Programmed Protection of Foreign DNA from Restriction Allows Pathogenicity Island Exchange during Pneumococcal Transformation
In bacteria, transformation and restriction-modification (R-M) systems play potentially antagonistic roles. While the former, proposed as a form of sexuality, relies on internalized foreign DNA to create genetic diversity, the latter degrade foreign DNA to protect from bacteriophage attack. The human pathogen Streptococcus pneumoniae is transformable and possesses either of two R-M systems, DpnI and DpnII, which respectively restrict methylated or unmethylated double-stranded (ds) DNA. S. pneumoniae DpnII strains possess DpnM, which methylates dsDNA to protect it from DpnII restriction, and a second methylase, DpnA, which is induced during competence for genetic transformation and is unusual in that it methylates single-stranded (ss) DNA. DpnA was tentatively ascribed the role of protecting internalized plasmids from DpnII restriction, but this seems unlikely in light of recent results establishing that pneumococcal transformation was not evolved to favor plasmid exchange. Here we validate an alternative hypothesis, showing that DpnA plays a crucial role in the protection of internalized foreign DNA, enabling exchange of pathogenicity islands and more generally of variable regions between pneumococcal isolates. We show that transformation of a 21.7 kb heterologous region is reduced by more than 4 logs in dpnA mutant cells and provide evidence that the specific induction of dpnA during competence is critical for full protection. We suggest that the integration of a restrictase/ssDNA-methylase couplet into the competence regulon maintains protection from bacteriophage attack whilst simultaneously enabling exchange of pathogenicicy islands. This protective role of DpnA is likely to be of particular importance for pneumococcal virulence by allowing free variation of capsule serotype in DpnII strains via integration of DpnI capsule loci, contributing to the documented escape of pneumococci from capsule-based vaccines. Generally, this finding is the first evidence for a mechanism that actively promotes genetic diversity of S. pneumoniae through programmed protection and incorporation of foreign DNA.
Vyšlo v časopise:
Programmed Protection of Foreign DNA from Restriction Allows Pathogenicity Island Exchange during Pneumococcal Transformation. PLoS Pathog 9(2): e32767. doi:10.1371/journal.ppat.1003178
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.ppat.1003178
Souhrn
In bacteria, transformation and restriction-modification (R-M) systems play potentially antagonistic roles. While the former, proposed as a form of sexuality, relies on internalized foreign DNA to create genetic diversity, the latter degrade foreign DNA to protect from bacteriophage attack. The human pathogen Streptococcus pneumoniae is transformable and possesses either of two R-M systems, DpnI and DpnII, which respectively restrict methylated or unmethylated double-stranded (ds) DNA. S. pneumoniae DpnII strains possess DpnM, which methylates dsDNA to protect it from DpnII restriction, and a second methylase, DpnA, which is induced during competence for genetic transformation and is unusual in that it methylates single-stranded (ss) DNA. DpnA was tentatively ascribed the role of protecting internalized plasmids from DpnII restriction, but this seems unlikely in light of recent results establishing that pneumococcal transformation was not evolved to favor plasmid exchange. Here we validate an alternative hypothesis, showing that DpnA plays a crucial role in the protection of internalized foreign DNA, enabling exchange of pathogenicity islands and more generally of variable regions between pneumococcal isolates. We show that transformation of a 21.7 kb heterologous region is reduced by more than 4 logs in dpnA mutant cells and provide evidence that the specific induction of dpnA during competence is critical for full protection. We suggest that the integration of a restrictase/ssDNA-methylase couplet into the competence regulon maintains protection from bacteriophage attack whilst simultaneously enabling exchange of pathogenicicy islands. This protective role of DpnA is likely to be of particular importance for pneumococcal virulence by allowing free variation of capsule serotype in DpnII strains via integration of DpnI capsule loci, contributing to the documented escape of pneumococci from capsule-based vaccines. Generally, this finding is the first evidence for a mechanism that actively promotes genetic diversity of S. pneumoniae through programmed protection and incorporation of foreign DNA.
