title: Deep sequencing reveals transcriptome re-programming of Taxus × media cells to the elicitation with methyl jasmonate.
abstract: BACKGROUND
  Plant cell culture represents an alternative source for producing high-value secondary metabolites including paclitaxel (Taxol®), which is mainly produced in Taxus and has been widely used in cancer chemotherapy. The phytohormone methyl jasmonate (MeJA) can significantly increase the production of paclitaxel, which is induced in plants as a secondary metabolite possibly in defense against herbivores and pathogens. In cell culture, MeJA also elicits the accumulation of paclitaxel; however, the mechanism is still largely unknown.
  
  
  RESULTS
  To obtain insight into the global regulation mechanism of MeJA in the steady state of paclitaxel production (7 days after MeJA addition), especially on paclitaxel biosynthesis, we sequenced the transcriptomes of MeJA-treated and untreated Taxus × media cells and obtained ∼ 32.5 M high quality reads, from which 40,348 unique sequences were obtained by de novo assembly. Expression level analysis indicated that a large number of genes were associated with transcriptional regulation, DNA and histone modification, and MeJA signaling network. All the 29 known genes involved in the biosynthesis of terpenoid backbone and paclitaxel were found with 18 genes showing increased transcript abundance following elicitation of MeJA. The significantly up-regulated changes of 9 genes in paclitaxel biosynthesis were validated by qRT-PCR assays. According to the expression changes and the previously proposed enzyme functions, multiple candidates for the unknown steps in paclitaxel biosynthesis were identified. We also found some genes putatively involved in the transport and degradation of paclitaxel. Potential target prediction of miRNAs indicated that miRNAs may play an important role in the gene expression regulation following the elicitation of MeJA.
  
  
  CONCLUSIONS
  Our results shed new light on the global regulation mechanism by which MeJA regulates the physiology of Taxus cells and is helpful to understand how MeJA elicits other plant species besides Taxus.
authors: Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
authors: Guiling
authors: G
authors: Sun
authors: Yanfang
authors: Y
authors: Yang
authors: Fuliang
authors: F
authors: Xie
authors: Jian-Fan
authors: JF
authors: Wen
authors: Jianqiang
authors: J
authors: Wu
authors: Iain W
authors: IW
authors: Wilson
authors: Qi
authors: Q
authors: Tang
authors: Hongwei
authors: H
authors: Liu
authors: Deyou
authors: D
authors: Qiu
mesh_terms: D000085:Acetates / Q000494:pharmacology*; D002460:Cell Line; D002478:Cells, Cultured; D019295:Computational Biology; D003517:Cyclopentanes / Q000378:metabolism / Q000494:pharmacology*; D030541:Databases, Genetic; D005030:Ethylenes / Q000096:biosynthesis; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D054883:Oxylipins / Q000378:metabolism / Q000494:pharmacology*; D017239:Paclitaxel / Q000096:biosynthesis; D059828:Plant Cells / Q000187:drug effects* / Q000378:metabolism*; D010937:Plant Growth Regulators / Q000494:pharmacology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020946:Taxus / Q000166:cytology*; D013729:Terpenes / Q000378:metabolism; D059467:Transcriptome
chemical_list: D000085:Acetates; D003517:Cyclopentanes; D005030:Ethylenes; D035683:MicroRNAs; D054883:Oxylipins; D010937:Plant Growth Regulators; D012333:RNA, Messenger; D013729:Terpenes; C011006:jasmonic acid; C072239:methyl jasmonate; C036216:ethylene; D017239:Paclitaxel
references: Biochem Eng J. 2012 Apr 15;63:50-56
references: 23180977
references: Nucleic Acids Res. 2002 May 1;30(9):e36
references: 11972351
references: Adv Biochem Eng Biotechnol. 2008;111:187-228
references: 18594786
references: J Nat Prod. 1990 Sep-Oct;53(5):1249-55
references: 1981374
