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Identification of early jasmonate-responsive genes in Taxus × media cells by analyzing time series digital gene expression data

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Abstract

Jasmonate, an effective elicitor, can induce the biosynthesis of paclitaxel, a well-known anticancer drug, in Taxus cell culture. The jasmonate signaling pathway has been well studied in Arabidopsis, and many early jasmonate-responsive genes have been found to be involved in signaling pathway. In Taxus, only a few late jasmonate-responsive genes related to paclitaxel biosynthesis were identified. So, identification of early responsive genes and knowledge of the jasmonate signaling pathway are essential for understanding the effects of jasmonate on paclitaxel biosynthesis and for improving paclitaxel production in Taxus cells. In this study, total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 h of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the paired-end method. A total of 45,583 transcript clusters were obtained by de novo assembly of the sequenced reads. Based on the transcriptome data, the digital gene expressions of each RNA sample were investigated. We found that after 0.5, 3, and 24 h of methyl jasmonate treatment; 134, 1008, and 987 unigenes were differentially expressed. For the secondary metabolism pathways, phenylalanine pathway unigenes were responsive to jasmonate after 3 h of treatment, while genes related to paclitaxel biosynthesis were induced after 0.5 h of treatment. The digital gene expression levels of candidate genes related to paclitaxel biosynthesis were confirmed by qRT-PCR. Transcriptome sequencing and digital gene expression profiling identified early jasmonate-responsive genes in cultured Taxus × media cells. The comprehensive time series jasmonate-responsive gene expression data have provided transcriptome-wide information about the mechanism of paclitaxel biosynthesis regulation by jasmonate signaling.

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References

  • Bustin SA, Vandesompele J, Pfaffl MW (2009) Standardization of qPCR and RT-qPCR. Genet Eng Biotechnol News 29:40–43

    Google Scholar 

  • Chen J, Yan YX, Guo ZG (2015) Identification of hydrogen peroxide responsive ESTs involved in phenylethanoid glycoside biosynthesis in Cistanche salsa cell culture. Biol Plant 59:695–700

    Article  CAS  Google Scholar 

  • Chini A, Fonseca S, Fernández G, Adie B, Chico JM, Lorenzo O, García-Casado G, López-Vidriero I, Lozano FM, Ponce MR, Micol JL, Solano R (2007) The JAZ family of repressors is the missing link in jasmonate signalling. Nature 448:666–671

    Article  PubMed  CAS  Google Scholar 

  • Croteau R, Ketchum REB, Long RM, Kaspera R, Wildung MR (2006) Taxol biosynthesis and molecular genetics. Phytochem Rev 5:75–97

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fernandez-Calvo P, Chini A, Fernandez-Barbero G, Chico J, Gimenez-Ibanez S, Geerinck J, Eeckhout D, Schweizer F, Godoy M, Manuel Franco-Zorrilla J, Pauwels L, Witters E, Isabel Puga M, Paz-Ares J, Goossens A, Reymond P, De Jaeger G, Solano R (2011) The Arabidopsis bHLH transcription factors MYC3 and MYC4 are targets of JAZ repressors and act additively with MYC2 in the activation of jasmonate responses. Plant Cell 23:701–715

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Frerigmann H, Gigolashvili T (2014) MYB34, MYB51, and MYB122 distinctly regulate indolic glucosinolate biosynthesis in Arabidopsis thaliana. Mol Plant 7:814–828

    Article  PubMed  CAS  Google Scholar 

  • Gfeller A, Liechti R, Farmer EE (2010) Arabidopsis jasmonate signaling pathway. Sci Signal 3(109):cm4

    PubMed  Google Scholar 

  • Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512

    Article  PubMed  CAS  Google Scholar 

  • Ishiga Y, Ishiga T, Uppalapati SR, Mysore KS (2013) Jasmonate ZIM-domain (JAZ) protein regulates host and nonhost pathogen-induced cell death in tomato and Nicotiana benthamiana. PLoS ONE 8:e75728

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jennewein S, Croteau R (2001) Taxol: biosynthesis, molecular genetics, and biotechnological applications. Appl Microbiol Biotechnol 57:13–19

    Article  PubMed  CAS  Google Scholar 

  • Kitaoka N, Matsubara T, Sato M, Takahashi K, Wakuta S, Kawaide H, Matsui H, Nabeta K, Matsuura H (2011) Arabidopsis CYP94B3 encodes jasmonyl-l-isoleucine 12-hydroxylase, a key enzyme in the oxidative catabolism of jasmonate. Plant Cell Physiol 52:1757–1765