Zdroje
1. Maynard SmithJ, DowsonCG, SprattBG (1991) Localized sex in bacteria. Nature 349: 29–31.
2. JohnsborgO, EldholmV, HåvarsteinLS (2007) Natural genetic transformation: prevalence, mechanisms and function. Res Microbiol 158: 767–778.
3. ClaverysJP, PrudhommeM, Mortier-BarrièreI, MartinB (2000) Adaptation to the environment: Streptococcus pneumoniae, a paradigm for recombination-mediated genetic plasticity? Mol Microbiol 35: 251–259.
4. CroucherNJ, HarrisSR, FraserC, QuailMA, BurtonJ, et al. (2011) Rapid pneumococcal evolution in response to clinical interventions. Science 331: 430–434.
5. BentleySD, AanensenDM, MavroidiA, SaundersD, RabbinowitschE, et al. (2006) Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet 2: e31.
6. TockMR, DrydenDT (2005) The biology of restriction and anti-restriction. Curr Opin Microbiol 8: 466–472.
7. LacksS, GreenbergB (1975) A deoxyribonuclease of Diplococcus pneumoniae specific for methylated DNA. J Biol Chem 250: 4060–4066.
8. LacksSA, MannarelliBM, SpringhornSS, GreenbergB (1986) Genetic basis of the complementary DpnI and DpnII restriction systems of S. pneumoniae: an intercellular cassette mechanism. Cell 46: 993–1000.
9. LeeMS, MorrisonDA (1999) Identification of a new regulator in Streptococcus pneumoniae linking quorum sensing to competence for genetic transformation. J Bacteriol 181: 5004–5016.
10. PetersonS, SungCK, ClineR, DesaiBV, SnesrudE, et al. (2004) Identification of competence pheromone responsive genes in Streptococcus pneumoniae. Mol Microbiol 51: 1051–1070.
11. LacksSA, AyalewS, de la CampaAG, GreenbergB (2000) Regulation of competence for genetic transformation in Streptococcus pneumoniae: expression of dpnA, a late competence gene encoding a DNA methyltransferase of the DpnII restriction system. Mol Microbiol 35: 1089–1098.
12. ClaverysJP, MartinB, PolardP (2009) The genetic transformation machinery: composition, localization and mechanism. FEMS Microbiol Rev 33: 643–656.
13. CerritelliS, SpringhornSS, LacksSA (1989) DpnA, a methylase for single-strand DNA in the Dpn II restriction system, and its biological function. Proc Natl Acad Sci USA 86: 9223–9227.
14. BerryAM, GlareEM, HansmanD, PatonJC (1989) Presence of a small plasmid in clinical isolates of Streptococcus pneumoniae. FEMS Microbiol Lett 65: 275–278.
15. SiboldC, MarkiewiczZ, LatorreC, HakenbeckR (1991) Novel plasmids in clinical strains of Streptococcus pneumoniae. FEMS Microbiol Lett 77: 91–96.
16. SaundersCW, GuildWR (1981) Pathway of plasmid transformation in pneumococcus: open circular and linear molecules are active. J Bacteriol 146: 517–526.
17. AttaiechL, OlivierA, Mortier-BarrièreI, SouletAL, GranadelC, et al. (2011) Role of the single-stranded DNA binding protein SsbB in pneumococcal transformation: maintenance of a reservoir for genetic plasticity. PLoS Genet 7: e1002156.
18. SallesC, CréancierL, ClaverysJP, MéjeanV (1992) The high level streptomycin resistance gene from Streptococcus pneumoniae is a homologue of the ribosomal protein S12 gene from Escherichia coli. Nucl Acids Res 20: 6103.
19. HåvarsteinLS, CoomaraswamyG, MorrisonDA (1995) An unmodified heptadecapeptide pheromone induces competence for genetic transformation in Streptococcus pneumoniae. Proc Natl Acad Sci USA 92: 11140–11144.
