The annotated complete DNA sequence of Enterococcus faecalis bacteriophage φEf11 and its comparison with all available phage and predicted prophage genomes

FEMS Microbiology Letters

Volumn 317, Issue 1, 2011, Pages 9-26

  Stevens, Roy H ^a   Ektefaie, Mahmoud R ^a   Fouts, Derrick E ^b  

^a TEMPLE UNIVERSITY   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

Author keywords

Bacteriophage Ef11; Enterococcus faecalis; Phage genome sequence and analysis

Indexed keywords

BACTERIAL DNA; CYTOSINE; GUANINE;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIOPHAGE; CONTROLLED STUDY; DNA CONTENT; DNA SEQUENCE; ENTEROCOCCUS FAECALIS; GENETIC ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE HOMOLOGY;

BASE COMPOSITION; CLUSTER ANALYSIS; DNA, VIRAL; ENTEROCOCCUS FAECALIS; GENE ORDER; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; PROMOTER REGIONS, GENETIC; PROPHAGES; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SYNTENY;

ENTEROCOCCUS FAECALIS; POSIBACTERIA; SIPHOVIRIDAE;

EID: 79952186125     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2010.02203.x     Document Type: Article

References (67)

1. Ackermann H-W, Caprioli T & Kasatiya SS (1975) A large new Streptococcus bacteriophage. Can J Microbiol 21: 571-574.
2. Alemayehu D, Ross RP, O'Sullivan OO, Stanton C, Gitzgerald GF & McAuliffe O (2009) Genome of a virulent bacteriophage Lb338-1 that lyses the probiotic Lactobacillus paracasei cheese strain. Gene 448: 29-39.
3. Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
4. Bachrach GT, Leizerovici-Zigmond M, Zlotkin A, Naor R & Steinberg D (2003) Bacteriophage isolation from human saliva. Lett Appl Microbiol 36: 50-53.
5. Bazient C & King J (1985) The DNA translocating vertex of dsDNA bacteriophage. Annu Rev Microbiol 39: 109-129.
6. Black LW (1989) DNA packaging in dsDNA bacteriophages. Annu Rev Microbiol 43: 267-292.
7. Bleiweis A & Zimmerman LN (1961) Formation of two types of osmotically fragile bodies from Streptococcus faecalis var liquefaciens. Can J Microbiol 77: 363-373.
8. Bonten MJM, Willems R & Weinstein RA (2001) Vancomycin-resistant enterococci: why are they here, and where do they come from? Lancet Infect Dis 1: 314-325.
9. Breuner A, Brøndsted L & Hammer K (1999) Novel organization of genes involved in prophage excision identified in the temperate lactococcal bacteriophage TP901-1. J Bacteriol 181: 7291-7297.
10. Brøndsted L, Østergaard S, Pedersen M, Hammer K & Vogensen FK (2001) Analysis of the complete DNA sequence of the temperate bacteriophage TP901-1: evolution, structure, and genome organization of lactococcal bacteriophages. Virology 283: 93-109.
11. Campbell A (1994) Comparative molecular biology of lambdoid phages. Annu Rev Microbiol 48: 193-222.
12. Canchaya C, Desiere F, McShan WM, Ferretti JJ, Parkhill J & Brüssow H (2002) Genome analysis of an inducible prophage and prophage remnants integrated in the Streptococcus pyogenes strain SF370. Virology 302: 245-258.
13. Casjens S, Hatfull G & Hendrix R (1992) Evolution of dsDNA tailed-bacteriophage genomes. Semin Virol 3: 383-397.
14. Casjens SR, Gilcrease EB, Winn-Stapley DA, Schicklmaier P, Schmieger H, Pedulla ML, Ford ME, Houtz JM, Hatfull GF & Hendrix RW (2005) The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J Bacteriol 187: 1091-1104.
15. Delcher AL, Phillippy A, Carlton J & Salzberg SL (2002) Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 30: 2478-2483.
16. Desiere F, Pridmore RD & Brüssow H (2000) Comparative genomics of the late gene cluster from Lactobacillus phages. Virology 275: 294-305.
17. Edgeworth JD, Treacher DF & Eykyn SJ (1999) A 25-year study of nosocomial bacteremia in an adult intensive care unit. Crit Care Med 28: 1421-1428.
18. Evans AC (1934) The prevalence of Streptococcus bacteriophage. Science 80: 40-41.
