Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao

BMC Genomics

Volumn 16, Issue 7, 2015, Pages

  Chen, Jing ^a   Wu, Xue Ting ^b   Xu, Yi Qin ^a   Zhong, Yang ^a,c   Li, Yi Xue ^d   Chen, Jia Kuan ^a   Li, Xuan ^b   Nan, Peng ^a  

^a FUDAN UNIVERSITY   (China)

^b INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^c TIBET UNIVERSITY   (China)

^d SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao; Herb; Isoflavonoids; Metabolites; Transcriptome; Triterpene saponins

Indexed keywords

CYCLOARTENOL SYNTHASE; CYTOCHROME P450; GLYCOSYLTRANSFERASE; ISOLAVONOID; PLANT MEDICINAL PRODUCT; PROTEIN MYB; SAPONIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR BHLH; TRANSCRIPTION FACTOR C3H; TRANSCRIPTION FACTOR WRKY; UNCLASSIFIED DRUG; ISOFLAVONE DERIVATIVE; PLANT PROTEIN;

ARABIDOPSIS THALIANA; ARTICLE; ASTRAGALUS MEMBRANACEUS; ASTRAGALUS MEMBRANACEUS BGE VAR MONGOLICUS BGE HSIAO; BARREL MEDIC; BIOSYNTHESIS; CONTROLLED STUDY; DNA SEQUENCE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ASSOCIATION; METABOLISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT LEAF; PLANT ROOT; PLANT STEM; PROTEIN ANALYSIS; PROTEIN FUNCTION; RNA ANALYSIS; RNA SEQUENCE; SPECIES COMPARISON; SPECIES DIVERSITY; TRANSCRIPTOME ANALYSIS; GENE EXPRESSION REGULATION; GENETIC VARIATION; GENETICS; PROCEDURES; SEQUENCE ANALYSIS;

ASTRAGALUS MEMBRANACEUS; CYTOCHROME P-450 ENZYME SYSTEM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENETIC VARIATION; ISOFLAVONES; METABOLIC NETWORKS AND PATHWAYS; PHYLOGENY; PLANT PROTEINS; SAPONINS; SEQUENCE ANALYSIS, RNA;

EID: 84969286391     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-16-S7-S15     Document Type: Article

References (80)

