Phage-inducible islands in the Gram-positive cocci

ISME Journal

Volumn 11, Issue 4, 2017, Pages 1029-1042

  Martínez Rubio, Roser ^a   Quiles Puchalt, Nuria ^b   Martí, Miguel ^c   Humphrey, Suzanne ^b   Ram, Geeta ^d   Smyth, Davida ^d   Chen, John ^e   Novick, Richard P ^d   Penadés, José R ^a,b  

^a UNIVERSIDAD CEU CARDENAL HERRERA   (Spain)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c INSTITUTO VALENCIANO DE INVESTIGACIONES AGRARIAS IVIA   (Spain)

^d NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; COLIFORM BACTERIUM; CONVERGENT EVOLUTION; GENE TRANSFER; GENETIC ANALYSIS; PARADIGM SHIFT; PROTEIN;

ENTEROCOCCUS FAECALIS; LACTOCOCCUS; MIRIDAE; POSIBACTERIA; STAPHYLOCOCCUS AUREUS;

BACTERIOPHAGE RECEPTOR;

BACTERIOPHAGE; GENE EXPRESSION REGULATION; GENOMIC ISLAND; GRAM POSITIVE COCCI; PHYSIOLOGY; VIROLOGY;

ATTACHMENT SITES, MICROBIOLOGICAL; BACTERIOPHAGES; GENE EXPRESSION REGULATION, BACTERIAL; GENOMIC ISLANDS; GRAM-POSITIVE COCCI;

EID: 85004090213     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2016.163     Document Type: Article

References (39)

1. Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J et al. (2001). The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res 11: 731-753.
2. Carpena N, Manning KA, Dokland T, Marina A, Penadés JR. (2016). Convergent evolution of pathogenicity islands in helper cos phage interference. Philos Trans R Soc Lond B 371: 20150505.
3. Charpentier E, Anton AI, Barry P, Alfonso B, Fang Y, Novick RP. (2004). Novel cassette-based shuttle vector system for gram-positive bacteria. Appl Environ Microbiol 70: 6076-6085.
4. Chen J, Novick RP. (2009). Phage-mediated intergeneric transfer of toxin genes. Science 323: 139-141.
5. Chen J, Carpena N, Quiles-Puchalt N, Ram G, Novick RP, Penadés JR. (2015a). Intra- and inter-generic transfer of pathogenicity island-encoded virulence genes by cos phages. ISME J 9: 1260-1263.
6. Chen J, Ram G, Penadés JR, Brown S, Novick RP. (2015b). Pathogenicity island-directed transfer of unlinked chromosomal virulence genes. Mol Cell 57: 138-149.
7. Chopin A, Bolotin A, Sorokin A, Ehrlich SD, Chopin M. (2001). Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations. Nucleic Acids Res 29: 644-651.
8. Claverys J-P, Martin B, Håvarstein LS. (2007). Competenceinduced fratricide in streptococci. Mol Microbiol 64: 1423-1433.
9. Duerkop BA, Clements CV, Rollins D, Rodrigues JLM, Hooper LV. (2012). A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proc Natl Acad Sci USA 109: 17621-17626.
10. Ferrer MD, Quiles-Puchalt N, Harwich MD, Tormo-Más MÁ, Campoy S, Barbé J et al. (2011). RinA controls phagemediated packaging and transfer of virulence genes in Gram-positive bacteria. Nucleic Acids Res 39: 5866-5878.
11. Frígols B, Quiles-Puchalt N, Mir-Sanchis I, Donderis J, Elena SF, Buckling A et al. (2015). Virus satellites drive viral evolution and ecology. PLoS Genet 11: e1005609.
12. Hamilton CM, Aldea M, Washburn BK, Babitzke P, Kushner SR. (1989). New method for generating deletions and gene replacements in Escherichia coli. J Bacteriol 171: 4617-4622.
13. Kanehisa M, Goto S. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30.
14. Lindsay JA, Ruzin A, Ross HF, Kurepina N, Novick RP. (1998). The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus. Mol Microbiol 29: 527-543.
15. Maiques E, Ubeda C, TormoMA, FerrerMD, Lasa I, Novick RP et al. (2007). Role of staphylococcal phage and SaPI integrase in intra- and interspecies SaPI transfer. J Bacteriol 189: 5608-5616.
16. Matos RC, Lapaque N, Rigottier-Gois L, Debarbieux L, Meylheuc T, Gonzalez-Zorn B et al. (2013). Enterococcus faecalis prophage dynamics and contributions to pathogenic traits. PLoS Genet 9: e1003539.
17. Nguyen SV, McShan WM. (2014). Chromosomal islands of Streptococcus pyogenes and related streptococci: molecular switches for survival and virulence. Front Cell Infect Microbiol 4: 109.
18. Novick RP, Ram G. (2015). The floating (pathogenicity) island: a genomic dessert. Trends Genet 32: 114-126.
19. Novick RP, Christie GE, Penadés JR. (2010). The phagerelated chromosomal islands of Gram-positive bacteria. Nat Rev Microbiol 8: 541-551.
20. O'Callaghan CH, Morris A, Kirby SM, Shingler AH. (1972). Novel method for detection of beta-lactamases by using a chromogenic cephalosporin substrate. Antimicrob Agents Chemother 1: 283-288.
21. Paulsen IT, Banerjei L, Myers GSA, Nelson KE, Seshadri R, Read TD et al. (2003). Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299: 2071-2074.
22. Penadés JR, Christie GE. (2015). The phage-inducible chromosomal islands: a family of highly evolved molecular parasites. Annu Rev Virol 2: 181-201.
23. Quiles-Puchalt N, Carpena N, Alonso JC, Novick RP, Marina A, Penadés JR. (2014). Staphylococcal pathogenicity island DNA packaging system involving cossite packaging and phage-encoded HNH endonucleases. Proc Natl Acad Sci USA 111: 6016-6021.
24. Quiles-Puchalt N, Tormo-MásMÁ, Campoy S, Toledo-Arana A, Monedero V, Lasa I et al. (2013). A super-family of transcriptional activators regulates bacteriophage packaging and lysis in Gram-positive bacteria. Nucleic Acids Res 41: 7260-7275.
25. Ram G, Chen J, Kumar K, Ross HF, Ubeda C, Damle PK et al. (2012). Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism. Proc Natl Acad Sci USA 109: 16300-16305.
26. Ram G, Chen J, Ross HF, Novick RP. (2014). Precisely modulated pathogenicity island interference with late phage gene transcription. Proc Natl Acad Sci USA 111: 14536-14541.
27. Ruzin A, Lindsay J, Novick RP. (2001). Molecular genetics of SaPI1-a mobile pathogenicity island in Staphylococcus aureus. Mol Microbiol 41: 365-377.
28. Scott J, Nguyen SV, King CJ, Hendrickson C, McShan WM. (2012). Phage-like Streptococcus pyogenes chromosomal islands (SpyCI) and mutator phenotypes: control by growth state and rescue by a SpyCI-encoded promoter. Front Microbiol 3: 317.
29. Scott J, Thompson-Mayberry P, Lahmamsi S, King CJ, McShan WM. (2008). Phage-associated mutator phenotype in group A streptococcus. J Bacteriol 190: 6290-6301.
30. Straume D, Stamsås GA, Håvarstein LS. (2015). Natural transformation and genome evolution in Streptococcus pneumoniae. Infect Genet Evol 33: 371-380.
31. Tormo-Más MÁ, Donderis J, García-Caballer M, Alt A, Mir- Sanchis I, Marina A et al. (2013). Phage dUTPases control transfer of virulence genes by a protooncogenic G protein-like mechanism. Mol Cell 49: 947-958.
32. Tormo MA, Ferrer MD, Maiques E, Ubeda C, Selva L, Lasa I et al. (2008). Staphylococcus aureus pathogenicity island DNA is packaged in particles composed of phage proteins. J Bacteriol 190: 2434-2440.
33. Tormo-Más MÁ, Mir I, Shrestha A, Tallent SM, Campoy S, Lasa I et al. (2010). Moonlighting bacteriophage proteins derepress staphylococcal pathogenicity islands. Nature 465: 779-782.
34. Ubeda C, Barry P, Penadés JR, Novick RP. (2007a). A pathogenicity island replicon in Staphylococcus aureus replicates as an unstable plasmid. Proc Natl Acad Sci USA 104: 14182-14188.
35. Ubeda C, Maiques E, Barry P, Matthews A, Tormo MA, Lasa I et al. (2008). SaPI mutations affecting replication and transfer and enabling autonomous replication in the absence of helper phage. Mol Microbiol 67: 493-503.
36. Ubeda C, Maiques E, Knecht E, Lasa I, Novick RP, Penadés JR. (2005). Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity islandencoded virulence factors in staphylococci. Mol Microbiol 56: 836-844.
37. Ubeda C, Maiques E, Tormo MA, Campoy S, Lasa I, Barbé J et al. (2007b). SaPI operon I is required for SaPI packaging and is controlled by LexA. Mol Microbiol 65: 41-50.
38. Ubeda C, Tormo MA, Cucarella C, Trotonda P, Foster TJ, Lasa I et al. (2003). Sip, an integrase protein with excision, circularization and integration activities, defines a new family of mobile Staphylococcus aureus pathogenicity islands. Mol Microbiol 49: 193-210.
39. Viana D, Blanco J, Tormo-Más MÁ, Selva L, Guinane CM, Baselga R et al. (2010). Adaptation of Staphylococcus aureus to ruminant and equine hosts involves SaPIcarried variants of von Willebrand factor-binding protein. Mol Microbiol 77: 1583-1594.