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BMC Bioinformatics. 2015 Nov 11;16:381. doi: 10.1186/s12859-015-0792-9.

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins.

Author information

1
Department of Computer Science and Software engineering, Miami University, Oxford, OH, USA. jamietmorton@gmail.com.
2
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA. jamietmorton@gmail.com.
3
Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, South Bend, IN, USA. stefan_freed@nd.edu.
4
Chemistry Biochemistry Biology Interface Program, University of Notre Dame, South Bend, IN, USA. stefan_freed@nd.edu.
5
Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, South Bend, IN, USA. shaun_lee@nd.edu.
6
Department of Computer Science and Software engineering, Miami University, Oxford, OH, USA. idoerg@iastate.edu.
7
Department of Microbiology, Miami University, Oxford, OH, USA. idoerg@iastate.edu.
8
Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA. idoerg@iastate.edu.

Abstract

BACKGROUND:

Bacteriocins 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.

METHODS:

Using 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 CONCLUSIONS:

We 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 AVAILABILITY:

https://github.com/idoerg/BOA.

PMID:
26558535
PMCID:
PMC4642626
DOI:
10.1186/s12859-015-0792-9
[Indexed for MEDLINE]
Free PMC Article

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