19. Facklam RR, Carvalho MGS & Teixeira LM (2002) History, taxonomy, biochemical characteristics and antibiotic susceptibility testing of enterococci. The Enterococci - Pathogenesis, Molecular Biology, and Antibiotic Resistance (Gilmore MS, ed), pp. 1-54. ASM Press, Washington, DC.
20. Finn RD, Tate J, Mistry J et al. (2008) The Pfam protein families database. Nucleic Acids Res 36: D281-D288.
21. Fouts DE (2006) Phage finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res 34: 5839-5851.
22. Fujisawa H & Morita M (1997) Phage DNA packaging. Genes Cells 2: 537-545.
23. Hogness DS (1966) The structure and function of the DNA from bacteriophage lambda. J Gen Physiol 49: 29-57.
24. Izquierdo E, Wagner C, Marchioni E, Aoude-Werner D & Ennahar S (2009) Enterocin 96, a novel class II bacteriocin produced by Enterococcus faecalis WHE96, isolated from munster cheese. Appl Environ Microb 75: 4273-4276.
25. Javed I, Ahme S, Ali MI, Ahmad B, Ghumro PB, Hameed A & Chaudry GJ (2009) Bacteriocinogenic potential of newly isolated strains of Enterococcus faecium and Enterococcus faecalis from dairy products of Pakistan. J Microbiol Biotechn 20: 153-160.
26. Katsura I (1987) Determination of bacteriophage lambda tail length by a protein ruler. Nature 327: 73-75.
27. Katsura I & Hendrix RW (1984) Length determination in bacteriophage lambda tails. Cell 39: 691-698.
28. Kjems E (1955) Studies on streptococcal bacteriophages. Acta Pathol Mic Sc 36: 433-444.
29. Klumpp J, Lavigne R, Loessner MJ & Ackermann HW (2010) The SPO1-related bacteriophages. Arch Virol 155: 1547-1561.
30. Lucchini S, Desiere F & Brüssow H (1999) The genetic relationship between virulent and temperate Streptococcus thermophilus bacteriophages whole genome comparison of cos-site phages Sfi19 and Sfi21. Virology 260: 232-243.
31. Madsen PL & Hammer K (1998) Temporal transcription of the lactococcal temperate phage TP901-1 and DNA sequence of the early promoter region. Microbiology 144: 2203-2215.
32. Majka J, Zakrzewsha-Czerwiñska J & Messer W (2001) Sequence recognition, cooperative interaction, and dimerization of the initiator protein DnaA of Streptomyces. J Biol Chem 276: 6243-6252.
33. Martín-Platero A, Valdivia E, Maqueda M & Martínez-Bueno M (2009) Characterization and safety evaluation of enterococci isolated from Spanish goats' milk cheese. Int J Food Microbiol 132: 24-32.
34. McShan WM & Shankar N (2002) The genome of Enterococcus faecalis V583: a tool for discovery. The Enterococci - Pathogenesis, Molecular Biology and Antibiotic Resistance (Gilmore MS, ed), pp. 409-415. ASM Press, Washington, DC.
35. Megran DW (1992) Enterococcal endocarditis. Clin Infect Dis 15: 63-71.
36. Missich R, Weise R, Chai S, Lurz R, Pedré X & Alonso JC (1997) The replisome organizer (G38P) of Bacillus subtilis bacteriophage SSP1 forms specialized nucleoprotein complexes with two discrete regions of the SPP1 genome. J Mol Biol 270: 50-64.
37. Moellering RC Jr (1992) Emergence of Enterococcus as a significant pathogen. Clin Infect Dis 14: 1173-1176.
38. Myers EW, Sutton GG, Delcher AL et al. (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
39. National Nosocomial Infections Surveillance System (1999) National Nosocomial Infections Surveillance (NNIS) System Report, data summary from January 1990-May 1999. June 1999. Am J Infect Control 27: 520-532.
40. Natkin E (1967) Isolation and host range of bacteriophages active against human oral enterococci. Archs Oral Biol 12: 669-680.
41. Paisano AF, Spira B, Cai S & Bombana AC (2004) In vitro antimicrobial effect of bacteriophages on human dentin infected with Enterococcus faecalis ATCC 29212. Oral Microbiol Immun 19: 327-330.
42. Paulsen IT, Benerjei L, Myers GSA et al. (2003) Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299: 2071-2074.
43. Poteete AR (1982) Location and sequence of the erf gene of phage P22. Virology 119: 422-429.