1. XY Z: Pharmacopoeia of the People's Republic of China 2005. 2005, People's Medical Publishing House, 1:
2. Ma X, Tu P, Chen Y, Zhang T, Wei Y, Ito Y: Preparative isolation and purification of two isoflavones from Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao by high-speed counter-current chromatography. Journal of Chromatography A. 2003, 992 (1): 193-197.
3. Wu T, Annie Bligh S, Gu Lh, Wang Zt, Liu Hp, Cheng Xm, Branford-White CJ, Hu Zb: Simultaneous determination of six isoflavonoids in commercial Radix Astragali by HPLC-UV. Fitoterapia. 2005, 76 (2): 157-165. 10.1016/j.fitote.2004.11.006.
4. Zhang Q, Gao W, Man S: Chemical composition and pharmacological activities of astragali radix. China journal of Chinese materia medica. 2012, 37 (21): 3203-3207.
5. Pan H, Wang Y, Zhang Y, Zhou T, Fang C, Nan P, Wang X, Li X, Wei Y, Chen J: Phenylalanine ammonia lyase functions as a switch directly controlling the accumulation of calycosin and calycosin-7-O-β-D-glucoside in Astragalus membranaceus var. mongholicus plants. Journal of experimental botany. 2008, 59 (11): 3027-3037. 10.1093/jxb/ern152.
6. Fan Y, Wu DZ, Gong YQ, Zhou JY, Hu ZB: Effects of calycosin on the impairment of barrier function induced by hypoxia in human umbilical vein endothelial cells. European journal of pharmacology. 2003, 481 (1): 33-40. 10.1016/j.ejphar.2003.09.007.
7. Lee YM, Lee , Yun-Mi , Choi SI, Choi , Soo-Im , Lee JW, Lee , Jae-Won , Jung SM, Jung , Sun-Mi , Park SM, Park , Sang-Min , Heo TR, Heo , Tae-Ryeon : Isolation of hyaluronidase inhibitory component from the roots of Astraglus membranaceus Bunge (Astragali Radix). Food Science and Biotechnology. 2005, 14 (2): 263-267.
8. CHOI S, PARK SR, HEO TR: Inhibitory effect of astragali radix on matrix degradation in human articular cartilage. Journal of microbiology and biotechnology. 2005, 15 (6): 1258-1266.
9. Pan H, Fang C, Zhou T, Wang Q, Chen J: Accumulation of calycosin and its 7-O-β-d-glucoside and related gene expression in seedlings of Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao induced by low temperature stress. Plant cell reports. 2007, 26 (7): 1111-1120. 10.1007/s00299-006-0301-8.
10. Liu CJ, Huhman D, Sumner LW, Dixon RA: Regiospecific hydroxylation of isoflavones by cytochrome p450 81E enzymes from Medicago truncatula. The Plant Journal. 2003, 36 (4): 471-484. 10.1046/j.1365-313X.2003.01893.x.
11. Liu CJ, Deavours BE, Richard SB, Ferrer JL, Blount JW, Huhman D, Dixon RA, Noel JP: Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses. The Plant Cell Online. 2006, 18 (12): 3656-3669. 10.1105/tpc.106.041376.
12. Du M, WX , Wang ZY, Hu ZB: Isolation and Identification of Genes Related to Astragaloside IV Differential Expressed Synthesis in Astragalus membranaceus. Pharmaceutical Biotechnology. 2005, 12 (2): 76-80.
13. Luo H, Sun C, Sun Y, Wu Q, Li Y, Song J, Niu Y, Cheng X, Xu H, Li C: Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers. BMC genomics. 2011, 12 (Suppl 5): S5-10.1186/1471-2164-12-S5-S5.
14. Dong H, Jiang B, Han Y, GENG Y, ZHAO Yq: Transformation of Compound K from Saponins in Leaves of Panax notoginseng by Immobilized β-Glucanase. Chin Herb Med. 2010, 2 (1): 41-47.
15. Wu D, Austin RS, Zhou S, Brown D: The root transcriptome for North American ginseng assembled and profiled across seasonal development. BMC genomics. 2013, 14 (1): 564-10.1186/1471-2164-14-564.
16. Wang S, Li J, Huang H, Gao W, Zhuang C, Li B, Zhou P, Kong D: Anti-hepatitis B virus activities of astragaloside IV isolated from radix Astragali. Biological & pharmaceutical bulletin. 2009, 32 (1): 132-135. 10.1248/bpb.32.132.
17. Augustin JM, Kuzina V, Andersen SB, Bak S: Molecular activities, biosynthesis and evolution of triterpenoid saponins. Phytochemistry. 2011, 72 (6): 435-457. 10.1016/j.phytochem.2011.01.015.
18. Kim O, Bang K, Jung S, Kim Y, Hyun D, Kim S, Cha S: Molecular characterization of ginseng farnesyl diphosphate synthase gene and its up-regulation by methyl jasmonate. Biologia plantarum. 2010, 54 (1): 47-53. 10.1007/s10535-010-0007-1.
