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

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About: The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance
Creator	Li, Qing Chen, Junfeng Zhang, Lei Chen, Wansheng Xiao, Ying Di, Peng
Source	Medline; PMC
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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-388) contains supplementary material, which is available to authorized users.
has issue date	2014-05-20(xsd:dateTime)
bibo:doi	10.1186/1471-2164-15-388
bibo:pmid	24885106
has license	cc-by
sha1sum (hex)	c8fae9fb3ab55e35384170c08c05fdcada6360e6
schema:url	https://doi.org/10.1186/1471-2164-15-388
resource representing a document's title	The dirigent multigene family in Isatis indigotica: gene discovery and differential transcript abundance
has PubMed Central identifier	PMC4052678
has PubMed identifier	24885106
schema:publication	BMC Genomics
resource representing a document's body	covid:c8fae9fb3ab55e35384170c08c05fdcada6360e6#body_text
is schema:about of	named entity 'proteins' named entity 'family' named entity 'compound' named entity 'family' named entity 'ANTIVIRAL' named entity 'STEREOSELECTIVITY' named entity 'COMPOUND' named entity 'LARGE FAMILY' named entity 'TIME' named entity 'They' named entity 'kind' named entity 'exist' named entity 'stereoselectivity' named entity 'optically active' named entity 'phenoxy' named entity 'stereoselectivity' named entity 'coupling reaction' named entity 'vascular plant' named entity 'Isatis indigotica' named entity 'gene' named entity 'focuses' named entity 'RNA' named entity 'protein' named entity 'Open Reading Frame' named entity 'antiviral' named entity 'protein' named entity 'amino acid sequences' named entity 'cDNA' named entity 'RNA' named entity 'pea' named entity 'N-terminus' named entity 'β-strands' named entity 'lignin' named entity 'epidemic' named entity 'melting curve analysis' named entity 'Secondary structure' named entity 'Isatis indigotica' named entity 'tertiary structures' named entity 'Thuja plicata' named entity 'signal peptide' named entity 'lignin' named entity 'sulfur' named entity 'Applied Biosystems' named entity 'alcohols' named entity 'gene' named entity 'homology' named entity 'signal peptide' named entity 'transcription' named entity 'reverse transcribed' named entity 'non-specific' named entity 'organ' named entity 'optically active' named entity 'molecular formula' named entity 'technical replicates' named entity 'X-ray' named entity 'protein sequences' named entity 'phenoxy' named entity 'TBLASTN' named entity 'Phyre2' named entity 'Real-time PCR' named entity 'Beijing' named entity 'transcription' named entity 'aromatic' named entity 'homologous' named entity 'protein' named entity 'antiviral' named entity 'corn' named entity 'expression analysis' named entity 'plant development' named entity 'tertiary structures' named entity 'China' named entity 'lignans' named entity 'anti-estrogenic' named entity 'infections of the upper respiratory tract' named entity 'amino acid sequences' named entity 'vacuolar'

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