44. Ptashne M (2004) A Genetic Switch, Phage Lambda Revisited, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
45. Rams TE, Feik D, Young V, Hammond BF & Slots J (1992) Enterococci in human periodontitis. Oral Microbiol Immun 7: 249-252.
46. Rasko DA, Myers GS & Ravel J (2005) Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics 6: 2.
47. Richards MJ, Edwards JR, Culver DH & Gaynes RP (2000) Nosocomial infections in combined medical-surgical intensive care units in the United States. Infect Cont Hosp Ep 21: 510-515.
48. Riedel HD, Heinric J, Heisig A, Choli T & Schuster H (1993) The antirepressor of phage P1. Isolation and interaction with CI repressor of P1 and P7. FEBS Lett 334: 165-169.
49. Rogers CG & Sarles WB (1963) Characterization of Enterococcus bacteriophages from the small intestine. J Bacteriol 85: 1378-1385.
50. Salzberg SL, Delcher AL, Kasif S & White O (1998) Microbial gene identification with interpolated Markov models. Nucleic Acids Res 26: 544-548.
51. Sambrook J, Fritsch FF & Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
52. SantaLucia J Jr (1998) A unified view of polymer, dumbell, and oligonucleotide DNA nearest-neighbor thermodynamics. P Natl Acad Sci USA 95: 1460-1465.
53. Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR & White O (2007) TIGRFAMs and genome properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 35: D260-D264.
54. Siboo IR, Bensing BA & Sullam PM (2003) Genomic organization and molecular characterization of SM1, a temperate bacteriophage of Streptococcus mitis. J Bacteriol 185: 6968-6975.
55. Son JS, Jun SY, Kim EB, Park JE, Paik HR, Yoon SJ, Kang SH & Choi Y-J (2009) Complete genome sequence of a newly isolated lytic bacteriophage, EFAP-1 of Enterococcus faecalis and antibacterial activity of its endolysin EFAL-1. J Appl Microbiol 108: 1769-1779.
56. Stevens RH, Porras OD & Delisle AL (2009) Bacteriophages induced from lysogenic root canal isolates of Enterococcus faecalis. Oral Microbiol Immun 24: 278-284.
57. Stuart CH, Schwartz SA, Beeson TJ & Owatz CB (2006) Enterococcus faecalis: its role in root canal treatment failures and current concepts in retreatment. J Endodont 32: 93-98.
58. Uchiyama J, Rashel M, Yoshihiro M, Takemura I, Sugihara S, Akechi K, Muraoka A, Wakiguchi H & Matsuzaki S (2007) Isolation and characterization of a novel Enterococcus faecalis bacteriophage φEF24C as a therapeutic candidate. FEMS Microbiol Lett 278: 200-206.
59. Uchiyama J, Rashel M, Maeda Y, Takemura I, Wakiguchi H & Matsuzaki S (2008) In silico and in vivo evaluation of bacteriophage φEF24C, a candidate for treatment of Enterococcus faecalis infections. Appl Environ Microb 74: 4149-4163.
60. van der Ploeg JR (2007) Genome sequence of Streptococcus mutans bacteriophage M102. FEMS Microbiol Lett 275: 130-138.
61. van Sinderen D, Karsens H, Kok J, Terpstra P, Ruiters MHJ, Venema G & Nauta A (1996) Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t. Mol Microbiol 19: 1343-1355.
62. Ventura M, Canchaya C, Pridmore RD & Brüssow H (2004) The prophages of Lactobacillus johnsonii NCC 533: comparative genomics and transcription analysis. Virology 320: 229-242.
63. Ventura M, Canchaya C, Bernini V et al. (2006) Comparative genomics and transcriptional analysis of prophages indentified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei. Appl Environ Microb 72: 3130-3146.
64. Yasmin A, Kenny JG, Shankar J, Darby AC, Hall N, Edwards C & Horsburgh MJ (2010) Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages. J Bacteriol 192: 1122-1130.
65. Yeo A & Feiss M (1995) Specific interaction of terminase, the DNA packaging enzyme of bacteriophage λ, with the portal protein of the prohead. J Mol Biol 245: 141-150.
66. Young R, Wang IN & Roof WD (2000) Phages will out: strategies of host cell lysis. Trends Microbiol 8: 120-128.
67. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.