Transcript expression profiling for adventitious roots of panax ginseng meyer

Gene

Volumn 546, Issue 1, 2014, Pages 89-96

  Subramaniyam, Sathiyamoorthy ^a,b   Mathiyalagan, Ramya ^a   Natarajan, Sathishkumar ^a   Kim, Yu Jin ^a   Jang, Moon gi ^a   Park, Jun Hyung ^b   Yang, Deok Chun ^a  

^a Kyung Hee University   (South Korea)

^b Insilicogen Inc   (South Korea)

Author keywords

Adventitious root; Gene regulation; MeJA; Panax ginseng

Indexed keywords

CYTOCHROME; DNA BINDING PROTEIN; GINSENOSIDE; GLUCOSYLTRANSFERASE; GLYCOSYLTRANSFERASE; JASMONIC ACID; PLANT EXTRACT; RNA; SAPONIN; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ADVENTITIOUS ROOT; ARTICLE; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GINSENG; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; NONHUMAN; PANAX GINSENG MEYER; PARTICLE SIZE; PLANT GENOME; PRIORITY JOURNAL; PYROSEQUENCING; RNA EXTRACTION; RNA SEQUENCE; SUSPENSION CELL CULTURE;

ARALIACEAE; PANAX; PANAX GINSENG;

ADVENTITIOUS ROOT; GENE REGULATION; MEJA; PANAX GINSENG;

ACETATES; CYCLOPENTANES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GINSENOSIDES; MOLECULAR SEQUENCE ANNOTATION; OXYLIPINS; PANAX; PLANT ROOTS; SECONDARY METABOLISM; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84901841595     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.05.024     Document Type: Article

References (58)

