Molecular Biology Reports

, Volume 43, Issue 12, pp 1395–1409 | Cite as

Comparative transcriptome analysis in different tissues of a medicinal herb, Picrorhiza kurroa pinpoints transcription factors regulating picrosides biosynthesis

  • Ira Vashisht
  • Tarun Pal
  • Hemant Sood
  • Rajinder S. Chauhan
Original Article
First Online:
Received:
Accepted:

Abstract

Transcriptional regulation of picrosides biosynthesis, the iridoid glycosides of an endangered medicinal herb, Picrorhiza kurroa, is completely unknown. P. kurroa plants obtained from natural habitat accumulate higher picrosides than in-vitro cultured plants, which necessitates identification of transcription factors (TFs) regulating their differential biosynthesis. The current study investigates complete spectrum of different TF classes in P. kurroa transcriptomes and discerns their association with picrosides biosynthesis. Transcriptomes of differential picroside-I content shoots and picroside-II content roots were mined for seven classes of TFs implicated in secondary metabolism regulation in plants. Key TFs were identified through in silico transcript abundance and qPCR analysis was performed to confirm transcript levels of TFs under study in differential content tissues and genotypes. Promoter regions of key picrosides biosynthetic pathway genes were explored to hypothesize which TFs can possibly regulate target genes. A total of 131, 137, 107, 82 and 101 transcripts encoding different TFs families were identified in PKS-25, PKS-15, PKSS, PKR-25 and PKSR transcriptomes, respectively. ERF-18, bHLH-104, NAC-25, 32, 94 and SUF-4 showed elevated expression in roots (up to 37 folds) and shoots (up to 195 folds) of plants obtained from natural habitat, indicating their role as activators of picrosides biosynthesis whereas, elevated expression of WRKY-17, 40, 71 and MYB-4 in low picrosides content conditions suggested their down-regulatory role. In silico analysis of key picrosides biosynthetic pathway gene promoter regions revealed binding domains for ERF-18, NAC-25, WRKY-40 and MYB-4. Identification of candidate TFs contributing towards picrosides biosynthesis is a pre-requisite for designing appropriate metabolic engineering strategies aimed at enhancing picrosides content in vitro and in vivo.

Keywords

Picrorhiza kurroa Picrosides Transcription factors Secondary metabolism Transcriptome 

Abbreviations

TF

Transcription factor

P. kurroa

Picrorhiza kurroa

PKS-25

P. kurroa in vitro-cultured shoots grown at 25 °C

PKS-15

P. kurroa in vitro-cultured shoots grown at 15 °C

PKR-25

P. kurroa in vitro-cultured roots grown at 25 °C

PKSS

P. kurroa shoots obtained from natural habitat

PKSR

P. kurroa roots obtained from natural habitat

P-I and II

Picroside I and II

HMGR

Hydroxymethyl glutaryl CoA reductase

ISPD

2-C-methylerythritol 4-phosphate cytidyl transferase

DXPS

1-Deoxy-d-xylulose 5-phosphate synthase

PMK

Phosphomevalonate kinase

HFD

2 Hydroxyisoflavanone dehydratase

DAHPS

3-Deoxy-d-arabinoheptulosonate 7-phosphate synthase

ISPE

4-(Cytidine-5′-diphospho)-2-C-methyl-d-erythritol kinase

CM

Chorismate mutase

GS

Geraniol synthase

G10H

Geraniol 10-hydroxylase

EPSPS

5-Enolpyruvylshikimic acid-3-phosphate synthase

PAL

Phenylalanine ammonia lyase

SK

Shikimate kinase

pkdoubleWRKY

Double WRKY type transcription factor sequenced from P. kurroa

pkWRKY

WRKY class transcription factor isolated from P. kurroa

CPRF2

Common plant regulatory factor 2 (CPRF2) transcription factor

NAP

NAC like activated by APETALA3/PISTILLATA

COL

Constans like TF

RSEM

RNA-Seq by Expectation Maximization

FPKM

Fragments per kilobase of exon per million fragments mapped

NGS

Next generation sequencing

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Notes

Acknowledgments

The authors are thankful to the Department of Biotechnology, Ministry of Science & Technology, Government of India, for providing research grant in the form of a program support on high value medicinal plants to RSC.

Author contributions

RSC, IV and HS conceived and designed the experiments. IV and TP performed the experiments and analyzed the data. IV was involved in writing the manuscript. RSC and HS revised the manuscript critically and finally approved the manuscript to be published.

Supplementary material

11033_2016_4073_MOESM1_ESM.docx (65 kb)
Supplementary material 1 (DOCX 64 KB)

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Ira Vashisht
    • 1
  • Tarun Pal
    • 1
  • Hemant Sood
    • 1
  • Rajinder S. Chauhan
    • 1
  1. 1.Department of Biotechnology & BioinformaticsJaypee University of Information TechnologySolanIndia

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