Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis
详细信息 查看全文
- 作者：Yanhong Xu (1)
Zheng Zhang (1) (2)
Mengxi Wang (3)
Jianhe Wei (1) (2)
Hongjiang Chen (2)
Zhihui Gao (1)
Chun Sui (1)
Hongmei Luo (1)
Xingli Zhang (1)
Yun Yang (2)
Hui Meng (2)
Wenlan Li (3) - 关键词：Agarwood ; Aquilaria sinensis ; GC ; MS ; Sesquiterpenes ; Transcriptome ; Wound signal transduction
- 刊名：BMC Genomics
- 出版年：2013
- 出版时间：December 2013
- 年：2013
- 卷：14
- 期：1
- 全文大小：743KB
- 参考文献：1. China pharmacopoeia Committee: / The Pharmacopoeia of People’s Republic of China(I). Beijing: Chemical Industry Press; 2010.
2. Hashimoto K, Nakahara S, Inoue T, Sumida Y, Takahashi M: A new chromone from agarwood and pyrolysis products of chromone derivatives. / Chem Pharm Bull 1985,33(11):5088-091. CrossRef
3. Ishihara M, Tsuneya T, Uneyama K: Fragrant sesquiterpenes from agarwood. / Phytochemistry 1993, 33:1147-155. CrossRef
4. Yagura T, Ito M, Kiuchi F, Honda G, Shimada Y: Four new 2-(2-phenylethyl) chromone derivatives from withered wood of Aquilaria sinensis . / Chem Pharm Bull(Tokyo) 2003, 51:560-64. CrossRef
5. Kumeta Y, Ito M: Characterization of δ-guaiene synthases from cultured cells of Aquilaria , responsible for the formation of the sesquiterpenes in agarwood. / Plant Physiol 2010, 154:1998-007. CrossRef
6. Chen HQ, Yang Y, Xue J, Wei JH, Zhang Z, Chen HJ: Comparison of compositions and antimicrobial activities of essential oils from chemically stimulated agarwood, wild agarwood and healthy Aquilaria sinensis (Lour.) Gilg trees. / Molecules 2011, 16:4884-896. CrossRef
7. Chen HQ, Wei JH, Yang JS, Zhang Z, Yang Y: Chemical constituents of agarwood originating from the endemic genus Aquilaria plants. / Chem Biodivers 2012,9(2):236-50. CrossRef
8. Gardner RG, Hampton RY: A highly conserved signal controls degradation of 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase in eukaryotes. / J Biol Chem 1999,274(44):31671-1678. CrossRef
9. Shang CH, Zhu F, Li N, OU-Yang X, Shi L, Zhao MW, Li YX: Cloning and characterization of a gene encoding HMG-CoA reductase from Ganoderma lucidum and its functional identification in yeast. / Biosci Biotech Bioch 2008,72(5):1333-339. CrossRef
10. Rohmer M: The discovery of a mevalonate independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. / Nat Prod Rep 1999, 16:565-74. CrossRef
11. Xu YH, Wang JW, Wang S, Wang JY, Chen XY: Characterization of GaWRKY1, a cotton transcription factor that regulates the sesquiterpene synthase gene (+)- δ -cadinene synthase-A. / Plant Physiol 2004, 135:507-15. CrossRef
12. Ma DM, Pu GB, Lei CY, Ma LQ, Wang HH, Guo YW, Chen JL, Du ZG, Wang H, Li GF, Ye HC, Liu BY: Isolation and characterization of AaWRKY1, an Artemisia annua transcription factor that regulates the Amorpha-4,11-diene synthase gene, a key gene of artemisinin biosynthesis. / Plant Cell Physiol 2009,50(12):2146-161. CrossRef
13. Hong GJ, Xue XY, Mao YB, Wang LJ, Chen XY: Arabidopsis MYC2 interacts with DELLA proteins in regulating sesquiterpene synthase gene expression. / Plant Cell 2012, 24:2635-648. CrossRef
14. Ng LT, Chang YS, Kadir AA: A review on agar (gaharu) producing Aquilaria species. / J Trop Forest Products 1997,2(2):272-85.
15. Itoh T, Tabata Y, Widjaja E, Mulyaningsih T, Parman , Wiriadinata H, Mandang YI: Structure and artificial induction of aloe wood. The Fifth Pacific Regional Wood Anatomy Conference. Abstracts of Papers and Posters. / IAWA Journal 2002,23(4):466-67.