19. Zhang WJ, Hufnagl P, Binder BR, Wojta J: Anti-inflammatory activity of astragaloside IV is mediated by inhibition of NF-qB activation and adhesion molecule expression. Thromb Haemost. 2003, 90 (5): 904-914.
20. Mardis ER: The impact of next-generation sequencing technology on genetics. Trends in genetics. 2008, 24 (3): 133-141. 10.1016/j.tig.2007.12.007.
21. Ping J, Wang Y, Yu Y, Li Y, Li X, Hao P: A comparative analysis of tissue gene expression data from high-throughput studies. Chinese Science Bulletin. 2012, 57 (22): 2920-2927. 10.1007/s11434-012-5077-3.
22. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH: Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular ecology. 2008, 17 (7): 1636-1647. 10.1111/j.1365-294X.2008.03666.x.
23. Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, Jiang CJ, Sun J, Li YY, Chen Q, Xia T: Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC genomics. 2011, 12 (1): 131-10.1186/1471-2164-12-131.
24. Wang XC, Zhao QY, Ma CL, Zhang ZH, Cao HL, Kong YM, Yue C, Hao XY, Chen L, Ma JQ: Global transcriptome profiles of Camellia sinensis during cold acclimation. BMC genomics. 2013, 14 (1): 415-10.1186/1471-2164-14-415.
25. Liu XB, Ma L, Zhang AH, Zhang YH, Jiang J, Ma W, Zhang LM, Ren WC, Kong XJ: High-Throughput Analysis and Characterization of Astragalus membranaceus Transcriptome Using 454 GS FLX. PloS one. 2014, 16 (5): e95831-
26. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology. 2011, 29 (7): 644-652. 10.1038/nbt.1883.
27. Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.
28. Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science. 1997, 278 (5338): 631-637. 10.1126/science.278.5338.631.
29. Jin J, Zhang H, Kong L, Gao G, Luo J: PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic acids research. 2014, 42 (D1): D1182-D1187. 10.1093/nar/gkt1016.
30. Lorenzo CP, Anahit G, Irma RV, F M-GJ, R B-CJ, L RD: Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiology. 2010, 3
31. Khanna R, Huq E, Kikis EA, Al-Sady B, Lanzatella C, Quail PH: A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors. The Plant Cell Online. 2004, 16 (11): 3033-3044. 10.1105/tpc.104.025643.
32. Chinnusamy V, Ohta M, Kanrar S, Lee Bh, Hong X, Agarwal M, Zhu JK: ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes & development. 2003, 17 (8): 1043-1054. 10.1101/gad.1077503.
33. Kiribuchi K, Sugimori M, Takeda M, Otani T, Okada K, Onodera H, Ugaki M, Tanaka Y, Tomiyama-Akimoto C, Yamaguchi T: RERJ1, a jasmonic acid-responsive gene from rice, encodes a basic helix-loop-helix protein. Biochemical and biophysical research communications. 2004, 325 (3): 857-863. 10.1016/j.bbrc.2004.10.126.
34. Wei Z, Yujin S, Ljudmilla T, Changbin C, Ueli G, Hong M: Regulation of Arabidopsis tapetum development and function by DYSFUNCTIONAL TAPETUM1 (DYT1) encoding a putative bHLH transcription factor. Development (Cambridge). 2006, 16
35. Nuno P, Liam D: Origin and diversification of basic-helix-loop-helix proteins in plants. Molecular Biology and Evolution. 2009, 4
36. Qian W, Tan G, Liu H, He S, Gao Y, An C: Identification of a bHLH-type G-box binding factor and its regulation activity with G-box and Box I elements of the PsCHS1 promoter. Plant cell reports. 2007, 26 (1): 85-93.
37. R LS, F HL, L DS, R WS: Lc, a member of the maize R gene family responsible for tissue-specific anthocyanin production, encodes a protein similar to transcriptional activators and contains the myc-homology region. Proceedings of the National Academy of Sciences of the United States of America. 1989, 18
38. Hu J, Anderson B, Wessler SR: Isolation and characterization of rice R genes: evidence for distinct evolutionary paths in rice and maize. Genetics. 1996, 142 (3): 1021-1031.
39. N N, I D, C J, G P, M C, L L: The TT8 gene encodes a basic helix-loop-helix domain protein required for expression of DFR and BAN genes in Arabidopsis siliques. The Plant Cell. 2000, 10
40. Feller A, Machemer K, Braun EL, Grotewold E: Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. The Plant Journal. 2011, 66 (1): 94-116. 10.1111/j.1365-313X.2010.04459.x.
