A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-11-11

AUTHORS

James T. Morton, Stefan D. Freed, Shaun W. Lee, Iddo Friedberg

ABSTRACT

BackgroundBacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signaling molecules as well as their better known roles as antibiotics. To date, close to five hundred bacteriocins have been identified and classified. Recent discoveries have shown that bacteriocins are highly diverse and widely distributed among bacterial species. Given the heterogeneity of bacteriocin compounds, many tools struggle with identifying novel bacteriocins due to their vast sequence and structural diversity. Many bacteriocins undergo post-translational processing or modifications necessary for the biosynthesis of the final mature form. Enzymatic modification of bacteriocins as well as their export is achieved by proteins whose genes are often located in a discrete gene cluster proximal to the bacteriocin precursor gene, referred to as context genes in this study. Although bacteriocins themselves are structurally diverse, context genes have been shown to be largely conserved across unrelated species.MethodsUsing this knowledge, we set out to identify new candidates for context genes which may clarify how bacteriocins are synthesized, and identify new candidates for bacteriocins that bear no sequence similarity to known toxins. To achieve these goals, we have developed a software tool, Bacteriocin Operon and gene block Associator (BOA) that can identify homologous bacteriocin associated gene blocks and predict novel ones. BOA generates profile Hidden Markov Models from the clusters of bacteriocin context genes, and uses them to identify novel bacteriocin gene blocks and operons.Results and conclusionsWe provide a novel dataset of predicted bacteriocins and context genes. We also discover that several phyla have a strong preference for bacteriocin genes, suggesting distinct functions for this group of molecules.Software Availabilityhttps://github.com/idoerg/BOA More... »

PAGES

381

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12859-015-0792-9

DOI

http://dx.doi.org/10.1186/s12859-015-0792-9

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1010349619

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/26558535


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207 schema:name Chemistry Biochemistry Biology Interface Program, University of Notre Dame, South Bend, IN, USA
208 Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, South Bend, IN, USA
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212 Department of Computer Science and Software engineering, Miami University, Oxford, OH, USA
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214 grid-institutes:grid.34421.30 schema:alternateName Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
215 schema:name Department of Computer Science and Software engineering, Miami University, Oxford, OH, USA
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