Diverse Ecological Strategies Are Encoded by Streptococcus pneumoniae Bacteriocin-Like Peptides

Genome Biology and Evolution

Volumn 8, Issue 4, 2016, Pages 1072-1090

  Miller, Eric L ^a,b   Abrudan, Monica I ^a,b   Roberts, Ian S ^a   Rozen, Daniel E ^a,b  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b LEIDEN UNIVERSITY   (Netherlands)

Author keywords

Antagonism.; Bacteriocin; Bioinformatics; Ecological strategies; Interference competition

Indexed keywords

BACTERIOCIN;

ALLELE; AMINO ACID SEQUENCE; ANTIBIOSIS; BACTERIAL GENOME; CHEMISTRY; GENE EXPRESSION REGULATION; GENETIC VARIATION; GENETICS; HUMAN; METABOLISM; MICROBIOLOGY; NASOPHARYNX; OPERON; PHYLOGENY; PHYSIOLOGY; PNEUMOCOCCAL INFECTION; STREPTOCOCCUS PNEUMONIAE;

ALLELES; AMINO ACID SEQUENCE; ANTIBIOSIS; BACTERIOCINS; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC VARIATION; GENOME, BACTERIAL; HUMANS; NASOPHARYNX; OPERON; PHYLOGENY; PNEUMOCOCCAL INFECTIONS; STREPTOCOCCUS PNEUMONIAE;

EID: 85015352699     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evw055     Document Type: Article

References (62)