    Article  PubMed  CAS  Google Scholar 

  • Koo AJK, Gao X, Daniel Jones A, Howe GA (2009) A rapid wound signal activates the systemic synthesis of bioactive jasmonates in Arabidopsis. Plant J 59:974–986

    Article  PubMed  CAS  Google Scholar 

  • Laskaris G, Bounkhay M, Theodoridis G, van der Heijden R, Verpoorte R, Jaziri M (1999) Induction of geranylgeranyl diphosphate synthase activity and taxane accumulation in Taxus baccata cell cultures after elicitation by methyl jasmonate. Plant Sci 147:1–8

    Article  CAS  Google Scholar 

  • Lenka SK, Boutaoui N, Paulose B, Vongpaseuth K, Normanly J, Roberts SC, Walker EL (2012) Identification and expression analysis of methyl jasmonate responsive ESTs in paclitaxel producing Taxus cuspidata suspension culture cells. BMC Genom 13:148

    Article  CAS  Google Scholar 

  • Li S, Zhang P, Zhang M, Fu C, Zhao C, Dong Y, Guo A, Yu L (2012) Transcriptional profile of Taxus chinensis cells in response to methyl jasmonate. BMC Genom 13:295

    Article  CAS  Google Scholar 

  • Onrubia M, Moyano E, Bonfill M, Cusidó RM, Goossens A, Palazón J (2013) Coronatine, a more powerful elicitor for inducing taxane biosynthesis in Taxus media cell cultures than methyl jasmonate. J Plant Physiol 170:211–219

    Article  PubMed  CAS  Google Scholar 

  • Qi T, Song S, Ren Q, Wu D, Huang H, Chen Y, Fan M, Peng W, Ren C, Xie D (2011) The Jasmonate-ZIM-domain proteins interact with the WD-repeat/bHLH/MYB complexes to regulate jasmonate-mediated anthocyanin accumulation and trichome initiation in Arabidopsis thaliana. Plant Cell 23:1795–1814

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sabater-Jara A, Onrubia M, Moyano E, Bonfill M, Palazón J, Pedreño MA, Cusidó RM (2014) Synergistic effect of cyclodextrins and methyl jasmonate on taxane production in Taxus × media cell cultures. Plant Biotechnol J 12:1075–1084

    Article  PubMed  CAS  Google Scholar 

  • Sasaki Y, Asamizu E, Shibata D, Nakamura Y, Kaneko T, Awai K, Amagai M, Kuwata C, Tsugane T, Masuda T, Shimada H, Takamiya X, Ohta H, Tabata S (2001) Monitoring of methyl jasmonate-responsive genes in Arabidopsis by cDNA macroarray: self-activation of jasmonic acid biosynthesis and crosstalk with other phytohormone signaling pathways. DNA Res 8:153–161

    Article  PubMed  CAS  Google Scholar 

  • Sasaki-Sekimoto Y, Taki N, Obayashi T, Ainai T, Kobayashi Y, Asamizu E, Nakamura Y, Kuromori T, Hirayama T, Shinozaki K, Masuda T, Shimada H, Takamiya K, Shibata D, Tabata S, Ohta H (2003) Analysis for methyl jasmonate-specific expression changes in Arabidopsis by cDNA macroarray. Plant Cell Physiol 44S:S112

    Google Scholar 

  • Seo J, Joo J, Kim M, Kim Y, Nahm BH, Song SI, Cheong J, Lee JS, Kim J, Choi YD (2011) OsbHLH148, a basic helix–loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice. Plant J 65:907–921

    Article  PubMed  CAS  Google Scholar 

  • Sheludko YV (2010) Recent advances in plant biotechnology and genetic engineering for production of secondary metabolites. Tsitol Genet 44:65–75

    PubMed  CAS  Google Scholar 

  • Shen Q, Lu X, Yan T, Fu X, Lv Z, Zhang F, Pan Q, Wang G, Sun X, Tang K (2016) The jasmonate-responsive AaMYC2 transcription factor positively regulates artemisinin biosynthesis in Artemisia annua. New Phytol 210:1269–1281

    Article  PubMed  CAS  Google Scholar 

  • Shoji T, Ogawa T, Hashimoto T (2008) Jasmonate-induced nicotine formation in tobacco is mediated by tobacco COI1 and JAZ genes. Plant Cell Physiol 49:1003–1012

    Article  PubMed  CAS  Google Scholar 

  • Song S, Qi T, Huang H, Ren Q, Wu D, Chang C, Peng W, Liu Y, Peng J, Xie D (2011) The jasmonate-ZIM domain proteins interact with the R2R3-MYB transcription factors MYB21 and MYB24 to affect jasmonate-regulated stamen development in Arabidopsis. Plant Cell 23:1000–1013

