In silico analysis of Ardmore, a novel mycobacteriophage isolated from soil

Gene

Volumn 453, Issue 1-2, 2010, Pages 9-23

  Henry, Marine ^a   O'Sullivan, Orla ^b   Sleator, Roy D ^a,c   Coffey, Aidan ^a   Ross, R Paul ^b   McAuliffe, Olivia ^b   O'Mahony, Jim M ^a  

^a Munster Technological University   (Ireland)

^b TEAGASC FOOD RESEARCH CENTRE   (Ireland)

^c UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

lactamase; Bacteriophage; Biocontrol; Genome; Lysin; Mycobacteria

Indexed keywords

BETA LACTAMASE; CYTOSINE; DOUBLE STRANDED DNA; GUANINE;

ARDMORE; ARTICLE; BACTERIAL GENOME; BACTERIUM ISOLATION; COMPUTER ANALYSIS; COMPUTER MODEL; CONTROLLED STUDY; DNA CONTENT; FRAMESHIFT MUTATION; GENE LOCATION; GENETIC CONSERVATION; IRELAND; MYCOBACTERIOPHAGE; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MOTIF; RIBOSOMAL FRAMESHIFTING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SOIL;

COMPUTATIONAL BIOLOGY; DNA, VIRAL; GENOME, VIRAL; MYCOBACTERIOPHAGES; OPEN READING FRAMES; SOIL MICROBIOLOGY;

CORYNEBACTERINEAE;

EID: 77949264338     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2009.12.007     Document Type: Article

References (85)

