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BMC Microbiology

, 12:294

Microbial genetics, genomics and proteomics

Abstract

BackgroundTo derive post-genomic, neutral insight into the peptidoglycan PG distribution among organisms, we mined 1,644 genomes listed in the Carbohydrate-Active Enzymes database for the presence of a minimal 3-gene set that is necessary for PG metabolism. This gene set consists of one gene from the glycosyltransferase family GT28, one from family GT51 and at least one gene belonging to one of five glycoside hydrolase families GH23, GH73, GH102, GH103 and GH104.

ResultsNone of the 103 Viruses or 101 Archaea examined possessed the minimal 3-gene set, but this set was detected in 1-42 of the Eukarya members Micromonas sp., coding for GT28, GT51 and GH103 and in 1,260-1,398 90.1% of Bacteria, with a 100% positive predictive value for the presence of PG. Pearson correlation test showed that GT51 family genes were significantly associated with PG with a value of 0.963 and a p value less than 10. This result was confirmed by a phylogenetic comparative analysis showing that the GT51-encoding gene was significantly associated with PG with a Pagels score of 60 and 51 percentage of error close to 0%. Phylogenetic analysis indicated that the GT51 gene history comprised eight loss and one gain events, and suggested a dynamic on-going process.

ConclusionsGenome analysis is a neutral approach to explore prospectively the presence of PG in uncultured, sequenced organisms with high predictive values.

KeywordsPeptidoglycanGenomeGlycoside hydrolaseGlycosyltransferaseGramBeta-lactaminesGlycopeptidesAbbreviationsBLASTBasic Local Alignment Search Tool

CazyCarbohydrate Active Enzymes

GHGglycoside hydrolase

GOLDGenome OnLine Database

GTGlycosyltransferase

HAMAPHigh-quality Automated and Manual Annotation of microbial Proteomes

NCBINational Center for Biotechnology Information

PCAPrincipal component analysis

PGPeptidoglycan.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2180-12-294 contains supplementary material, which is available to authorized users.

An erratum to this article is available at http:-dx.doi.org-10.1186-1471-2180-14-123.

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Autor: CarolineCayrou - BernardHenrissat - PhilippeGouret - PierrePontarotti - MichelDrancourt

Fuente: https://link.springer.com/



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