41. J PA, D G, U W, A PP, H S: The regulatory c1 locus of Zea mays encodes a protein with homology to myb proto-oncogene products and with structural similarities to transcriptional activators. The EMBO Journal. 1987, 12
42. Hartmann U, Sagasser M, Mehrtens F, Stracke R, Weisshaar B: Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes. Plant molecular biology. 2005, 57 (2): 155-171. 10.1007/s11103-004-6910-0.
43. Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V, Bansal KC: Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC genomics. 2012, 13 (1): 544-10.1186/1471-2164-13-544.
44. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L: MYB transcription factors in Arabidopsis. Trends in plant science. 2010, 15 (10): 573-581. 10.1016/j.tplants.2010.06.005.
45. Chai G, Hu R, Zhang D, Qi G, Zuo R, Cao Y, Chen P, Kong Y, Zhou G: Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa). BMC genomics. 2012, 13 (1): 253-10.1186/1471-2164-13-253.
46. Dong W, Yinghui G, Changai W, Guodong Y, Yingying L, Chengchao Z: Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics. 2008, 1
47. I CS, R HT, B-H M, H CJ, H CB, R PS: Alleviation of osteoarthritis by calycosin-7-O-beta-D-glucopyranoside (CG) isolated from Astragali radix (AR) in rabbit osteoarthritis (OA) model. Osteoarthritis and Cartilage. 2007, 9
48. M MS, K HT, K GR, K BH: Phytoestrogens and breast cancer prevention: possible mechanisms of action. Environmental Health Perspectives. 2008, 4
49. Yu O, McGonigle B: Metabolic Engineering of Isoflavone Biosynthesis. Advances in Agronomy. 2005
50. Werck-Reichhart D, Batard Y, Kochs G, Lesot A, Durst F: Monospecific polyclonal antibodies directed against purified cinnamate 4-hydroxylase from Helianthus tuberosus (immunopurification, immunoquantitation, and interspecies cross-reactivity). Plant physiology. 1993, 102 (4): 1291-1298. 10.1104/pp.102.4.1291.
51. Jae-youl J, Mangai KG, Ji-young P, Won-jin K, Hyun-soon K, Bong-sik Y, Hyouk J, Jae-heung J: An overexpression of chalcone reductase of Pueraria montana var. lobata alters biosynthesis of anthocyanin and 5'-deoxyflavonoids in transgenic tobacco. Biochemical and Biophysical Research Communications. 2003, 1
52. Xu RY, Nan P, Yang Y, Pan H, Zhou T, Chen J: Ultraviolet irradiation induces accumulation of isoflavonoids and transcription of genes of enzymes involved in the calycosin-7-O-β-d-glucoside pathway in Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao. Physiologia plantarum. 2011, 142 (3): 265-273. 10.1111/j.1399-3054.2011.01474.x.
53. Gillissen B, Bürkle L, André B, Kühn C, Rentsch D, Brandl B, Frommer WB: A new family of high-affinity transporters for adenine, cytosine, and purine derivatives in Arabidopsis. The Plant Cell Online. 2000, 12 (2): 291-300. 10.1105/tpc.12.2.291.
54. Kim YB, Thwe AA, Li X, Tuan PA, Zhao S, Park CG, Lee JW, Park SU: Accumulation of Flavonoids and Related Gene Expressions in Different Organs of Astragalus membranaceus Bge. Applied Biochemistry and Biotechnology. 2014, 1-10.
55. Dubey VS, Bhalla R, Luthra R: An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants. Journal of biosciences. 2003, 28 (5): 637-646. 10.1007/BF02703339.
56. Lichtenthaler HK, Schwender J, Disch A, Rohmer M: Biosynthesis of isoprenoids in higher plant chloroplasts proceeds via a mevalonate-independent pathway. Febs Letters. 1997, 400 (3): 271-274. 10.1016/S0014-5793(96)01404-4.
57. Wolff M, Seemann M, Tse Sum Bui B, Frapart Y, Tritsch D, Estrabot AG, Rodríguez-Concepción M, Boronat A, Marquet A, Rohmer M: Isoprenoid biosynthesis via the methylerythritol phosphate pathway: the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (LytB/IspH) from Escherichia coli is a [4Fe-4S] protein. FEBS letters. 2003, 541 (1): 115-120.
58. Vincken JP, Heng L, de Groot A, Gruppen H: Saponins, classification and occurrence in the plant kingdom. Phytochemistry. 2007, 68 (3): 275-297. 10.1016/j.phytochem.2006.10.008.
59. CHIOU Wf, ZHANG Jt: Comparison of the pharmacological effects of Panax ginseng and Panax quinquefolium. Acta Pharmacologica Sinica. 2008, 29 (9): 1103-1108. 10.1111/j.1745-7254.2008.00868.x.