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sun G, Yang Y, Xie F, Wen J, Wu J, Wilson IW, Tang Q, Liu H, Qiu D (2013) Deep sequencing reveals transcriptome re-programming of Taxus × media cells to the elicitation with methyl jasmonate. PLoS ONE 8(4):e62865

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Thines B, Katsir L, Melotto M, Niu Y, Mandaokar A, Liu G, Nomura K, He SY, Howe GA, Browse J (2007) JAZ repressor proteins are targets of the SCFCOI1 complex during jasmonate signalling. Nature 448:661–665

    Article  PubMed  CAS  Google Scholar 

  • Wani MC, Horwitz SB (2014) Nature as a remarkable chemist. Anti-Cancer Drug 25:482–487

    Article  CAS  Google Scholar 

  • Wilson SA, Roberts SC (2012) Recent advances towards development and commercialization of plant cell culture processes for the synthesis of biomolecules. Plant Biotechnol J 10:249–268

    Article  PubMed  CAS  Google Scholar 

  • Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ying F, Zhigang G (1999) Low ammomium medium used in Taxus SSP. callus inducement and taxol biosynthesis. Nat Prod Res Dev 11(4):7–13

    Google Scholar 

  • Yukimune Y, Tabata H, Higashi Y, Hara Y (1996) Methyl jasmonate-induced overproduction of paclitaxel and baccatin III in Taxus cell suspension cultures. Nat Biotechnol 14:1129–1132

    Article  PubMed  CAS  Google Scholar 

  • Zhou Y, Sun W, Chen J, Tan H, Xiao Y, Li Q, Ji Q, Gao S, Chen L, Chen S, Zhang L, Chen W (2016) SmMYC2a and SmMYC2b played similar but irreplaceable roles in regulating the biosynthesis of tanshinones and phenolic acids in Salvia miltiorrhiza. Sci Rep 6:22852

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Acknowledgements

We thank Annoroad (Beijing, China, http://www.annoroad.com/) for providing the sequencing service.

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Authors and Affiliations

  1. Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China

    Rongjia Mao, Jing Chen, Yuejun Chen & Zhigang Guo

Authors
  1. Rongjia Mao
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  2. Jing Chen
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  3. Yuejun Chen
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  4. Zhigang Guo
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Contributions

ZG designed research: RM and YC perpfomed research: JC analyzed the data: RM and JC wrote the paper.

Corresponding author

Correspondence to Zhigang Guo.

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The authors declare that they have no conflict of interests.

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Fig. S1

GO classification of the transcriptome unigenes (TIFF 1040 kb)

Fig. S2

GO classification of the DEGs in the 12 MeJA treated samples (TIFF 1172 kb)

Table S1

Primers used in the qRT-PCR (XLSX 10 kb)

Table S2

Transcriptome and digital gene expression sequencing statistics (XLSX 11 kb)

Table S3

The sequences of the unigenes which clustered by Trinity (XLSX 29217 kb)

Table S4

Annotation details of the transcripts and unigenes (XLSX 4248 kb)

Table S5

KEGG mapping of the transcriptome unigenes (XLSX 160 kb)

Table S6

Unigenes expression level estimated based on average RPKM values (XLSX 5095 kb)

Table S7

Correlation coefficients between 12 MeJA treated samples calculated based on RPKM values (XLSX 10 kb)

Table S8

DEGs in the 12 MeJA treated samples based on RPKM values (XLSX 619 kb)

Table S9

KEGG mapping of the DEGs in the 12 MeJA treated samples (XLSX 24 kb)

Table S10

Paclitaxel biosynthesis pathway gene expression levels after jasmonate treatment based on average RPKM values (XLSX 12 kb)

Table S11

Potential paclitaxel biosynthesis-related unigenes induced by jasmonate treatment (XLSX 14 kb)

Table S12

Phenylalanine metabolism pathway unigenes induced by jasmonate treatment (XLSX 12 kb)

Table S13

Transcription factors identified in the transcriptome and DEGs (XLSX 89 kb)

Table S14

Paclitaxel biosynthesis pathway gene expression levels evaluated by qRT-PCR (XLSX 22 kb)

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Mao, R., Chen, J., Chen, Y. et al. Identification of early jasmonate-responsive genes in Taxus × media cells by analyzing time series digital gene expression data. Physiol Mol Biol Plants 24, 715–727 (2018). https://doi.org/10.1007/s12298-018-0527-2

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  • DOI: https://doi.org/10.1007/s12298-018-0527-2

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