学方法, 鉴定出43个萜类合成酶全长基因, 并对这些基因的分子进化、结构、复制、表达及功能分化的机理进行了探究。 结果表明, 中粒咖啡萜类合成酶基因可以分为5个亚家族(a、b、c、e/f、g), 不同亚家族的基因结构差异很大; 串联复制是基因家族扩增的主要原因; 表达分析结果表明, 萜类合成酶基因在不同组织中的表达差异明显; 中粒咖啡萜类合成酶基因启动子区的顺式调控元件可能与基因的功能分化相关; 不同亚家族之间的功能差异主要由亚家族特异的氨基酸决定。
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 . DOI: 10.11983/CBB15022
Terpenoids are catalyzed by terpenoid synthase and have important physiological, ecological and medicinal value. By integrating data for the Coffee canephora genome and transcriptome, terpenoid synthase genes from C. canephora were identified. Then, the molecular evolution, structure, duplication and expression pattern of the genes were analyzed. Finally, functional differentiation among the terpenoid synthase subfamilies was investigated. C. canephora contains 43 full-length terpenoid synthase genes, which can be divided into 5 subfamilies (a, b, c, e/f, g), with largely different gene structure. Amplification of the genes is mainly caused by tandem duplication. Also the expression pattern of C. canephora terpenoid synthases differs in different tissues. Functional differentiation between each terpenoid synthase subfamily may have several reasons; cis-regulatory elements in the gene promoter region may be strongly related to functional differentiation and the differentiation is mainly caused by the subfamily-specific amino acid.
| [1] | 郭安源, 朱其慧, 陈新, 罗静初 (2007). GSDS: 基因结构显示系统. 遗传 29, 1023-1026. |
| [2] | Argüello-Astorga GR, Herrera-Estrella LR (1996). Ancestral multipartite units in light-responsive plant promoters have structural features correlating with specific phototransduction pathways. Plant Physiol 112, 1151-1166. |
| [3] | Aubourg S, Lecharny A, Bohlmann J (2002). Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana. Mol Genet Genomics 267, 730-745. |
| [4] | Bohlmann J, Meyer-Gauen G, Croteau R (1998). Plant terpenoid synthases: molecular biology and phylogenetic analysis. Proc Natl Acad Sci USA 95, 4126-4133. |
| [5] | Cardenas C, Quesada AR, Medina MA (2011). Antiangio- genic and anti-inflammatory properties of kahweol, a coffee diterpene. PLoS One 6, e23407. |
| [6] | Chartier A, Beaumesnil M, de Oliveira AL, Elfakir C, Bostyn S (2013). Optimization of the isolation and quantitation of kahweol and cafestol in green coffee oil. Talanta 117, 102-111. |
| [7] | Chen F, Tholl D, Bohlmann J, Pichersky E (2011). The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified through out the kingdom. Plant J 66, 212-229. |
| [8] | Chen H, Li G, K?llner TG, Jia Q, Gershenzon J, Chen F (2014). Positive Darwinian selection is a driving force for the diversification of terpenoid biosynthesis in the genus Oryza. BMC Plant Biol 14, 239. |
| [9] | Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Jo?t T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Mu?oz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono RM, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama MR, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P (2014). The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345, 1181-1184. |
| [10] | Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G (2015). The coffee genome hub: a resource for coffee genomes. Nucleic Acids Res 43, D1028-D1035. |
| [11] | Eddy SR (1998). Profile hidden Markov models. Bioinformatics 14, 755-763. |
| [12] | Falara V, Akhtar T, Nguyen TT, Spyropoulou EA, Bleeker PM, Schauvinhold I, Matsuba Y, Bonini ME, Schilmiller AL, Last RL, Schuurink RC, Pichersky E (2011). The tomato terpene synthase gene family. Plant Physiol 157, 770-789. |
| [13] | Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006). Pfam: clans, web tools and services. Nucleic Acids Res 34, D247-D251. |
| [14] | Gu X (1999). Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol 16, 1664-1674. |
| [15] | Gu X (2006). A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol 23, 1937-1945. |
| [16] | Gu X, Zou Y, Su Z, Huang W, Zhou Z, Arendsee Z, Zeng Y (2013). An update of DIVERGE software for functional divergence analysis of protein family. Mol Biol Evol 30, 1713-1719. |
| [17] | Gubler F, Jacobsen JV (1992). Gibberellin-responsive ele- ments in the promoter of a barley high-pI alphaamylase gene. Plant Cell 4, 1435-1441. |
| [18] | Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999). Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27, 297-300. |
| [19] | Irmisch S, Jiang Y, Chen F, Gershenzon J, Kollner TG (2014). Terpene synthases and their contribution to herbivore-induced volatile emission in western balsam poplar (Populus trichocarpa). BMC Plant Biol 14, 270. |
| [20] | Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S (2014). InterProScan 5: genome-scale protein function classification. Bioinforma- tics 30, 1236-1240. |
| [21] | Katoh K, Misawa K, Kuma K, Miyata T (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30, 3059-3066. |
