Analysis of deoxynucleosides in bacteriophages φ{symbol}EF24C and K and the frequency of a specific restriction site in the genomes of members of the bacteriophage subfamily Spounavirinae

Archives of Virology

Volumn 157, Issue 8, 2012, Pages 1587-1592

  Uchiyama, Jumpei ^a   Maeda, Yusuke ^b   Takemura, Iyo ^a   Gamoh, Keiji ^b   Matsuzaki, Shigenobu ^a   Daibata, Masanori ^a  

^a KOCHI MEDICAL SCHOOL   (Japan)

^b KOCHI UNIVERSITY   (Japan)

Author keywords

Bacteriophage; Nucleoside analysis; SPO1 related viruses

Indexed keywords

VIRUS DNA; VIRUS PROTEIN;

ARTICLE; BACTERIOPHAGE; CHEMISTRY; CLASSIFICATION; DNA BASE COMPOSITION; GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RESTRICTION MAPPING; VIRUS GENOME;

BASE COMPOSITION; BASE SEQUENCE; DNA, VIRAL; GENOME, VIRAL; MYOVIRIDAE; PHYLOGENY; RESTRICTION MAPPING; VIRAL PROTEINS;

MYOVIRIDAE; STAPHYLOCOCCUS PHAGE TWORT;

EID: 84864487506     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-012-1324-9     Document Type: Article

References (34)