1. Adler-Biassette H, et al. Non tuberculous mycobacterial diseases. Ann. Pathol. 2003, 23(3):216-235.
2. Ahmad S. Treatment of post-burns bacterial infections by bacteriophages, specifically ubiquitous Pseudomonas spp. notoriously resistant to antibiotics. Med. Hypotheses 2002, 58(4):327-331. Apr.
3. Altermann E., Klaenhammer T.K. GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes. Omics 2003, 7:161-169.
4. Altschul S.F, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25(17):3389-3402. Sep 1.
5. Arcus V.L., Bäckbo K., Roos A., Daniel E.L., Baker E.N. Distant structural homology leads to the functional characterisation of an archeal PIN domain as an exonuclease. J. Biol. Chem. 2004, 279(16):16471-16478.
6. Biswas B., et al. Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium. Infect Immun. 2002, 70(1):204-210. Jan.
7. Boyd E.F., Davis B.M., Hochhut B. Bacteriophage-bacteriophage interactions in the evolution of pathogenic bacteria. Trends Microbiol. 2001, 9(3):137-144. Mar.
8. Brillard J., Boyer-Giglio M.H., Boemare N., Givaudan A. Holin locus characterisation from lysogenic Xenorhabdus nematophila and its involvement in Escherichia coli SheA haemolytic phenotype. FEMS Microbiol. Lett. 2003, 218(1):107-113. Jan 21.
9. Brüssow H., Desiere F. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol. Microbiol. 2001, 39(2):213-222. Jan.
10. Brüssow H., Canchaya C., Hardt W.D. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 2004, 68(3):560-602. Sep.
11. Canchaya C., Fournous G., Chibani-Chennoufi S., Dillmann M.L., Brüssow H. Phage as agents of lateral gene transfer. Curr. Opin. Microbiol. 2003, (4):417-424. Aug 6.
12. Carver T., et al. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 2008.
13. Casjens S. Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol. 2003, 49(2):277-300. Jul.
14. Christiansen B, Brøndsted L, Vogensen FK, Hammer K., 1996 A resolvase-like protein is required for the site-specific integration of the temperate lactococcal bacteriophage TP901-1. J. Bacteriol. 1996, 178(17):5164-5173. Sep.
15. Christie G.E., Temple L.M., Bartlett B.A., Goodwin T.S. Programmed translational frameshift in the bacteriophage P2 FETUD tail gene operon. J. Bacteriol. 2002, 184(23):6522-6531. Dec.
16. Coetzee J.N., Sacks T.G. Transduction of streptomycin resistance in Proteus mirabilis. J. Gen. Microbiol. 1960, 23:445-455.
17. Condron B.G., Atkins J.F., Gesteland R.F. Frameshifting in gene 10 of bacteriophage T7. J. Bacteriol. 1991, 173(21):6998-7003. Nov.
18. Creevey C.J., McInerney J.O. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 2005, 21:390-392.
19. D 'Herelle F.H. Sur un microbe invisible antagoniste des bacillus dysenteriques. Les comptes rendus de l'Academie des Sciences 1917, 165:373-375.
20. De Rossi E, Aínsa JA, Riccardi G. Role of mycobacterial efflux transporters in drug resistance: an unresolved question. FEMS Microbiol. Rev. 2006, 30(1):36-52. Jan.
21. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23(6):673-679.
22. Farabaugh P.J. Programmed translational frameshifting. Annu. Rev. Genet. 1996, 30:507-528.
23. Fattorini L., et al. Resistance to beta-lactams in Mycobacterium fortuitum. Antimicrob. Agents Chemother. 1992, 36(5):1068-1072. May.
24. Felsentein J. Phylip; Phylogeny Inference Package Version 3.2. Cladistics 1989, 5:164-166.
25. Fenton M., Ross R.P., McAuliffe O., O'Mahony J., Coffey A. Recombinant bacteriophage lysins as antibacterials. Bioengineered Bugs 2010, 1(1):9-16.
26. Finn R.D., et al. The Pfam protein families database. Nucleic Acids Res., Database Issue 2008, 36:D281-D288.
27. Flores A.R., Parsons L.M., Pavelka M.J. Genetic analysis of the beta-lactamases of Mycobacterium tuberculosis and Mycobacterium smegmatis and susceptibility to beta-lactam antibiotics. Microbiology 2005, 151(Pt 2):521-532. Feb.
28. Freitas-Vieira A., Anes E., Moniz-Pereira J. The site-specific recombination locus of mycobacteriophage Ms6 determines DNA integration at the tRNA(Ala) gene of Mycobacterium spp. Microbiology 1998, 144(Pt 12):3397-3406. Dec.
29. Gaudelus J., De Pontual L. Epidemiology of tuberculosis in France. Arch. Pediatr. 2005, 12(Suppl 2):S83-S87. Aug.
30. Ghosh P, Kim A.I, Hatfull G.F The orientation of mycobacteriophage Bxb1 integration is solely dependent on the central dinucleotide of attP and attB. Mol Cell. 2003, 12(5):1101-1111.