16. Pojanagaroon S, Kaewrak C: Mechanical methods to stimulate aloes wood formation in Aquilaria crassna Pierre ex H.Lec. (Kritsana) trees. / ISHS Acta Horticuturae 2005, 676:161-66.
17. Persoon GA: Growing 'the wood of the gods': agarwood production in Southeast Asia. / Smallholder Tree Growing for Rural Development and Environmental Service. Advance in Agroforesty 2008, 5:245-62. CrossRef
18. Zhang Z, Yang Y, Wei JH, Meng H, Sui C, Chen HQ: Advances in studies on mechanism of agarwood formation in Aquilaria sinensis and its hypothesis of agarwood formation induced by defense response. / Chinese Traditional and Herbal Drugs 2010,41(1):156-59.
19. Romualdi C, Bortoluzzi S, DAlessi F, Danieli GA: IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. / Physiol Genomics 2003,12(2):159-62.
20. Matsushita Y, Kang WK, Charlwood BV: Cloning and analysis of a cDNA encoding farnesyl diphosphate synthase from Artemisia annua . / Gene 1996, 172:207-09. CrossRef
21. Delourme D, Lacroute F, Karst F: Cloning of an Arabidopsis thaliana cDNA coding for farnesyl diphosphate synthase by functional complementation in yeast. / Plant Mol Biol 1994, 26:1867-873. CrossRef
22. Cao XY, Yin T, Miao Q, Li HG, Ju XY, Sun Y, Jiang JH: Molecular characterization and expression analysis of a gene encoding for farnesyl diphosphate synthase from Euphorbia pekinensis Rupr. / Mol Biol Rep 2012,39(2):1487-492. CrossRef
23. Kumeta Y, Ito M: Genomic organization of δ-guaiene synthase genes in Aquilaria crassna and its possible use for the identification of Aquilaria species. / J Nat Med 2011,65(3):508-13. CrossRef
24. Reymond P, Farmer EE: Jasmonate and salicylate as global signals for defense gene expression. / Curr Opin Plant Biol 1998, 1:404-11. CrossRef
25. Leon J, Rojo E, Sánchez-Serrano JJ: Wound signalling in plants. / J Exp Bot 2001, 52:1-. CrossRef
26. Zhao J, Davis LC, Verpoorte R: Elicitor signal transduction leading to production of plant secondary metabolites. / Biotechnol Adv 2005, 23:283-33. CrossRef
27. Ito M, Okimoto K, Yagura T, Honda G: Induction of sesquiterpenoid production by methyl-jasmonate in Aquilaria sinensis cell suspension culture. / J Essent Oil Res 2005,17(2):175-80. CrossRef
28. Okudera Y, Ito M: Production of agarwood fragrant constituents in Aquilaria calli and cell suspension cultures. / Plant Biotechnol 2009,26(3):307-15. CrossRef
29. Hussain SS, Kayani MA, Amjad M: Transcription factors as tools to engineer enhanced drought stress tolerance in plants. / Biotechnol Progr 2011,27(2):297-06. CrossRef