1. Akagi T., Ikegami A., Tsujimoto T., Kobayashi S., Sato A., Kono A., Yonemori K. DkMyb4 is a Myb transcription factor involved in proanthocyanidin biosynthesis in persimmon fruit. Plant Physiology 2009, 151:2028-2045.
2. Ali M., Hahn E.J., Paek K.Y. Copper-induced changes in the growth, oxidative metabolism, and saponin production in suspension culture roots of Panax ginseng in bioreactors. Plant Cell Reports 2006, 25:1122-1132.
3. Ali M., Yu K.W., Hahn E.J., Paek K.Y. Methyl jasmonate and salicylic acid elicitation induces ginsenosides accumulation, enzymatic and non-enzymatic antioxidant in suspension culture Panax ginseng roots in bioreactors. Plant Cell Reports 2006, 25:613-620.
4. Asaka I., Ii I., Hirotani M., Asada Y., Furuya T. Production of ginsenoside saponins by culturing ginseng (Panax ginseng) embryogenic tissues in bioreactors. Biotechnology Letters 1993, 15:1259-1264.
5. Audic S., Claverie J.M. The significance of digital gene expression profiles. Genome Research 1997, 7:986-995.
6. Bae K.H., Choi Y.E., Shin C.G., Kim Y.Y., Kim Y.S. Enhanced ginsenoside productivity by combination of ethephon and methyl jasmonate in ginseng (Panax ginseng C.A. Meyer) adventitious root cultures. Biotechnology Letters 2006, 28:1163-1166.
7. Chen S., Luo H., Li Y., Sun Y., Wu Q., Niu Y., Song J., Lv A., Zhu Y., Sun C., Steinmetz A., Qian Z. 454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng. Plant Cell Reports 2011, 30:1593-1601.
8. Choi K.T. Botanical characteristics, pharmacological effects and medicinal components of Korean Panax ginseng C A Meyer. Acta Pharmacologica Sinica 2008, 29:1109-1118.
9. Choi D.W., Jung J., Ha Y.I., Park H.W., In D.S., Chung H.J., Liu J.R. Analysis of transcripts in methyl jasmonate-treated ginseng hairy roots to identify genes involved in the biosynthesis of ginsenosides and other secondary metabolites. Plant Cell Reports 2005, 23:557-566.
10. De Geyter N., Gholami A., Goormachtig S., Goossens A. Transcriptional machineries in jasmonate-elicited plant secondary metabolism. Trends in Plant Science 2012, 17:349-359.
11. de Hoon M.J., Imoto S., Nolan J., Miyano S. Open source clustering software. Bioinformatics 2004, 20:1453-1454.
12. Devi B.S., Kim Y.J., Sathiyamoorthy S., Khorolragchaa A., Gayathri S., Parvin S., Yang D.U., Selvi S.K., Lee O.R., Lee S., Yang D.C. Classification and characterization of putative cytochrome P450 genes from Panax ginseng C. A. Meyer. Biochemistry (Mosc) 2011, 76:1347-1359.
13. Foster T., Kirk C., Jones W., Allan A., Espley R., Karunairetnam S., Rakonjac J. Characterisation of the DELLA subfamily in apple (Malus×domestica Borkh.). Tree Genetics & Genomes 2007, 3:187-197.
14. Han J.Y., In J.G., Kwon Y.S., Choi Y.E. Regulation of ginsenoside and phytosterol biosynthesis by RNA interferences of squalene epoxidase gene in Panax ginseng. Phytochemistry 2010, 71:36-46.
15. Han J.Y., Kim H.J., Kwon Y.S., Choi Y.E. The cytochrome P450 enzyme CYP716A47 catalyzes the formation of protopanaxadiol from dammarenediol-II during ginsenoside biosynthesis in Panax ginseng. Plant and Cell Physiology 2011, 52:2062-2073.
16. Han J.Y., Hwang H.S., Choi S.W., Kim H.J., Choi Y.E. Cytochrome P450 CYP716A53v2 catalyzes the formation of protopanaxatriol from protopanaxadiol during ginsenoside biosynthesis in Panax ginseng. Plant & Cell Physiology 2012, 53:1535-1545.
17. Hu F.X., Zhong J.J. Role of jasmonic acid in alteration of ginsenoside heterogeneity in elicited cell cultures of Panax notoginseng. Journal of Bioscience and Bioengineering 2007, 104:513-516.
18. Hu F.X., Zhong J.J. Jasmonic acid mediates gene transcription of ginsenoside biosynthesis in cell cultures of Panax notoginseng treated with chemically synthesized 2-hydroxyethyl jasmonate. Process Biochemistry 2008, 43:113-118.
19. Hu X., Neill S.J., Cai W., Tang Z. Nitric oxide mediates elicitor-induced saponin synthesis in cell cultures of Panax ginseng. Functional Plant Biology 2003, 30:901-907.
20. Huang X., Madan A. CAP3: a DNA sequence assembly program. Genome Research 1999, 9:868-877.