1. Abrudan MI, Brown S, Rozen DE. 2012. Killing as means of promoting biodiversity. Biochem Soc Trans. 40:1512–1516.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403–410.
3. Aziz RK, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75.
4. Bakkal S, Robinson SM, Ordonez CL, Waltz DA, Riley MA. 2010. Role of bacteriocins in mediating interactions of bacterial isolates taken from cystic fibrosis patients. Microbiology 156:2058–2067.
5. Black S, et al. 2000. Efficacy, safety and immunogenicity of heptavalent pneumococcal conjugate vaccine in children. Northern California Kaiser Permanente Vaccine Study Center Group. Pediatr Infect Dis J. 19:187–195.
6. Bogaardt C, van Tonder AJ, Brueggemann AB. 2015. Genomic analyses of pneumococci reveal a wide diversity of bacteriocins—including pneumocyclicin, a novel circular bacteriocin. BMC Genomics 16:554.
7. Bogaert D, et al. 2001. Pneumococcal carriage in children in the Netherlands: a molecular epidemiological study. J Clin Microbiol. 39:3316–3320.
8. Brugger SD, Frey P, Aebi S, Hinds J, Muhlemann K. 2010. Multiple colonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal polysaccharide vaccine. PLoS One 5:e11638.
9. Chancey ST, et al. 2015. Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae. Front Microbiol. 6:1–14.
10. Chewapreecha C, et al. 2014. Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet. 46:305–309.
11. Croucher NJ, Finkelstein JA, et al. 2013. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet. 45:656–663.
12. Croucher NJ, Mitchell AM, et al. 2013. Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection. PLoS Genet. 9:e1003868.
13. Croucher NJ, et al. 2011. Rapid pneumococcal evolution in response to clinical interventions. Science 331:430–434.
14. Cutts FT, et al. 2005. Efficacy of nine-valent pneumococcal conjugate vaccine against pneumonia and invasive pneumococcal disease in The Gambia: randomised, double-blind, placebo-controlled trial. Lancet 365:1139–1146.
15. Czárán TL, Hoekstra RF, Pagie L. 2002. Chemical warfare between microbes promotes biodiversity. Proc Natl Acad Sci U S A. 99:786–790.
16. Davis SM, Deloria-Knoll M, Kassa HT, O’Brien KL. 2013. Impact of pneumococcal conjugate vaccines on nasopharyngeal carriage and invasive disease among unvaccinated people: review of evidence on indirect effects. Vaccine 32:133–145.
17. Dawid S, Roche AM, Weiser JN. 2007. The blp bacteriocins of Streptococcus pneumoniae mediate intraspecies competition both in vitro and in vivo. Infect Immun. 75:443–451.
18. De Saizieu A, et al. 2000. Microarray-based identification of a novel Streptococcus pneumoniae regulon controlled by an autoinduced peptide. J Bacteriol. 182:4696–4703.
19. Feil EJ, Li BC, Aanensen DM, Hanage WP, Spratt BG. 2004. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol. 186:1518–1530.
20. García-Rodríguez JA, Fresnadillo Martínez MJ. 2002. Dynamics of nasopharyngeal colonization by potential respiratory pathogens. J Antimicrob Chemother. 50(Suppl. S):59–73.
21. Gladman S, Seemann T. 2008. VelvetOptimiser. http://www.vicbioinformatics.com/software.velvetoptimiser.shtml [last accessed November 20, 2013].
22. Guiral S, Mitchell TJ, Martin B, Claverys JP. 2005. Competence-programmed predation of noncompetent cells in the human pathogen Streptococcus pneumoniae: genetic requirements. Proc Natl Acad Sci U S A. 102:8710–8715.
23. Håvarstein LS, Diep DB, Nes IF. 1995. A family of bacteriocin ABC transporters carry out proteolytic processing of their substrates concomitant with export. Mol Microbiol. 16:229–240.
24. Hawlena H, Bashey F, Lively CM. 2012. Bacteriocin-mediated interactions within and between coexisting species. Ecol Evol. 2:2521–2526.
25. Holm S. 1979. A simple sequentially rejective multiple test procedure. Scand J Stat. 6:65–70.
26. Hoover SE, et al. 2015. A new quorum-sensing system (TprA/PhrA) for Streptococcus pneumoniae D39 that regulates a lantibiotic biosynthe-sis gene cluster. Mol Microbiol. 97:229–243.
27. Johnston C, Campo N, Bergé MJ, Polard P, Claverys JP. 2014. Streptococcus pneumoniae, le transformiste. Trends Microbiol. 22:113–119.
28. Jolley KA, Maiden MC. 2010. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595.
29. Kearse M, et al. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649.
30. Kerr B, Riley MA, Feldman MW, Bohannan BJM. 2002. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418:171–174.
31. Kirkup BC, Riley MA. 2004. Antibiotic-mediated antagonism leads to a bacterial game of rock-paper-scissors in vivo. Nature 428:412–414.
32. Kjos M, Snipen L, Salehian Z, Nes IF, Diep DB. 2010. The Abi proteins and their involvement in bacteriocin self-immunity. J Bacteriol. 192:2068–2076.
33. Kjos M, et al. 2011. Target recognition, resistance, immunity and genome mining of class II bacteriocins from Gram-positive bacteria. Microbiology 157:3256–3267.
34. Kjos M, et al. 2016. Expression of Streptococcus pneumoniae bacteriocins is induced by antibiotics via regulatory interplay with the competence system. PLoS Pathog. 12:e1005422.
35. Klugman KP, et al. 2003. A trial of a 9-valent pneumococcal conjugate vaccine in children with and those without HIV infection. N Engl J Med. 349:1341–1348.
36. Kozlov AM, Aberer AJ, Stamatakis A. 2015. ExaML version 3: a tool for phylogenomic analyses on supercomputers. Bioinformatics 31:2577–2579.
37. Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452.
38. Lunter G, Goodson M. 2011. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 21:936–939.
39. Lux T, Nuhn M, Hakenbeck R, Reichmann P. 2007. Diversity of bacteriocins and activity spectrum in Streptococcus pneumoniae. J Bacteriol. 189:7741–7751.
40. Majeed H, Gillor O, Kerr B, Riley MA. 2011. Competitive interactions in Escherichia coli populations: the role of bacteriocins. ISME J. 5:71–81.
41. McGee L, et al. 2001. Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network. J Clin Microbiol. 39:2565–2571.
42. Nissen-Meyer J, Oppegård C, Rogne P, Haugen HS, Kristiansen PE. 2010. Structure and mode-of-action of the two-peptide (class-IIb) bacteriocins. Probiotics Antimicrob Proteins. 2:52–60.
43. O’Brien KL, et al. 2003. Efficacy and safety of seven-valent conjugate pneumococcal vaccine in American Indian children: group randomised trial. Lancet 362:355–361.
44. O’Brien KL, et al. 2009. Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. Lancet 374:893–902.
45. Pagel M, Meade A, Barker D. 2004. Bayesian estimation of ancestral character states on phylogenies. Syst Biol. 53:673–684.
46. Pei J, Grishin NV. 2001. Type II CAAX prenyl endopeptidases belong to a novel superfamily of putative membrane-bound metalloproteases. Trends Biochem Sci. 26:275–277.
47. Pinchas MD, LaCross NC, Dawid S. 2015. An electrostatic interaction between BlpC and BlpH dictates pheromone specificity in the control of bacteriocin production and immunity in Streptococcus pneumoniae. J Bacteriol. 197:1236–1248.
48. R Core Team. 2013. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing. Available from: http://www.R–project.org/.
49. Regev-Yochay G, et al. 2004. Nasopharyngeal carriage of Streptococcus pneumoniae by adults and children in community and family settings. Clin Infect Dis. 38:632–639.
50. Reichmann P, Hakenbeck R. 2000. Allelic variation in a peptide-inducible two-component system of Streptococcus pneumoniae. FEMS Microbiol Lett. 190:231–236.
51. Riley MA, Gordon DM. 1999. The ecological role of bacteriocins in bacterial competition. Trends Microbiol. 7:129–133.
52. Riley MA, Wertz JE. 2002. Bacteriocins: evolution, ecology, and application. Annu Rev Microbiol. 56:117–137.
53. RStudio Team. 2015. RStudio: integrated development environment for R. Boston (MA): RStudio, Inc. Available from: http://www.rstudio.com/.
54. Sauver JS, et al. 2000. Risk factors for otitis media and carriage of multiple strains of Haemophilus influenzae and Streptococcus pneumoniae. Emerg Infect Dis. 6:622–630.
55. Spijkerman J, et al. 2012. Long-term effects of pneumococcal conjugate vaccine on nasopharyngeal carriage of S. pneumoniae, S. aureus, H. influenzae and M. catarrhalis. PLoS One 7:3–8.
56. Spratt BG, Hanage WP, Li B, Aanensen DM, Feil EJ. 2004. Displaying the relatedness among isolates of bacterial species—the eBURST approach. FEMS Microbiol Lett. 241:129–134.
57. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690.
58. Tocheva AS, et al. 2011. Declining serotype coverage of new pneumococcal conjugate vaccines relating to the carriage of Streptococcus pneumoniae in young children. Vaccine 29:4400–4404.
59. Turner KME, Hanage WP, Fraser C, Connor TR, Spratt BG. 2007. Assessing the reliability of eBURST using simulated populations with known ancestry. BMC Microbiol. 7:30.
60. Wyllie AL, et al. 2014. Streptococcus pneumoniae in saliva of Dutch primary school children. PLoS One 9:1–8.
61. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829.
62. Zhao X, van der Donk WA. 2016. Structural characterization and bioac-tivity analysis of the two-component lantibiotic Flv system from a ruminant bacterium. Cell Chem Biol. 23:1–11.