60. Han JY, Kwon YS, Yang DC, Jung YR, Choi YE: Expression and RNA interference-induced silencing of the dammarenediol synthase gene in Panax ginseng. Plant and cell physiology. 2006, 47 (12): 1653-1662. 10.1093/pcp/pcl032.
61. Y.H. L, Shi. S, H.Q. Z, Y.D. Z, B. X: 2D NMR study on cycloartane triterpenoids from Astragalus membranaceus var. mongholicus. Journal of China Pharmaceutical University. 2008, 39 (1): 15-19.
62. Phillips DR, Rasbery JM, Bartel B, Matsuda S: Biosynthetic diversity in plant triterpene cyclization. Current opinion in plant biology. 2006, 16 (3): 305-314.
63. Corey E, Matsuda S, Bartel B: Isolation of an Arabidopsis thaliana gene encoding cycloartenol synthase by functional expression in a yeast mutant lacking lanosterol synthase by the use of a chromatographic screen. Proceedings of the National Academy of Sciences. 1993, 90 (24): 11628-11632. 10.1073/pnas.90.24.11628.
64. Nelson DR, Schuler MA, Paquette SM, Werck-Reichhart D, Bak S: Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot. Plant Physiology. 2004, 135 (2): 756-772. 10.1104/pp.104.039826.
65. Masaaki S, Masaki H, Yuji K, Hiroaki H, Tetsuo K, Yutaka E: Identification of beta-amyrin and sophoradiol 24-hydroxylase by expressed sequence tag mining and functional expression assay. The FEBS Journal. 2006, 5
66. Hikaru S, Kiyoshi O, Satoru S, Masaharu M, Toshiyuki O, Hiroshi S, Tomoyoshi A, Toshio A, Kazuki S, Toshiya M: Licorice beta-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin. Proceedings of the National Academy of Sciences of the United States of America. 2008, 37
67. Lahoucine A, V HD, A FM, W SL, W BJ, A DR: Genomics-based selection and functional characterization of triterpene glycosyltransferases from the model legume Medicago truncatula. The Plant Journal. 2005, 6
68. WANG YP, LI XY, SONG CQ, HU ZB: Effect of astragaloside F on T, B lymphocyte proliferation and peritoneal macrophage function in mice1. Acta Pharmacol Sin. 2002, 23 (3): 263-266.
69. Luo H, Dai R, Li Y: Nuclear cardiology study on effective ingredients of Astragalus membranaceus in treating heart failure. Chinese journal of integrated traditional and Western medicine. 1995, 15 (12): 707-709.
70. Luo Y, Qin Z, Hong Z, Zhang X, Ding D, Fu JH, Zhang WD, Chen J: Astragaloside IV protects against ischemic brain injury in a murine model of transient focal ischemia. Neuroscience letters. 2004, 363 (3): 218-223. 10.1016/j.neulet.2004.03.036.
71. Zhou J, Fan Y, Kong J, Wu D, Hu Z: Effects of components isolated from Astragalus membranaceus Bunge on cardiac function injured by myocardial ischemia reperfusion in rats. China journal of Chinese materia medica. 2000, 25 (5): 300-302.
72. Bak S, Beisson F, Bishop G, Hamberger B, Höfer R, Paquette S, Werck-Reichhart D: Cytochromes P450. The Arabidopsis Book/American Society of Plant Biologists. 2011, 16:
73. Bernhardt R: Cytochromes P450 as versatile biocatalysts. Journal of biotechnology. 2006, 124 (1): 128-145. 10.1016/j.jbiotec.2006.01.026.
74. Nelson D, Werck-Reichhart D: A P450-centric view of plant evolution. The Plant Journal. 2011, 66 (1): 194-211. 10.1111/j.1365-313X.2011.04529.x.
75. K AG, Shigeru T, Oksoo H, Hitoshi I, Randeep R: Rice octadecanoid pathway. Biochemical and Biophysical Research Communications. 2004, 1
76. K HR, Stefania DD, Angelo S: Plant cytochrome CYP74 family: biochemical features, endocellular localisation, activation mechanism in plant defence and improvements for industrial applications. ChemBioChem. 2009, 7
77. Li T, Valeria M, Joonyul K, Maria ML, Dean D: The Arabidopsis LUT1 locus encodes a member of the cytochrome p450 family that is required for carotenoid epsilon-ring hydroxylation activity. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2004, 1
78. M TE, Shozo F, Hideharu S, Yukihisa S, Suguru T, Shigeo Y, A DM, I TQ, M NM: CYP72B1 inactivates brassinosteroid hormones: an intersection between photomorphogenesis and plant steroid signal transduction. Plant Physiology. 2003, 4
79. J BG, Csaba K: Brassinosteroids and plant steroid hormone signaling. The Plant Cell. 2002
80. Franck P, Fred B: Cytochrome P450 metabolizing fatty acids in plants: characterization and physiological roles. The FEBS Journal (Online). 2010, 2