21. Hwang S.H., Shin T.J., Choi S.H., Cho H.J., Lee B.H., Pyo M.K., Lee J.H., Kang J., Kim H.J., Park C.W., Shin H.C., Nah S.Y. Gintonin, newly identified compounds from ginseng, is novel lysophosphatidic acids-protein complexes and activates G protein-coupled lysophosphatidic acid receptors with high affinity. Molecules and Cells 2012, 33:151-162.
22. Jeong G.T., Park D.H. Enhancement of growth and secondary metabolite biosynthesis: effect of elicitors derived from plants and insects. Biotechnology and Bioprocess Engineering 2005, 10:73-77.
23. Jeong G.T., Park D.H. Enhanced secondary metabolite biosynthesis by elicitation in transformed plant root system. Applied Biochemistry and Biotechnology 2006, 130:436-446.
24. Jeong G.T., Park D.H., Ryu H.W., Hwang B., Woo J.C., Kim D., Kim S.W. Production of antioxidant compounds by culture of Panax ginseng C.A. Meyer hairy roots: I. Enhanced production of secondary metabolite in hairy root cultures by elicitation. Applied Biochemistry and Biotechnology 2005, 121-124:1147-1157.
25. Jung J.D., Park H.W., Hahn Y., Hur C.G., In D.S., Chung H.J., Liu J.R., Choi D.W. Discovery of genes for ginsenoside biosynthesis by analysis of ginseng expressed sequence tags. Plant Cell Reports 2003, 22:224-230.
26. Khorolragchaa A., Kim Y.J., Rahimi S., Sukweenadhi J., Jang M.G., Yang D.C. Grouping and characterization of putative glycosyltransferase genes from Panax ginseng Meyer. Gene 2014, 536:186-192.
27. Kim O., Kim S., Ohyama K., Muranaka T., Choi Y., Lee H., Kim M., Hwang B. Upregulation of phytosterol and triterpene biosynthesis in Centella asiatica hairy roots overexpressed ginseng farnesyl diphosphate synthase. Plant Cell Reports 2010, 29:403-411.
28. Kim Y.K., Kim J.K., Kim Y.B., Lee S., Kim S.U., Park S.U. Enhanced accumulation of phytosterol and triterpene in hairy root cultures of Platycodon grandiflorum by overexpression of Panax ginseng 3-hydroxy-3-methylglutaryl-coenzyme A reductase. Journal of Agricultural and Food Chemistry 2013, 61:1928-1934. 10.1104//pp.113.22596.
29. Kim Y.J., Jeon J.N., Jang M.G., Oh J.Y., Kwon W.S., Jung S.K., Yang D.C. Ginsenoside profiles and related gene expression during foliation in Panax ginseng Meyer. Journal of Ginseng Research 2014, 38:66-72.
30. Kim Y.J., Lee O.R., Oh J.Y., Jang M.G., Yang D.C. Functional analysis of HMGR encoding genes in triterpene saponin-producing Panax ginseng Meyer. Plant Physiology 2014.
31. Lee M.H., Jeong J.-H., Seo J.W., Shin C.G., Kim Y.S., In J.G., Yang D.C., Yi J.S., Choi Y.E. Enhanced triterpene and phytosterol biosynthesis in Panax ginseng overexpressing squalene synthase gene. Plant and Cell Physiology 2004, 45:976-984.
32. Li C., Zhu Y., Guo X., Sun C., Luo H., Song J., Li Y., Wang L., Qian J., Chen S. Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C. A. Meyer. BMC Genomics 2013, 14:245.
33. Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method. Methods 2001, 25:402-408.
34. Lu, Wong, Teng Effects of elicitation on the production of saponin in cell culture of Panax ginseng. Plant Cell Reports 2001, 20:674-677.
35. Luo H., Sun C., Sun Y., Wu Q., Li Y., Song J., Niu Y., Cheng X., Xu H., Li C., Liu J., Steinmetz A., Chen S. Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers. BMC Genomics 2011, 12(Suppl. 5):S5.
36. Mathiyalagan R., Subramaniyam S., Natarajan S., Kim Y.J., Sun M.S., Kim S.Y., Kim Y.J., Yang D.C. In silico profiling of microRNAs in Korean ginseng (Panax ginseng Meyer). Journal of Ginseng Research 2013, 37:227-247.
37. Mathiyalagan R., Subramaniyam S., Kim Y.J., Natarajan S., Min J.W., Kim S.Y., Yang D.C. Synthesis and pharmacokinetic characterization of a pH-sensitive polyethylene glycol ginsenoside CK (PEG-CK) conjugate. Bioscience, Biotechnology, and Biochemistry 2014, 1-3.
38. Niu Y., Luo H., Sun C., Yang T.J., Dong L., Huang L., Chen S. Expression profiling of the triterpene saponin biosynthesis genes FPS, SS, SE, and DS in the medicinal plant Panax notoginseng. Gene 2014, 533:295-303.