31. Gil F., Catalao M.J., Moniz-Pereira J., Leandro P., McNeils M., Pimentel M. The lytic cassette of mycobacteriophage Ms6 encodes an enzyme with lipolytic activity. Microbiology 2008, 154:1364-1371.
32. Hatfull G.F., et al. Bacteriophages as tools for vaccine development. Dev. Biol. Stand. 1994, 82:43-47.
33. Hatfull G.F. Mycobacteriophages. The Bacteriophages 2006, 602-620. Oxford University Press. 2nd edition. R. Calendar, S.T. Abedon (Eds.).
34. Hatfull G.F., et al. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2006, 2(6):e92. Jun.
35. Hendrix R.W. Bacteriophage genomics. Curr. Opin. Microbiol. 2003, 6(5):506-511. Oct.
36. Hertwig S., Klein I., Schmidt V., Beck S., Hammerl J., Appel B. Sequence analysis of the genome of the temperate Yersinia enterocolitica phage PY54. J. Mol. Biol. 2003, 331(3):605-622. Aug 15.
37. Huson D., Richter D., Rausch C., Dezulian T., Franz M., Rupp R. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinform. 2007, 8:460.
38. Hussain T. Leprosy and tuberculosis: an insight-review. Crit. Rev. Microbiol. 2007, 33(1):15-66.
39. Inal J.M. Phage therapy: a reappraisal of bacteriophages as antibiotics. Arch. Immunol. Ther. Exp. 2003, 51(4):237-244.
40. Jagusztyn-Krynicka E.K., Wyszyńska A. The decline of antibiotic era-new approaches for antibacterial drug discovery. Pol. J. Microbiol. 2008, 57(2):91-98.
41. Jain S, Hatfull GF. Transcriptional regulation and immunity in mycobacteriophage Bxb1. Mol Microbiol. 2000, 38(5):971-985.
42. Jarlier V, Nikaido H. Mycobacterial cell wall: structure and role in natural resistance to antibiotics. FEMS Microbiol. Lett. 1994, 123(1-2):11-18. Oct. 15.
43. Juhala R.J., Ford M.E., Duda R.L., Youlton A., Hatfull G.F., Hendrix R.W. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 2000, May 26.
44. Katsura I., Hendrix R.W. Length determination in bacteriophage lambda tails. Cell. 1984, 39(3 Pt 2):691-698. Dec.
45. Kurtz S., et al. Versatile and open software for comparing large genomes. Genome Biol. 2004, 5:R12.
46. Kutateladze M., Adamia R. Phage therapy experience at the Eliava Institute. Med. Mal. Infect. 2008, 38(8):426-430. Aug 6.
47. Lambert P.A. Cellular impermeability and uptake of biocides and antibiotics in gram-positive bacteria and mycobacteria. Symp. Ser. Soc. Appl. Microbiol. 2002, 31:46S-54S.
48. Laslett D., Canback B. ARAGORN, a program for the detection of transfer RNA and transfer-messenger RNA genes in nucleotide sequences. Nucleic Acids Res. 2004, 32:11-16.
49. Levin M.E., Hendrix R.W., Casjens S.R. A programmed translational frameshift is required for the synthesis of a bacteriophage lambda tail assembly protein. J. Mol. Biol. 1993, 234(1):124-139. Nov 5.
50. Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
51. Malke H. Transduction of Streptococcus pyogenes K 56 by temperature-sensitive mutants of the transducing phage A 25. Z. Naturforsch. B. 1969, 24(12):1556-1561.
52. Markine-Goriaynoff N., Gillet L., Van Etten J.L., Korres H., Verma N., Vanderplasschen A. Glycosyltransferases encoded by viruses. J. Gen. Virol. 2004, Oct, 85(Pt 10):2741-2754.
53. Mathur M.D., Vidhani S., Mehndiratta P.L. Bacteriophage therapy: an alternative to conventional antibiotics. J. Assoc. Physicians India 2003, 51:593-596. Jun.
54. McShan W.M., Ferretti J.J. Prophages and their Contribution to host cell Phenotype. Bacteriophages 2007, 229-250. Bcateriophage, genetics and Molecular Biology, Caister Academic Press, Norfolk. S. McGrath, D. Van Sinderen (Eds.).
55. Mediavilla J., et al. Genome organisation and characterisation of mycobacteriophage Bxb1. Mol. Microbiol. 2000, 38(5):955-970.
56. Merril C.R., Scholl D., Adhya S.L. The prospect for bacteriophage therapy in Western medicine. Nat. Rev. Drug Discov. 2003, 2(6):489-497.
57. Morris P., Marinelli L.J., Jacobs-Sera D., Hendrix R.W., Hatfull G.F. Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination. J. Bacteriol. 2008, 190(6):2172-2182. Mar 4.
58. Muniesa M, et al. Bacteriophages and diffusion of beta-lactamase genes. Emerg. Infect. Dis. 2004, 10(6):1134-1137.
59. Nesbit C.E., Levin M.E., Donnelly-Wu M.K., Hatfull G.F. Transcriptional regulation of repressor synthesis in mycobacteriophage L5. Mol. Microbiol. 1995, 17(6):1045-1056.
