Characterization of staphylococcus epidermidis phage vB_SepS_SEP9 - a unique member of the siphoviridae family

Research in Microbiology

Volumn 165, Issue 8, 2014, Pages 679-685

  Melo, Luís D R ^a   Sillankorva, Sanna ^a   Ackermann, Hans Wolfgang ^b   Kropinski, Andrew M ^c,d   Azeredo, Joana ^a   Cerca, Nuno ^a  

^a UNIVERSITY OF MINHO   (Portugal)

^b UNIVERSITÉ LAVAL   (Canada)

^c PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^d UNIVERSITY OF GUELPH   (Canada)

Author keywords

Bacteriophages; Genomics; Siphoviridae; Staphylococcus epidermidis

Indexed keywords

INTEGRASE; VIRUS DNA;

ARTICLE; BACTERIAL GENOME; BACTERIUM EXAMINATION; BACTERIUM ISOLATION; DATA BASE; GENOMICS; GROWTH CURVE; HOST RANGE; LYSOGENIZATION; MICROBIAL MORPHOLOGY; NONHUMAN; PHYLOGENY; STAPHYLOCOCCUS EPIDERMIDIS; STAPHYLOCOCCUS PHAGE; STAPHYLOCOCCUS PHAGE SEP9; START CODON; CHEMISTRY; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; SIPHOVIRIDAE; ULTRASTRUCTURE; VIROLOGY; VIRUS GENE; VIRUS GENOME;

DNA, VIRAL; GENES, VIRAL; GENOME, VIRAL; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SIPHOVIRIDAE; STAPHYLOCOCCUS EPIDERMIDIS; STAPHYLOCOCCUS PHAGES;

EID: 84910020657     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2014.09.012     Document Type: Article

References (51)

