Genomic analyses of pneumococci reveal a wide diversity of bacteriocins - including pneumocyclicin, a novel circular bacteriocin
File(s)
Published version
Author(s)
Bogaardt, C
van Tonder, AJ
Brueggemann, AB
Type
Journal Article
Abstract
Background: One of the most important global pathogens infecting all age groups is Streptococcus pneumoniae
(the ‘pneumococcus’). Pneumococci reside in the paediatric nasopharynx, where they compete for space and
resources, and one competition strategy is to produce a bacteriocin (antimicrobial peptide or protein) to attack
other bacteria and an immunity protein to protect against self-destruction. We analysed a collection of 336 diverse
pneumococcal genomes dating from 1916 onwards, identified bacteriocin cassettes, detailed their genetic composition
and sequence diversity, and evaluated the data in the context of the pneumococcal population structure.
Results: We found that all genomes maintained a blp bacteriocin cassette and we identified several novel blp cassettes
and genes. The composition of the ‘bacteriocin/immunity region’ of the blp cassette was highly variable: one cassette
possessed six bacteriocin genes and eight putative immunity genes, whereas another cassette had only one of each.
Both widely-distributed and highly clonal blp cassettes were identified. Most surprisingly, one-third of pneumococcal
genomes also possessed a cassette encoding a novel circular bacteriocin that we called pneumocyclicin, which
shared a similar genetic organisation to well-characterised circular bacteriocin cassettes in other bacterial species.
Pneumocyclicin cassettes were mainly of one genetic cluster and largely found among seven major pneumococcal
clonal complexes.
Conclusions: These detailed genomic analyses revealed a novel pneumocyclicin cassette and a wide variety of blp
bacteriocin cassettes, suggesting that competition in the nasopharynx is a complex biological phenomenon.
(the ‘pneumococcus’). Pneumococci reside in the paediatric nasopharynx, where they compete for space and
resources, and one competition strategy is to produce a bacteriocin (antimicrobial peptide or protein) to attack
other bacteria and an immunity protein to protect against self-destruction. We analysed a collection of 336 diverse
pneumococcal genomes dating from 1916 onwards, identified bacteriocin cassettes, detailed their genetic composition
and sequence diversity, and evaluated the data in the context of the pneumococcal population structure.
Results: We found that all genomes maintained a blp bacteriocin cassette and we identified several novel blp cassettes
and genes. The composition of the ‘bacteriocin/immunity region’ of the blp cassette was highly variable: one cassette
possessed six bacteriocin genes and eight putative immunity genes, whereas another cassette had only one of each.
Both widely-distributed and highly clonal blp cassettes were identified. Most surprisingly, one-third of pneumococcal
genomes also possessed a cassette encoding a novel circular bacteriocin that we called pneumocyclicin, which
shared a similar genetic organisation to well-characterised circular bacteriocin cassettes in other bacterial species.
Pneumocyclicin cassettes were mainly of one genetic cluster and largely found among seven major pneumococcal
clonal complexes.
Conclusions: These detailed genomic analyses revealed a novel pneumocyclicin cassette and a wide variety of blp
bacteriocin cassettes, suggesting that competition in the nasopharynx is a complex biological phenomenon.
Date Issued
2015-07-28
Date Acceptance
2015-06-26
Citation
BMC Genomics, 2015, 16 (1)
ISSN
1471-2164
Publisher
BioMed Central
Journal / Book Title
BMC Genomics
Volume
16
Issue
1
Copyright Statement
© 2015 Bogaardt et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution
License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://
creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://
creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Identifier
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Subjects
Science & Technology
Life Sciences & Biomedicine
Biotechnology & Applied Microbiology
Genetics & Heredity
STREPTOCOCCUS-PNEUMONIAE
GENETIC-TRANSFORMATION
PEPTIDE
RECOMBINATION
COMPETENCE
IMMUNITY
SEROTYPE
DISEASE
IDENTIFICATION
VISUALIZATION
Bacterial Proteins
Bacteriocins
Base Composition
Genome, Bacterial
Multigene Family
Sequence Homology, Nucleic Acid
Streptococcus pneumoniae
Bioinformatics
06 Biological Sciences
11 Medical And Health Sciences
08 Information And Computing Sciences
Publication Status
Published
Article Number
ARTN 554