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Open Access Research article

The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance

Qing Li1, Junfeng Chen1, Ying Xiao13, Peng Di1, Lei Zhang2* and Wansheng Chen1*

Author Affiliations

1 Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, No. 415 Fengyang Road, Huangpu District, Shanghai 200003, China

2 Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, No. 325 Guohe Road, Yangpu District, Shanghai 200433, China

3 The MOE Key Laboratory of Standardization of Chinese Medicines, Institute of Chinese Materia Medica,Shanghai University of Traditional Chinese Medicine, Shanghai 201210, China

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BMC Genomics 2014, 15:388  doi:10.1186/1471-2164-15-388

Published: 20 May 2014

Abstract

Background

Isatis indigotica Fort. is one of the most commonly used traditional Chinese medicines. Its antiviral compound is a kind of lignan, which is formed with the action of dirigent proteins (DIR). DIR proteins are members of a large family of proteins which impart stereoselectivity on the phenoxy radical-coupling reaction, yielding optically active lignans from two molecules of E-coniferyl alcohol. They exist in almost every vascular plant. However, the DIR and DIR-like protein gene family in I. indigotica has not been analyzed in detail yet. This study focuses on discovery and analysis of this protein gene family in I. indigotica for the first time.

Results

Analysis of transcription profiling database from I. indigotica revealed a family of 19 full-length unique DIR and DIR-like proteins. Sequence analysis found that I. indigotica DIR and DIR-like proteins (IiDIR) were all-beta strand proteins, with a signal peptide at the N-terminus. Phylogenetic analysis of the 19 proteins indicated that the IiDIR genes cluster into three distinct subfamilies, DIR-a, DIR-b/d, and DIR-e, of a larger plant DIR and DIR-like gene family. Gene-specific primers were designed for 19 unique IiDIRs and were used to evaluate patterns of constitutive expression in different organs. It showed that most IiDIR genes were expressed comparatively higher in roots and flowers than stems and leaves.

Conclusions

New DIR and DIR-like proteins were discovered from the transcription profiling database of I. indigotica through bioinformatics methods for the first time. Sequence characteristics and transcript abundance of these new genes were analyzed. This study will provide basic data necessary for further studies.

Keywords:
Dirigent and dirigent-like proteins; Isatis indigotica; Bioinformatics; Secondary structures; Tertiary structures; Phylogenetic analysis; Transcript abundance