1. Otto M. Staphylococcus epidermidis-the 'accidental' pathogen. Nat Rev Microbiol 2009, 7:555-567.
2. Otto M. Basis of virulence in community-associated methicillin-resistant Staphylococcus aureus. Annu Rev Microbiol 2010, 64:143-162.
3. Sulakvelidze A., Morris J.G. Bacteriophages as therapeutic agents. Ann Med 2001, 33:507-509.
4. King A.M.Q., Adams M.J., Carstens E.B., Lefkowitz E.J. Virus taxonomy: ninth report of the international committee on taxonomy of viruses 2011, Elsevier.
5. Deghorain M., Bobay L.M., Smeesters P.R., Bousbata S., Vermeersch M., Perez-Morga D., et al. Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages. J Bacteriol 2012, 194:5829-5839.
6. Deghorain M., Van Melderen L. The staphylococci phages family: an overview. Viruses 2012, 4:3316-3335.
7. Lavigne R., Darius P., Summer E.J., Seto D., Mahadevan P., Nilsson A.S., et al. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol 2009, 9:224.
8. Lavigne R., Seto D., Mahadevan P., Ackermann H.-W., Kropinski A.M. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res Microbiol 2008, 159:406-414.
9. Gutierrez D., Adriaenssens E.M., Martinez B., Rodriguez A., Lavigne R., Kropinski A.M., et al. Three proposed new bacteriophage genera of staphylococcal phages: "3alikevirus", "77likevirus" and "Phietalikevirus". Arch Virol 2013, 159(2):389-398.
10. Daniel A., Bonnen P.E., Fischetti V.A. First complete genome sequence of two Staphylococcus epidermidis bacteriophages. J Bacteriol 2007, 189:2086-2100.
11. Gutierrez D., Martinez B., Rodriguez A., Garcia P. Genomic characterization of two Staphylococcus epidermidis bacteriophages with anti-biofilm potential. BMC Genomics 2012, 13:228.
12. Madhusoodanan J., Seo K.S., Remortel B., Park J.Y., Hwang S.Y., Fox L.K., et al. An enterotoxin-bearing pathogenicity island in Staphylococcus epidermidis. J Bacteriol 2011, 193:1854-1862.
13. Melo L.D., Sillankorva S., Ackermann H.-W., Kropinski A.M., Azeredo J., Cerca N. Isolation and characterization of a new Staphylococcus epidermidis broad-spectrum bacteriophage. J Gen Virol 2014, 95:506-515.
14. Luzzaro F., Ortisi G., Larosa M., Drago M., Brigante G., Gesu G. Prevalence and epidemiology of microbial pathogens causing bloodstream infections: results of the OASIS multicenter study. Diagn Microbiol Infect Dis 2011, 69:363-369.
15. Sillankorva S., Neubauer P., Azeredo J. Phage control of dual species biofilms of Pseudomonas fluorescens and Staphylococcus lentus. Biofouling 2010, 26:567-575.
16. Ackermann H.-W. Basic phage electron microscopy. Methods Mol Biol 2009, 501:113-126.
17. Cavalli-Sforza L.L., Lederberg J. Isolation of pre-adaptive mutants in bacteria by sib selection. Genetics 1956, 41:367-381.
18. Aziz R.K., Bartels D., Best A.A., DeJongh M., Disz T., Edwards R.A., et al. The RAST server: rapid annotations using subsystems technology. BMC genomics 2008, 9:75.
19. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
20. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
21. Soding J., Biegert A., Lupas A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005, 33:W244-W248.
22. Kall L., Sonnhammer E.L. Reliability of transmembrane predictions in whole-genome data. FEBS Lett 2002, 532:415-418.
23. Kall L., Krogh A., Sonnhammer E.L. A combined transmembrane topology and signal peptide prediction method. J Mol Biol 2004, 338:1027-1036.
24. Wilkins M.R., Gasteiger E., Bairoch A., Sanchez J.C., Williams K.L., Appel R.D., et al. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol 1999, 112:531-552.
25. Laslett D., Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 2004, 32:11-16.
26. Schattner P., Brooks A.N., Lowe T.M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005, 33:W686-W689.
27. Bailey T.L., Boden M., Buske F.A., Frith M., Grant C.E., Clementi L., et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009, 37:W202-W208.
28. Naville M., Ghuillot-Gaudeffroy A., Marchais A., Gautheret D. ARNold: a web tool for the prediction of rho-independent transcription terminators. RNA Biol 2011, 8:11-13.
29. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-3415.
30. Hughes K.A., Sutherland I.W., Jones M.V. Biofilm susceptibility to bacteriophage attack: the role of phage-borne polysaccharide depolymerase. Microbiology 1998, 144(Pt 11):3039-3047.
31. Kropinski A.M., Prangishvili D., Lavigne R. Position paper: the creation of a rational scheme for the nomenclature of viruses of bacteria and archaea. Environ Microbiol 2009, 11:2775-2777.
32. Walker D.H., Anderson T.F. Morphological variants of coliphage P1. JVirol 1970, 5:765-782.
33. Gutierrez D., Martinez B., Rodriguez A., Garcia P. Isolation and characterization of bacteriophages infecting Staphylococcus epidermidis. Curr Microbiol 2010, 61:601-608.
34. Lobocka M., Hejnowicz M.S., Dabrowski K., Gozdek A., Kosakowski J., Witkowska M., et al. Genomics of staphylococcal twort-like phages-potential therapeutics of the post-antibiotic era. Adv Virus Res 2012, 83:143-216.
35. Wang I.N. Lysis timing and bacteriophage fitness. Genetics 2006, 172:17-26.
36. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res 2009, 37:D26-D31.
37. Hatfull G.F. Bacteriophage genomics. Curr Opin Microbiol 2008, 11:447-453.
38. Casjens S.R., Gilcrease E.B. Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods Mol Biol 2009, 502:91-111.
39. Dereeper A., Guignon V., Blanc G., Audic S., Buffet S., Chevenet F., et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008, 36:W465-W469.
40. Riipinen K.A., Forsman P., Alatossava T. The genomes and comparative genomics of Lactobacillus delbrueckii phages. Arch Virol 2011, 156:1217-1233.
41. Katsura I., Hendrix R.W. Length determination in bacteriophage lambda tails. Cell 1984, 39:691-698.
42. Tavares P., Zinn-Justin S., Orlova E.V. Genome gating in tailed bacteriophage capsids. Adv Exp Med Biol 2012, 726:585-600.
43. Oliveira H., Melo L.D., Santos S.B., Nobrega F.L., Ferreira E.C., Cerca N., et al. Molecular aspects and comparative genomics of bacteriophage endolysins. J Virol 2013, 87:4558-4570.
44. Birkeland N.K. Cloning, molecular characterization, and expression of the genes encoding the lytic functions of lactococcal bacteriophage phi LC3: a dual lysis system of modular design. Can J Microbiol 1994, 40:658-665.
45. Donovan D.M., Foster-Frey J., Garrett W.M., Blomberg L. Resolving the database sequence discrepancies for the Staphylococcus aureus bacteriophage ϕ11 amidase. J Basic Microbiol 2008, 48:48-52.
46. Garcia P., Martinez B., Obeso J.M., Lavigne R., Lurz R., Rodriguez A. Functional genomic analysis of two Staphylococcus aureus phages isolated from the dairy environment. Appl Environ Microbiol 2009, 75:7663-7673.
47. Hargreaves K.R., Kropinski A.M., Clokie M.R. What does the talking?: quorum sensing signalling genes discovered in a bacteriophage genome. PLoS One 2014, 9:e85131.
48. Mayer M.J., Payne J., Gasson M.J., Narbad A. Genomic sequence and characterization of the virulent bacteriophage phiCTP1 from Clostridium tyrobutyricum and heterologous expression of its endolysin. Appl Environ Microbiol 2010, 76:5415-5422.
49. Kwan T., Liu J., DuBow M., Gros P., Pelletier J. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc Natl Acad Sci U S A 2005, 102:5174-5179.
50. Ceyssens P.J., Hertveldt K., Ackermann H.W., Noben J.P., Demeke M., Volckaert G., et al. The intron-containing genome of the lytic Pseudomonas phage LUZ24 resembles the temperate phage PaP3. Virology 2008, 377:233-238.
51. Loc-Carrillo C., Abedon S.T. Pros and cons of phage therapy. Bacteriophage 2011, 1:111-114.