20. BrueggemannAB, PaiR, CrookDW, BeallB (2007) Vaccine escape recombinants emerge after pneumococcal vaccination in the United States. PLoS Pathog 3: e168.
21. VarvioSL, AuranenK, ArjasE, MakelaPH (2009) Evolution of the capsular regulatory genes in Streptococcus pneumoniae. J Infect Dis 200: 1144–1151.
22. HåvarsteinLS, HakenbeckR, GaustadP (1997) Natural competence in the genus Streptococcus: evidence that streptococci can change pherotype by interspecies recombinational exchanges. J Bacteriol 179: 6589–6594.
23. DenapaiteD, BrucknerR, NuhnM, ReichmannP, HenrichB, et al. (2010) The genome of Streptococcus mitis B6–what is a commensal? PLoS ONE 5: e9426.
24. VilkaitisG, LubysA, MerkieneE, TiminskasA, JanulaitisA, et al. (2002) Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation. Nucleic Acids Res 30: 1547–1557.
25. HumbertO, DorerMS, SalamaNR (2011) Characterization of Helicobacter pylori factors that control transformation frequency and integration length during inter-strain DNA recombination. Mol Microbiol 79: 387–401.
26. DorerMS, SesslerTH, SalamaNR (2011) Recombination and DNA repair in Helicobacter pylori. Annu Rev Microbiol 65: 329–348.
27. MarraffiniLA, SontheimerEJ (2008) CRISPR interference limits horizontal gene transfer in taphylococci by targeting DNA. Science 322: 1843–1845.
28. BikardD, Hatoum-AslanA, MucidaD, MarraffiniLA (2012) CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 12: 177–186.
29. DubnauD (1999) DNA uptake in bacteria. Annu Rev Microbiol 53: 217–244.
30. CharpentierX, PolardP, ClaverysJP (2012) Induction of competence for genetic transformation by antibiotics: convergent evolution of distant bacterial species lacking SOS? Curr Op Microbiol 15: 570–6.
31. RedfieldRJ (2001) Do bacteria have sex? Nat Rev Genet 2: 634–639.
32. ClaverysJP, PrudhommeM, MartinB (2006) Induction of competence regulons as general stress responses in Gram-positive bacteria. Annu Rev Microbiol 60: 451–475.
33. MartinB, PrudhommeM, AlloingG, GranadelC, ClaverysJP (2000) Cross-regulation of competence pheromone production and export in the early control of transformation in Streptococcus pneumoniae. Mol Microbiol 38: 867–878.
34. Mortier-BarrièreI, de SaizieuA, ClaverysJP, MartinB (1998) Competence-specific induction of recA is required for full recombination proficiency during transformation in Streptococcus pneumoniae. Mol Microbiol 27: 159–170.
35. ClaverysJP, LacksSA (1986) Heteroduplex deoxyribonucleic acid base mismatch repair in bacteria. Microbiol Rev 50: 133–165.
36. SungCK, LiH, ClaverysJP, MorrisonDA (2001) An rpsL Cassette, Janus, for Gene Replacement through Negative Selection in Streptococcus pneumoniae. Appl Environ Microbiol 67: 5190–5196.
37. LanieJA, NgWL, KazmierczakKM, AndrzejewskiTM, DavidsenTM, et al. (2007) Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain R6. J Bacteriol 189: 38–51.
38. TettelinH, NelsonKE, PaulsenIT, EisenJA, ReadTD, et al. (2001) Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293: 498–506.
39. DonatiC, HillerNL, TettelinH, MuzziA, CroucherNJ, et al. (2010) Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol 11: R107.
40. NelsonKE, WeinstockGM, HighlanderSK, WorleyKC, CreasyHH, et al. (2010) A catalog of reference genomes from the human microbiome. Science 328: 994–999.
41. HillerNL, JantoB, HoggJS, BoissyR, YuS, et al. (2007) Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol 189: 8186–8195.
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
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