60. O'Flaherty S., Ross R.P., Meaney W., Fitzgerald G.F., Elbreki M.F., Coffey A. Potential of the polyvalent anti-Staphylococcus bacteriophage K for control of antibiotic-resistant staphylococci from hospitals. Appl. Environ. Microbiol. 2005, 71(4):1836-1842. Apr.
61. Olia A.S., Cingolani G. A shifty stop for a hairy tail. Mol. Microbiol. 2008, 70(3):549-553. Nov 12.
62. Orengo C.A., Michie A.D., Jones D.T., Swindells M.B., Thornton J.M. CATH: a hierarchic classification of protein domain structures. Structure 1997, 5:1093-1108.
63. Pattee P.A., Baldwin J.N. Transduction of resistance to chlortetracycline and novobiocin in Staphylococcus aureus. J. Bacteriol. 1961, 82:875-881.
64. Payne K., Sun Q., Sacchettini J., Hatfull G.F. Mycobacteriophage Lysin B is a novel mycolylarabinogalactan esterase. Mol. Microbiol. 2009, 73(3):367-381.
65. Pedulla M.L., et al. Origins of highly mosaic mycobacteriophage genomes. Cell 2003, 113(2):171-182. Apr 18.
66. Pham T.T., Jacobs-Sera D., Pedulla M.L., Hendrix R.W, Hatfull G.F. Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria. Microbiology 2007, 153(Pt 8):2711-2723. Aug.
67. Pimentel M., Anes A., Garcia M., Moniz-Pereira J. Identification of a transmembranar protein encoded by the gene Pin of mycobacteriophage Ms6: role in superinfection exclusion. Workshop on Molecular Approaches to Tuberculosis 2000, Instituto Juan March de studios e Investigationes, Madrid, Dez (P).
68. Redmond W.B., Ward D.M. Media and methods for phage-typing mycobacteria. Bull. World Health Organ. 1966, 35(4):563-568.
69. Rybniker J, Plum G, Robinson N, Small PL, Hartmann P. Identification of three cytotoxic early proteins of mycobacteriophage L5 leading to growth inhibition in Mycobacterium smegmatis. Microbiology 2008, 154(Pt 8):2304-2314.
70. Sam MD, Cascio D, Johnson RC, Clubb RT. Crystal structure of the excisionase-DNA complex from bacteriophage lambda. J. Mol. Biol. 2004, 338(2):229-240.
71. Sehgal V.N., Sardana K., Dogra S. The imperatives of leprosy treatment in the pre- and post-global leprosy elimination era: appraisal of changing the scenario to current status. J. Dermatolog. Treat. 2008, 19(2):82-91.
72. Snider D.E., Jones W.D., Good R.C. The usefulness of phage typing Mycobacterium tuberculosis isolates. Am. Rev. Respir. Dis. 1984, 130(1095):1099.
73. Stone R. Bacteriophage therapy. Stalin's forgotten cure. Science 2002, 298(5594):728-731. Oct 25.
74. Sulakvelidze A. Phage therapy: an attractive option for dealing with antibiotic-resistant bacterial infections. Drug Discov. Today 2005, 10(12):807-809. Jun 15.
75. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
76. Uchiyama J., et al. Isolation and characterization of a novel Enterococcus faecalis bacteriophage phiEF24C as a therapeutic candidate. FEMS Microbiol. Lett. 2008, 278(2):200-206. Jan.
77. Unligil UM, Rini JM. Glycosyltransferase structure and mechanism. Curr. Opin. Struct. Biol. 2000, 10(5):510-517.
78. Vinodkumar C.S., Neelagund Y.F., Kalsurmath S. Bacteriophage in the treatment of experimental septicemic mice from a clinical isolate of multidrug resistant Klebsiella pneumoniae. J. Commun. Dis. 2005, 37(1):18-29. Mar.
79. Vinodkumar C.S., Kalsurmath S., Neelagund Y.F. Utility of lytic bacteriophage in the treatment of multidrug-resistant Pseudomonas aeruginosa septicemia in mice. Indian J. Pathol. Microbiol. 2008, 51(3):360-366. Jul-Sep.
80. Viscardi M., et al. Isolation and characterisation of two novel coliphages with high potential to control antibiotic-resistant pathogenic Escherichia coli (EHEC and EPEC). Int. J. Antimicrob. Agents 2008, 31(2):152-157. Feb.
81. Wang J., et al. Use of bacteriophage in the treatment of experimental animal bacteremia from imipenem-resistant Pseudomonas aeruginosa. Int. J. Mol. Med. 2006, 17(2):309-317. Feb.
82. Watanabe T., Watanabe M. Transduction of streptomycin sensitivity into resistant mutants of Salmonella typhimurium. J. Gen. Microbiol. 1959, 21:30-39.
83. Weber-Dabrowska B., Mulczyk M., Górski A. Bacteriophages as an efficient therapy for antibiotic-resistant septicemia in man. Transplant. Proc. 2003, 35(4):1385-1386. Jun.
84. Xu J., Hendrix R.W., Duda R.L. Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol. Cell. 2004, 16(1):11-21. Oct 8.
85. Zimmer M., Sattelberger E., Inman R.B., Calendar R., Loessner M.J. Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed + 1 translational frameshifting in structural protein synthesis. Mol. Microbiol. 2003, 50(1):303-317. Oct.