| [22] | Kessler A, Baldwin IT (2001). Defensive function of herbivore-induced plant volatile emissions in nature. Science 291, 2141-2144. |
| [23] | Lam LK, Sparnins VL, Wattenberg LW (1982). Isolation and identification of kahweol palmitate and cafestol pa- lmitate as active constituents of green coffee beans that enhance glutathione S-transferase activity in the mouse. Cancer Res 42, 1193-1198. |
| [24] | Lee KJ, Choi JH, Jeong HG (2007). Hepatoprotective and antioxidant effects of the coffee diterpenes kahweol and cafestol on carbon tetrachloride-induced liver damage in mice. Food Chem Toxicol 45, 2118-2125. |
| [25] | Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002). PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30, 325-327. |
| [26] | Liu J, Huang F, Wang X, Zhang M, Zheng R, Wang J, Yu D (2014). Genome-wide analysis of terpene synthases in soybean: functional characterization of GmTPS3. Gene 544, 83-92. |
| [27] | Liu Y, Jiang HY, Chen WJ, Qian YX, Ma Q, Cheng BJ, Zhu SW (2011). Genome-wide analysis of the auxin response factor (ARF) gene family in maize (Zea mays). Plant Gro- wth Regul 63, 225-234. |
| [28] | Lois R, Dietrich A, Hahlbrock K, Schulz W (1989). A phenylalanine ammonia-lyase gene from parsley: structure, regulation and identification of elicitor and light responsive cis-acting elements. EMBO J 8, 1641-1648. |
| [29] | Martin DM, Aubourg S, Schouwey MB, Daviet L, Schalk M, Toub O, Lund ST, Bohlmann J (2010). Functional annotation, genome organization and phylogeny of the grapevine (Vitis vinifera) terpene synthase gene family based on genome assembly, FLcDNA cloning, and enzyme assays. BMC Plant Biol 10, 226. |
| [30] | Menkens AE, Schindler U, Cashmore AR (1995). The G-box: a ubiquitous regulatory DNA element in plants bound by the GBF family of bZIP proteins. Trends Biochem Sci 20, 506-510. |
| [31] | Parker MT, Zhong Y, Dai X, Wang S, Zhao P (2014). Comparative genomic and transcriptomic analysis of terpene synthases in Arabidopsis and Medicago. IET Syst Biol 8, 146-153. |
| [32] | Pastuglia M, Roby D, Dumas C, Cock JM (1997). Rapid induction by wounding and bacterial infection of an S gene family receptor-like kinase gene in Brassica oleracea. Plant Cell 9, 49-60. |
| [33] | Pichersky E, Bernatzky R, Tanksley SD, Breidenbach RB, Kausch AP, Cashmore AR (1985). Molecular characterization and genetic mapping of two clusters of genes encoding chlorophyll a/b-binding proteins in Lycopersicon esculentum (tomato). Gene 40, 247-258. |
| [34] | Pichersky E, Gershenzon J (2002). The formation and function of plant volatiles: perfumes for pollinator attraction and defense. Curr Opin Plant Biol 5, 237-243. |
| [35] | Pichersky E, Noel JP, Dudareva N (2006). Biosynthesis of plant volatiles: nature’s diversity and ingenuity. Science 311, 808-811. |
| [36] | Rebers M, Kaneta T, Kawaide H, Yamaguchi S, Yang YY, Imai R, Sekimoto H, Kamiya Y (1999). Regulation of gibberellin biosynthesis genes during flower and early fruit development of tomato. Plant J 17, 241-250. |
| [37] | Rouster J, Leah R, Mundy J, Cameron-Mills V (1997). Identification of a methyl jasmonate-responsive region in the promoter of a lipoxygenase 1 gene expressed in barley grain. Plant J 11, 513-523. |
| [38] | Shu Y, Liu JQ, Peng XR, Wan LS, Zhou L, Zhang T, Qiu MH (2014). Characterization of diterpenoid glucosides in roasted puer coffee beans. J Agric Food Chem 62, 2631-2637. |
| [39] | Simpson SD, Nakashima K, Narusaka Y, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003). Two different novel cis-acting elements of erd1, a clpA homologous Arabidopsis gene function in induction by dehydration stress and dark-induced senescence. Plant J 33, 259-270. |
| [40] | Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006). Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7, 1-12. |
| [41] | Takaiwa F, Oono K, Wing D, Kato A (1991). Sequence of three members and expression of a new major subfamily of glutelin genes from rice. Plant Mol Biol 17, 875-885. |
| [42] | Wu C, Washida H, Onodera Y, Harada K, Takaiwa F (2000). Quantitative nature of the Prolamin-box, ACGT and AACA motifs in a rice glutelin gene promoter: minimal cis-element requirements for endosperm-specific gene ex- pression. Plant J 23, 415-421. |
| [43] | Yang CQ, Wu XM, Ruan JX, Hu WL, Mao YB, Chen XY, Wang LJ (2013). Isolation and characterization of terpene synthases in cotton (Gossypium hirsutum). Phytochemistry 96, 46-56. |
| [44] | Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2015). The I-TASSER Suite: protein structure and function prediction. Nat Methods 12, 7-8. |
| [45] | Yin G, Xu H, Xiao S, Qin Y, Li Y, Yan Y, Hu Y (2013). The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups. BMC Plant Biol 13, 148. |
/
| 〈 |
|
〉 |
首页