1. Alemayehu D, Ross RP, O'Sullivan O, Coffey A, Stanton C, Fitzgerald GF, McAuliffe O (2009) Genome of a virulent bacteriophage Lb338-1 that lyses the probiotic Lactobacillus paracasei cheese strain. Gene 448: 29-39.
2. Bikard D, Marraffini LA (2011) Innate and adaptive immunity in bacteria: mechanisms of programmed genetic variation to fight bacteriophages. Curr Opin Immunol. doi: 10. 1016/j. coi. 2011. 10. 005.
3. Blumentha RM, Cheng X (2002) Chapter 7 Restriction-modification systems. In: Streips UN, Yasbin RE (eds) Modern microbial genetics, 2nd edn. Wiley-Liss, Inc., New York, pp 177-225.
4. Boorstein RJ, Teebor GW (1989) Effects of 5-hydroxymethyluracil and 3-aminobenzamide on the repair and toxicity of 5-hydroxymethyl-2'-deoxyuridine in mammalian cells. Cancer Res 49: 1509-1514.
5. Carlton RM, Noordman WH, Biswas B, de Meester ED, Loessner MJ (2005) Bacteriophage P100 for control of Listeria monocytogenes in foods: genome sequence, bioinformatic analyses, oral toxicity study, and application. Regul Toxicol Pharmacol 43: 301-312.
6. Chibani-Chennoufi S, Dillmann ML, Marvin-Guy L, Rami-Shojaei S, Brüssow H (2004) Lactobacillus plantarum bacteriophage LP65: a new member of the SPO1-like genus of the family Myoviridae. J Bacteriol 186: 7069-7083.
7. de Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds) (2009) Bergey's manual of systemic bacteriology, 2nd edn: the Firmicutes. Springer, New York.
8. Fauquet C, Mayo M, Maniloff J, Desselberger U, Ball L (eds) (2011) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier, New York.
9. Huang LH, Farnet CM, Ehrlich KC, Ehrlich M (1982) Digestion of highly modified bacteriophage DNA by restriction endonucleases. Nucleic Acids Res 10: 1579-1591.
10. Kilcher S, Loessner MJ, Klumpp J (2010) Brochothrix thermosphacta bacteriophages feature heterogeneous and highly mosaic genomes and utilize unique prophage insertion sites. J Bacteriol 192: 5441-5453.
11. Klumpp J, Dorscht J, Lurz R, Bielmann R, Wieland M, Zimmer M, Calendar R, Loessner MJ (2008) The terminally redundant, nonpermuted genome of Listeria bacteriophage A511: a model for the SPO1-like myoviruses of gram-positive bacteria. J Bacteriol 190: 5753-5765.
12. Klumpp J, Lavigne R, Loessner MJ, Ackermann HW (2010) The SPO1-related bacteriophages. Arch Virol 155: 1547-1561.
13. Kwan T, Liu J, DuBow M, Gros P, Pelletier J (2005) The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc Natl Acad Sci USA 102: 5174-5179.
14. Labrie SJ, Samson JE, Moineau S (2010) Bacteriophage resistance mechanisms. Nat Rev Microbiol 8: 317-327.
15. Lavigne R, Ackermann HW, Kropinski AM, McAuliffe O, Calendar R, Stewart CR, Klumpp J (2009) Create the subfamily Spounavirinae in the family Myoviridae, order Caudovirales. Taxonomy proposals-prokaryote, International Committee on Taxonomy of viruses. On line: http://talk. ictvonline. org/files/proposals/taxonomy_proposals_prokaryote1/m/bact04/3950. aspx.
16. Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, Nilsson AS, Ackermann HW, Kropinski AM (2009) Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol 9: 224.
17. Matsuzaki S, Yasuda M, Nishikawa H et al (2003) Experimental protection of mice against lethal Staphylococcus aureus infection by novel bacteriophage φ{symbol}MR11. J Infect Dis 187: 613-624.
18. O'Flaherty S, Coffey A, Edwards R, Meaney W, Fitzgerald GF, Ross RP (2004) Genome of staphylococcal phage K: a new lineage of Myoviridae infecting gram-positive bacteria with a low G+C content. J Bacteriol 186: 2862-2871.
19. O'Flaherty S, Coffey A, Meaney W, Fitzgerald GF, Ross RP (2005) The recombinant phage lysin LysK has a broad spectrum of lytic activity against clinically relevant staphylococci, including methicillin-resistant Staphylococcus aureus. J Bacteriol 187: 7161-7164.
20. O'Flaherty S, Coffey A, Meaney WJ, Fitzgerald GF, Ross RP (2005) Inhibition of bacteriophage K proliferation on Staphylococcus aureus in raw bovine milk. Lett Appl Microbiol 41: 274-279.
21. O'Flaherty S, Ross RP, Meaney W, Fitzgerald GF, Elbreki MF, Coffey A (2005) Potential of the polyvalent anti-Staphylococcus bacteriophage K for control of antibiotic-resistant staphylococci from hospitals. Appl Environ Microbiol 71: 1836-1842.
22. Roberts RJ, Vincze T, Posfai J, Macelis D (2010) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38: D234-D236.
23. Rocha EP, Danchin A, Viari A (2001) Evolutionary role of restriction/modification systems as revealed by comparative genome analysis. Genome Res 11: 946-958.
24. Stern A, Sorek R (2011) The phage-host arms race: shaping the evolution of microbes. BioEssays 33: 43-51.
25. Stewart CR, Casjens SR, Cresawn SG et al (2009) The genome of Bacillus subtilis bacteriophage SPO1. J Mol Biol 388: 48-70.
26. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
27. Uchiyama J, Maeda Y, Takemura I, Chess-Williams R, Wakiguchi H, Matsuzaki S (2009) Blood kinetics of four intraperitoneally administered therapeutic candidate bacteriophages in healthy and neutropenic mice. Microbiol Immunol 53: 301-304.
28. Uchiyama J, Rashel M, Maeda Y et al (2008) Isolation and characterization of a novel Enterococcus faecalis bacteriophage φ{symbol}EF24C as a therapeutic candidate. FEMS Microbiol Lett 278: 200-206.
29. Uchiyama J, Rashel M, Takemura I, Wakiguchi H, Matsuzaki S (2008) In silico and in vivo evaluation of bacteriophage φ{symbol}EF24C, a candidate for treatment of Enterococcus faecalis infections. Appl Environ Microbiol 74: 4149-4163.
30. Uchiyama J, Takemura I, Hayashi I et al (2011) Characterization of lytic enzyme open reading frame 9 (ORF9) derived from Enterococcus faecalis bacteriophage φ{symbol}EF24C. Appl Environ Microbiol 77: 580-585.
31. Uchiyama J, Takemura I, Satoh M, Kato S, Ujihara T, Akechi K, Matsuzaki S, Daibata M (2011) Improved adsorption of an Enterococcus faecalis bacteriophage φ{symbol}EF24C with a spontaneous point mutation. PLoS ONE 6: e26648.
32. Vincze T, Posfai J, Roberts RJ (2003) NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res 31: 3688-3691.
33. Warren RA (1980) Modified bases in bacteriophage DNAs. Annu Rev Microbiol 34: 137-158.
34. Yee LM, Matsumoto T, Yano K, Matsuoka S, Sadaie Y, Yoshikawa H, Asai K (2011) The genome of Bacillus subtilis phage SP10: a comparative analysis with phage SPO1. Biosci Biotechnol Biochem 75: 944-952.