About: EST analysis reveals putative genes involved in glycyrrhizin biosynthesis

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

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	EST analysis reveals putative genes involved in glycyrrhizin biosynthesis
Creator	Wang, Ning Sun, Chao Li, Ying Chen, Shi-Lin Luo, Hong-Mei Song, Jing-Yuan Steinmetz, André Sun, Yong-Zhen Wu, Qiong Yao, Hui
Source	Medline; PMC
abstract	BACKGROUND: Glycyrrhiza uralensis is one of the most popular medicinal plants in the world and is also widely used in the flavoring of food and tobacco. Due to limited genomic and transcriptomic data, the biosynthetic pathway of glycyrrhizin, the major bioactive compound in G. uralensis, is currently unclear. Identification of candidate genes involved in the glycyrrhizin biosynthetic pathway will significantly contribute to the understanding of the biosynthetic and medicinal chemistry of this compound. RESULTS: We used the 454 GS FLX platform and Titanium regents to produce a substantial expressed sequence tag (EST) dataset from the vegetative organs of G. uralensis. A total of 59,219 ESTs with an average read length of 409 bp were generated. 454 ESTs were combined with the 50,666 G. uralensis ESTs in GenBank. The combined ESTs were assembled into 27,229 unique sequences (11,694 contigs and 15,535 singletons). A total of 20,437 unique gene elements representing approximately 10,000 independent transcripts were annotated using BLAST searches (e-value ≤ 1e-5) against the SwissProt, KEGG, TAIR, Nr and Nt databases. The assembled sequences were annotated with gene names and Gene Ontology (GO) terms. With respect to the genes related to glycyrrhizin metabolism, genes encoding 16 enzymes of the 18 total steps of the glycyrrhizin skeleton synthesis pathway were found. To identify novel genes that encode cytochrome P450 enzymes and glycosyltransferases, which are related to glycyrrhizin metabolism, a total of 125 and 172 unigenes were found to be homologous to cytochrome P450s and glycosyltransferases, respectively. The cytochrome P450 candidate genes were classified into 32 CYP families, while the glycosyltransferase candidate genes were classified into 45 categories by GO analysis. Finally, 3 cytochrome P450 enzymes and 6 glycosyltransferases were selected as the candidates most likely to be involved in glycyrrhizin biosynthesis through an organ-specific expression pattern analysis based on real-time PCR. CONCLUSIONS: Using the 454 GS FLX platform and Titanium reagents, our study provides a high-quality EST database for G. uralensis. Based on the EST analysis, novel candidate genes related to the secondary metabolite pathway of glycyrrhizin, including novel genes encoding cytochrome P450s and glycosyltransferases, were found. With the assistance of organ-specific expression pattern analysis, 3 unigenes encoding cytochrome P450s and 6 unigenes encoding glycosyltransferases were selected as the candidates most likely to be involved in glycyrrhizin biosynthesis.
has issue date	2010-04-28(xsd:dateTime)
bibo:doi	10.1186/1471-2164-11-268
bibo:pmid	20423525
has license	cc-by
sha1sum (hex)	9bbf07c4bf022a0695b79b87cb4299f6a8d18831
schema:url	https://doi.org/10.1186/1471-2164-11-268
resource representing a document's title	EST analysis reveals putative genes involved in glycyrrhizin biosynthesis
has PubMed Central identifier	PMC2886062
has PubMed identifier	20423525
schema:publication	BMC Genomics
resource representing a document's body	covid:9bbf07c4bf022a0695b79b87cb4299f6a8d18831#body_text
is schema:about of	named entity 'glycyrrhizin' named entity 'involved' named entity 'GLYCYRRHIZIN' named entity 'GENES' named entity 'WORLD' named entity 'UNCLEAR' named entity 'FOOD' named entity 'GLYCYRRHIZA URALENSIS' named entity 'USED' named entity 'BIOSYNTHETIC' named entity 'FLAVORING' named entity 'MEDICINAL CHEMISTRY' named entity 'ONE OF' named entity 'INVOLVED' named entity 'GENOMIC' named entity 'CURRENTLY' named entity 'CONTRIBUTE ' named entity 'TRANSCRIPTOMIC DATA' named entity 'PATHWAY' named entity 'LIMITED' named entity 'UNDERSTANDING' named entity 'INVOLVED' named entity 'REVEALS' named entity 'BIOSYNTHESIS' named entity 'EST ANALYSIS' named entity 'DUE TO' named entity 'MEDICINAL PLANTS' named entity 'GLYCYRRHIZIN' named entity 'CANDIDATE GENES' named entity 'MAJOR' named entity 'BACKGROUND' named entity 'TOBACCO' named entity 'COMPOUND' named entity 'IDENTIFICATION' named entity 'Identification' named entity 'glycyrrhizin' named entity 'biosynthetic pathway' named entity 'bioactive compound' named entity 'cytochrome P450 monooxygenase' named entity 'biosynthetic pathway' named entity 'triterpene' named entity 'EC 2.2.1.7' named entity 'tissue sample' named entity 'DNase' named entity 'oxidation' named entity 'biosynthetic pathway' named entity 'glycyrrhizin' named entity 'Glycosyltransferases' named entity 'β-amyrin' named entity 'glycosyltransferase' named entity 'glycyrrhizin' named entity 'cytosolic' named entity 'glycyrrhizin' named entity 'RNA extraction' named entity 'glycyrrhizin' named entity 'gene' named entity 'unigenes' named entity 'biosynthesis' named entity 'secondary metabolism' named entity 'biosynthesis' named entity 'glycyrrhizin' named entity 'gene' named entity 'flavonoids' named entity 'Arabidopsis thaliana' named entity 'absorbance' named entity '0.01' named entity 'Triterpenoids' named entity 'contigs' named entity 'EC 2.2.1.7' named entity 'Ningxia' named entity 'unigenes' named entity 'cDNA library'

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