title: The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance.
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.
authors.forename: Qing
authors.initials: Q
authors.lastname: Li
authors.forename: Junfeng
authors.initials: J
authors.lastname: Chen
authors.forename: Ying
authors.initials: Y
authors.lastname: Xiao
authors.forename: Peng
authors.initials: P
authors.lastname: Di
authors.affiliation: Department of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, No, 415 Fengyang Road, Huangpu District, Shanghai 200003, China. zhanglei@smmu.edu.cn.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.forename: Wansheng
authors.initials: W
authors.lastname: Chen
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D030541:Databases, Genetic; D031219:Isatis / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D016366:Open Reading Frames; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
chemical_list: D010940:Plant Proteins