30. Riechmann JL, Meyerowitz EM: The AP2/EREBP family of plant transcription factors. / Biol Chem 1998,379(6):633-46.
31. Shigyo M, Hasebe M, Ito M: Molecular evolution of the AP2 subfamily. / Gene 2006, 366:256-65. CrossRef
32. Jakoby M, Weisshaar B, Dr?ge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F: bZIP transcription factors in Arabidops . / Trends Plant Sci 2002,7(3):106-11. CrossRef
33. Chen YH, Yang XY, He K, Liu MH, Li JG, Gao ZF, Lin ZQ, Zhang YF, Wang XX, Qiu XM, Shen YP, Zhang L, Deng XH, Luo JC, Deng XW, Chen ZL, Gu HY, Qu LJ: The MYB transcription factor superfamily of Arabidopsis : expression analysis and phylogenetic comparison with the rice MYB family. / Plant Mol Biol 2006, 60:107-24. CrossRef
34. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L: MYB transcription factors in Arabidopsis . / Trends Plant Sci 2010,15(10):573-81. CrossRef
35. Feller A, Machemer K, Braun EL, Grotewold E: Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. / Plant J 2011,66(1):94-16. CrossRef
36. Pandey SP, Somssich IE: The role of WRKY transcription factors in plant immunity. / Plant Physiol 2009, 150:1648-655. CrossRef
37. Rushton PJ, Somssich IE, Ringler P, She QJ: WRKY transcription factors. / Trends Plant Sci 2010,15(5):247-58. CrossRef
38. Schwechheimer C, Zourelidou M, Bevan MW: Plant transcription factor studies. / Annu Rev Plant Physiol Plant Mol Biol 1998, 49:127-50. CrossRef
39. Singh KB, Foley RC, O?ate-Sánchez L: Transcription factors in plant defense and stress responses. / Curr Opin Plant Biol 2002, 5:430-36. CrossRef
40. Bradley JM, Davies KM, Doles SC, Bloor SJ, Lewis DH: The maize regulatory gene up-regulates the flavonoid biosynthetic pathway of petunia. / Plant J 1998, 13:381-92. CrossRef
41. Grotewold E, Chamberlain M, Snook M, Siame B, Butler L, Swenson J, Maddock S, Claire GS, Bowen B: Engineering secondary metabolism in maize cells by ectopic expression of transcription factors. / Plant Cell 1998, 10:721-40.
42. Van der Fits L, Memelink J: ORCA3, a jasmonate responsive transcriptional regulator of plant primary and secondary metabolism. / Science 2000, 289:295-97. CrossRef
43. Jonak C, Ligterink W, Hirt H: MAP kinases in plant signal transduction. / Cell Mol Life Sci 1999, 55:204-13. CrossRef
44. Pitzschke A, Schikora A, Hirt H: MAPK cascade signalling networks in plant defence. / Curr Opin Plant Biol 2009, 12:1-. CrossRef
45. Teige M, Scheik E, Eulgem T, Doczi R, Ichimura K, Shinozaki K, Dang JL, Hirt H: The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis . / Mol Cell 2004, 15:141-52. CrossRef
46. Pasquali G, Biricolti S, Locatelli F, Baldoni E, Mattana M: Osmyb4 expression improves adaptive responses to drought and cold stress in transgenic apples. / Plant Cell Rep 2008, 27:677-686. CrossRef
47. Babior BM: NADPH oxidase. / Curr Opin Immunol 2004, 16:42-7. CrossRef
48. Mittler R, Vanderauwera S, Gollery M, Breusegem FV: Reactive oxygen gene network of plants. / Trends Plant Sci 2004,9(10):490-98. CrossRef
49. CITES: / Amendments to Appendix I and II of CITES. Bangkok, Thailand: Proceedings of Thirteenth Meeting of the Conference of the Parties; 2004:2-4.
50. Rojo E, Titarenko E, Leon J, Berger S, Vancanneyt G, Sánchez-Serrano JJ: Reversible protein phosphorylation regulates JA-dependent and –independent wound signal transduction pathway in Arabidopsis thaliana . / Plant J 1998, 13:153-65. CrossRef
51. Orozco-Cárdenas ML, Ryan CA: Hydrogen peroxide is generated systemically in plant leaves by wounding and systemin via the octadecanoid pathway. / Proc Natl Acad Sci USA 1999, 96:6553-557. CrossRef
52. Orozco-Cárdenas ML, Narváez-Vásquez J, Ryan CA: Hydrogen peroxide acts as a second messenger for the induction of defense genes in tomato plants in response to wounding, systemin, and methyl jasmonate. / Plant Cell 2001, 13:179-91.
53. Hung KT, Kao CH: Nitric oxide acts as an antioxidant and delays methyl jasmonate -induced senescence of rice leaves. / J Plant Physiol 2004a, 161:43-2. CrossRef
54. Hung KT, Hsu YT, Kao CH: Hydrogen peroxide is involved in methyl jasmonate-induced senescence of rice leaves. / Physiol Plantarum 2006, 127:293-03. CrossRef
55. Nakagami H, Pitzschke A, Hirt H: Emerging MAP kinase pathways in plant stress signaling. / Trends in Plant Science 2005,10(7):339-46. CrossRef
56. Colcombet J, Hirt H: Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes. / Biochem J 2008, 413:217-26. CrossRef
57. Kazan K, Manners JM: Jasmonate Signaling: Toward an Integrated View. / Plant Physiol 2008, 146:1459-468. CrossRef
58. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J: Genome sequencing in microfabricated high-density picolitre reactors. / Nature 2005, 437:376-0.
59. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S: Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. / Genome Res 2004, 14:1147-159. CrossRef
60. Trivedi N, Bischof J, Davis S, Pedretti K, Scheetz TE, Braun TA, Roberts CA, Robinson NL, Sheffield VC, Soares MB, Casavant TL: Parallel creation of non-redundant gene indices from partial mRNA transcript. / Fut Generation Comput Syst 2002, 18:863-70. CrossRef
61. Huang X, Madan A: CAP3: a DNA sequence assembly program. / Genome Res 1999, 9:868-7. CrossRef
62. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. / Nucleic Acids Res 2006, 34:D354-D357. CrossRef
63. Zdobnov EM, Apweiler R: InterProScan an integration platform for the signature-recognition methods in InterPro. / Bioinformatics 2001,17(9):847-48. CrossRef
64. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS: The Gene Ontology (GO) database and informatics resource. / Nucleic Acids Res 2004, 32:D258-D261. CrossRef
65. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang L: WEGO: a web tool for plotting GO annotations. / Acids Research 2006, 34:293-97. CrossRef
66. Vencio RZ, Brentani H, Pereira CA: Using credibility intervals instead of hypothesis tests in SAGE analysis. / Bioinformatics 2003, 19:2461-464. CrossRef
67. Perez-Rodriguez P, Riano-Pachon DM, Correa LGG, Rensing SA, Kersten B, Mueller-Roeber B: PlnTFDB: updated content and new features of the plant transcription factor database. / Nucleic Acids Res 2010, 38:D822-D827. CrossRef
68. Sui C, Zhang J, Wei JH, Chen SH, Li Y, Xu JS, Jin Y, Xie CX, Gao ZH, Chen HJ, Yang CM, Zhang Z, Xu YH: Transcriptome analysis of Bupleurum chinese focusing on genes involved in the biosynthesis of saikosaponins. / BMC Genomics 2011, 12:539. CrossRef - 作者单位：Yanhong Xu (1)
Zheng Zhang (1) (2)
Mengxi Wang (3)
Jianhe Wei (1) (2)
Hongjiang Chen (2)
Zhihui Gao (1)
Chun Sui (1)
Hongmei Luo (1)
Xingli Zhang (1)
Yun Yang (2)
Hui Meng (2)
Wenlan Li (3)
1. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193, China
2. Hainan Branch Institute of Medicinal Plant (Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine), Chinese Academy of Medical Sciences & Peking Union Medical College, Wanning, 571533, China
3. Research Center on Life Sciences and Environmental Sciences, Harbin University of Commerce, Harbin, 150076, China
文摘
Background Agarwood is an expensive resinous heartwood derived from Aquilaria plants that is widely used in traditional medicines, incense and perfume. Only wounded trees can produce agarwood, and the huge demand for the agarwood products has led all Aquilaria spp. being endangered and listed in the Appendix II of the CITES (http://www.cites.org). The major components of agarwood are sesquiterpenes and phenylethyl chromones. Owing to a lack of genomic information, the molecular basis of wound-induced sesquiterpenes biosynthesis and agarwood formation remains unknown. Results To identify the primary genes that maybe related to agarwood formation, we sequenced 2 cDNA libraries generated from healthy and wounded A. sinensis (Lour.) Gilg. A total of 89,137 unigenes with an average length of 678.65?bp were obtained, and they were annotated in detail at bioinformatics levels. Of those associated with agarwood formation, 30 putatively encoded enzymes in the sesquiterpene biosynthesis pathway, and a handful of transcription factors and protein kinases were related to wound signal transduction. Three full-length cDNAs of sesquiterpene synthases (ASS1-3) were cloned and expressed in Escherichia coli, and enzyme assays revealed that they are active enzymes, with the major products being δ-guaiene. A methyl jasmonate (MJ) induction experiment revealed that the expression of ASS was significantly induced by MJ, and the production of sesquiterpenes was elevated accordingly. The expression of some transcription factors and protein kinases, especially MYB4, WRKY4, MPKK2 and MAPK2, was also induced by MJ and coordinated with ASS expression, suggesting they maybe positive regulators of ASS. Conclusions This study provides extensive transcriptome information for Aquilaria spp. and valuable clues for elucidating the mechanism of wound-induced agarwood sesquiterpenes biosynthesis and their regulation.