39. Ok R.L., Gayathri S., Yu j.k, In J.G., Kwon W.S., Kim J.H., Yang D.C. Defense genes induced by pathogens and abiotic stresses in Panax ginseng C.A. Meyer. Journal of Ginseng Research 2011, 35:1-11.
40. Pauwels L., Inze D., Goossens A. Jasmonate-inducible gene: what does it mean?. Trends in Plant Science 2009, 14:87-91.
41. Pollier J., Moses T., Gonzalez-Guzman M., De Geyter N., Lippens S., Vanden Bossche R., Marhavy P., Kremer A., Morreel K., Guerin C.J., Tava A., Oleszek W., Thevelein J.M., Campos N., Goormachtig S., Goossens A. The protein quality control system manages plant defence compound synthesis. Nature 2013, 504:148-152.
42. Qian Z.G., Zhao Z.J., Xu Y.F., Qian X.H., Zhong J.J. Novel chemically synthesized hydroxyl-containing jasmonates as powerful inducing signals for plant secondary metabolism. Biotechnology and Bioengineering 2004, 86:809-816.
43. Quan L.H., Min J.W., Sathiyamoorthy S., Yang D.U., Kim Y.J., Yang D.C. Biotransformation of ginsenosides Re and Rg1 into ginsenosides Rg2 and Rh1 by recombinant beta-glucosidase. Biotechnology Letters 2012, 34:913-917.
44. Sathiyamoorthy S., In J.G., Gayathri S., Kim Y.J., Yang D. Gene ontology study of methyl jasmonate-treated and non-treated hairy roots of Panax ginseng to identify genes involved in secondary metabolic pathway. Genetika 2010, 46:932-939.
45. Sathiyamoorthy S., In J.G., Gayathri S., Kim Y.J., Yang D.C. Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. Molecular Biology Reports 2010, 37:3465-3472.
46. Sathiyamoorthy S., In J.G., Lee B.S., Kwon W.S., Yang D.U., Kim J.H., Yang D.C. In silico analysis for expressed sequence tags from embryogenic callus and flower buds of Panax ginseng C. A. Meyer. Journal of Ginseng Research 2011, 35:21-30.
47. Sathiyaraj G., Lee O., Parvin S., Khorolragchaa A., Kim Y.-J., Yang D. Transcript profiling of antioxidant genes during biotic and abiotic stresses in Panax ginseng C. A. Meyer. Molecular Biology Reports 2011, 38:2761-2769.
48. Sawai S., Saito K. Triterpenoid biosynthesis and engineering in plants. Frontiers in Plant Science 2011, 2.
49. Shi W., Wang Y., Li J., Zhang H., Ding L. Investigation of ginsenosides in different parts and ages of Panax ginseng. Food Chemistry 2007, 102:664-668.
50. Shim J.S., Lee O.R., Kim Y.J., Lee J.H., Kim J.H., Jung D.Y., In J.G., Lee B.-S., Yang D.C. Overexpression of PgSQS1 increases ginsenoside production and negatively affects ginseng growth rate in Panax ginseng. Journal of Ginseng Research 2010, 34:99-103.
51. Sun C., Li Y., Wu Q., Luo H., Sun Y., Song J., Lui E.M., Chen S. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 2010, 11:262.
52. Sun Y., Niu Y., Xu J., Li Y., Luo H., Zhu Y., Liu M., Wu Q., Song J., Sun C., Chen S. Discovery of WRKY transcription factors through transcriptome analysis and characterization of a novel methyl jasmonate-inducible PqWRKY1 gene from Panax quinquefolius. Plant Cell, Tissue and Organ Culture (PCTOC) 2013, 114:269-277.
53. Suttipanta N., Pattanaik S., Kulshrestha M., Patra B., Singh S.K., Yuan L. The transcription factor CrWRKY1 positively regulates the terpenoid indole alkaloid biosynthesis in Catharanthus roseus. Plant Physiology 2011, 157:2081-2093.
54. Wu J., Zhong J.-J. Production of ginseng and its bioactive components in plant cell culture: current technological and applied aspects. Journal of Biotechnology 1999, 68:89-99.
55. Wu B., Wang M., Ma Y., Yuan L., Lu S. High-throughput sequencing and characterization of the small RNA transcriptome reveal features of novel and conserved microRNAs in Panax ginseng. PLoS One 2012, 7:e44385.
56. Wu D., Austin R.S., Zhou S., Brown D. The root transcriptome for North American ginseng assembled and profiled across seasonal development. BMC Genomics 2013, 14:564.
57. Yu K.W., Murthy H.N., Jeong C.S., Hahn E.J., Paek K.Y. Organic germanium stimulates the growth of ginseng adventitious roots and ginsenoside production. Process Biochemistry 2005, 40:2959-2961.
58. Zhao J., Davis L.C., Verpoorte R. Elicitor signal transduction leading to production of plant secondary metabolites. Biotechnology Advances 2005, 23:283-333.