references: Plant Cell. 2009 Aug;21(8):2323-40
references: 19684242
references: Plant Physiol. 2008 Apr;146(4):1459-68
references: 18390489
references: DNA Res. 2001 Aug 31;8(4):153-61
references: 11572481
references: Genome Res. 1999 Sep;9(9):868-77
references: 10508846
references: Biotechnol Adv. 2002 May;20(2):101-53
references: 14538059
references: Biotechnol Adv. 2005 Jun;23(4):283-333
references: 15848039
references: Bioinformatics. 2010 Dec 1;26(23):3002-3
references: 20934992
references: Genomics. 2008 Nov;92(5):255-64
references: 18703132
references: Science. 1993 Apr 9;260(5105):214-6
references: 8097061
references: Methods Mol Biol. 2000;132:365-86
references: 10547847
references: Plant Cell. 2011 Feb;23(2):701-15
references: 21335373
references: BMC Bioinformatics. 2003 Sep 11;4:41
references: 12969510
references: BMC Genomics. 2011 Dec 13;12:600
references: 22151917
references: Plant Cell. 2002;14 Suppl:S131-51
references: 12045274
references: Gene. 2009 May 1;436(1-2):37-44
references: 19393185
references: Curr Opin Plant Biol. 2008 Aug;11(4):428-35
references: 18583180
references: Plant Cell. 2005 Apr;17(4):1196-204
references: 15749761
references: Adv Biochem Eng Biotechnol. 2004;87:1-23
references: 15217102
references: Phytochemistry. 2007 Feb;68(3):335-41
references: 17157336
references: Plant Physiol. 1995 Apr;107(4):1333-41
references: 7770527
references: Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2447-52
references: 19168636
references: Planta. 1989 Jan;177(1):58-65
references: 24212272
references: Biotechnol Bioeng. 1999 Jan 5;62(1):97-105
references: 10099517
references: BMC Genomics. 2012 Apr 24;13:148
references: 22530557
references: Biol Pharm Bull. 2008 Feb;31(2):260-5
references: 18239284
references: Nat Biotechnol. 2008 Oct;26(10):1135-45
references: 18846087
references: Phytochemistry. 2003 Mar;62(6):901-9
references: 12590117
references: Trends Plant Sci. 2005 Feb;10(2):51-4
references: 15708340
references: PLoS One. 2011;6(6):e21220
references: 21731678
references: Plant Physiol. 2009 Jun;150(2):658-69
references: 19357199
references: Plant J. 2006 May;46(4):573-92
references: 16640595
references: Trends Plant Sci. 2000 May;5(5):199-206
references: 10785665
references: Nat Biotechnol. 1996 Sep;14(9):1129-32
references: 9631065
references: Nature. 2010 Jan 21;463(7279):311-7
references: 20010809
references: Biotechnol Prog. 2010 Jul-Aug;26(4):1145-53
references: 20730769
references: Mol Biol (Mosk). 2005 Jan-Feb;39(1):14-20
references: 15773543
references: BMC Bioinformatics. 2011 Aug 04;12:323
references: 21816040
references: Trends Plant Sci. 2009 Feb;14(2):87-91
references: 19162528
references: Bioinformatics. 2010 Jan 1;26(1):139-40
references: 19910308
references: Plant Cell Rep. 2009 Jan;28(1):83-93
references: 18813931
references: Plant Cell. 2011 Apr;23(4):1536-55
references: 21467581
references: Phytochem Rev. 2006 Feb;5(1):75-97
references: 20622989
references: Biotechnol Prog. 1996 Jan-Feb;12(1):110-8
references: 8845101
references: Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13591-6
references: 11095755
references: Anticancer Drugs. 1991 Dec;2(6):519-30
references: 1687206
references: Plant Physiol. 2002 Jan;128(1):201-11
references: 11788766
references: Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9149-54
references: 15178753
references: BMC Genomics. 2012 Jul 02;13:295
references: 22748077
references: Planta. 2000 May;210(6):979-84
references: 10872231
references: Planta Med. 2011 Mar;77(4):394-400
references: 20862637
references: BMC Plant Biol. 2012 Mar 17;12:37
references: 22424472
references: Trends Plant Sci. 2002 Mar;7(3):106-11
references: 11906833
references: Genome Res. 2009 Jun;19(6):1117-23
references: 19251739
references: Plant Mol Biol. 2012 Sep;80(1):17-36
references: 21874378
references: Plant J. 2005 Dec;44(6):1065-76
references: 16359398