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Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

Lookup NU author(s): Emeritus Professor Harry Gilbert

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Abstract

Motivation: A bacterial polysaccharide utilization locus (PUL) is a set of physically linked genes that orchestrate the breakdown of a specific glycan. PULs are prevalent in the Bacteroidetes phylum and are key to the digestion of complex carbohydrates, notably by the human gut microbiota. A given Bacteroidetes genome can encode dozens of different PULs whose boundaries and precise gene content are difficult to predict.Results: Here, we present a fully automated approach for PUL prediction using genomic context and domain annotation alone. By combining the detection of a pair of marker genes with operon prediction using intergenic distances, and queries to the carbohydrate-active enzymes database (www.cazy.org), our predictor achieved above 86% accuracy in two Bacteroides species with extensive experimental PUL characterization.

Publication metadata

Author(s): Terrapon N, Lombard V, Gilbert HJ, Henrissat B

Publication type: Article

Publication status: Published

Journal: Bioinformatics

Year: 2015

Volume: 31

Issue: 5

Pages: 647-655

Print publication date: 01/03/2015

Online publication date: 28/10/2014

Acceptance date: 23/10/2014

ISSN (print): 1367-4803

ISSN (electronic): 1460-2059

Publisher: Oxford University Press

URL: http://dx.doi.org/10.1093/bioinformatics/btu716

DOI: 10.1093/bioinformatics/btu716

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