The genome of bacteriophage φKMV, a T7-like virus infecting Pseudomonas aeruginosa

Virology

Volumn 312, Issue 1, 2003, Pages 49-59

  Lavigne, Rob ^a   Burkal'tseva, Maria V ^b   Robben, Johan ^a,d   Sykilinda, Nina N ^c   Kurochkina, Lidia P ^c   Grymonprez, Barbara ^a   Jonckx, Bart ^a   Krylov, Victor N ^b   Mesyanzhinov, Vadim V ^a,c   Volckaert, Guido ^a  

^a LABORATORY OF GENE TECHNOLOGY   (Belgium)

^b STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

^c SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^d HASSELT UNIVERSITY   (Belgium)

Author keywords

Endolysin; Genome sequence; Phage evolution; Phage therapy; Pseudomonas aeruginosa; RNA polymerase; T7 bacteriophage

Indexed keywords

DOUBLE STRANDED DNA; GENOMIC DNA; RNA POLYMERASE;

ARTICLE; BACTERIAL GENOME; BACTERIOPHAGE; BACTERIOPHAGE T7; BACTERIUM ISOLATION; DNA REPLICATION; DNA SEQUENCE; GENE SEQUENCE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN FUNCTION; PSEUDOMONAS AERUGINOSA; SEQUENCE HOMOLOGY;

BACTERIOPHAGE PHIKMV; PODOVIRIDAE; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA;

EID: 0043169693     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0042-6822(03)00123-5     Document Type: Article

References (60)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST a new generation of protein database search programs . Nucleic Acids Res. 25:1997;3389-3402.
2. Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29:2001;37-40.
3. Bairoch A., Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28:2000;45-48.
4. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., Sonnhammer E.L. Nucleic Acids Res. 30:2002;276-280.
5. Besemer J., Borodovsky M. Heuristic approach to deriving models for gene finding. Nucleic Acids Res. 27:1999;3911-3920.
6. Bonner G., Patra D., Lafer E.M., Sousa R. Mutations in T7 RNA polymerase that support the proposal for a common polymerase active site structure. EMBO J. 11:1992;3767-3775.
7. Borodovsky M., McIninch J. Recognition of genes in DNA sequence with ambiguities. Biosystems. 30:1993;161-171.
8. Brieba L.G., Padilla R., Sousa R. Role of t7 RNA polymerase his784 in start site selection and initial transcription. Biochemistry. 41:2002;5144-5149.
9. Cerritelli M.E., Studier F.W. Purification and characterization of T7 head-tail connectors expressed from the cloned gene. J. Mol. Biol. 258:1996;299-307.
10. Cheetham G.M., Jeruzalmi D., Steitz T.A. Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature. 399:1999;80-83.
11. Cheetham G.M., Steitz T.A. Structure of a transcribing T7 RNA polymerase initiation complex. Science. 286:1999;2305-2309.
12. Condron B.G., Atkins J.F., Gesteland R.F. Frameshifting in gene 10 of bacteriophage T7. J. Bacteriol. 173:1991;6998-7003.
13. d'Aubenton C.Y., Brody E., Thermes C. Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol. 216:1990;835-858.
14. Dunn J.J., Studier F.W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166:1983;477-535.
15. Dunn J.J., Studier F.W. Organization and expression of bacteriophage T7 DNA. CSH Symp. Quant. Biol. 47:1983;999-1007.
16. el Mabrouk N., Lisacek F. Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome. J. Mol. Biol. 264:1996;46-55.
17. Endy D., You L., Yin J., Molineux I.J. Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Proc. Natl. Acad. Sci. USA. 97:2000;5375-5380.
18. Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., Bairoch A. The PROSITE database, its status in 2002. Nucleic Acids Res. 30:2002;235-238.
19. Garcia L.R., Molineux I.J. Rate of translocation of bacteriophage T7 DNA across the membranes of Escherichia coli. J. Bacteriol. 177:1995;4066-4076.
20. Giamarellou H. Therapeutic guidelines for Pseudomonas aeruginosa infections. Int. J. Antimicrob. Agents. 16:2000;103-106.
21. Grundling A., Manson M.D., Young R. Holins kill without warning. Proc. Natl. Acad. Sci. USA. 98:2001;9348-9352.
22. Hendrix R.W., Smith M.C., Burns R.N., Ford M.E., Hatfull G.F. Evolutionary relationships among diverse bacteriophages and prophages all the world's a phage . Proc. Natl. Acad. Sci. USA. 96:1999;2192-2197.
23. Higgins D., Thompson J., Gibson T., 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. 22:1994;4673-4680.
24. Izawa M., Sasaki N., Watahiki M., Ohara E., Yoneda Y., Muramatsu M., Okazaki Y., Hayashizaki Y. Recognition sites of 3′-OH group by T7 RNA polymerase and its application to transcriptional sequencing. J. Biol. Chem. 273:1998;14242-14246.
25. Jeruzalmi D., Steitz T.A. Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J. 17:1998;4101-4113.
26. 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. 299:2000;27-51.
27. Kanamaru S., Leiman P.G., Kostyuchenko V.A., Chipman P.R., Mesyanzhinov V.V., Arisaka F., Rossmann M.G. Structure of the cell-puncturing device of bacteriophage T4. Nature. 415:2002;553-557.
28. Kessler C., Manta V. Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3). Gene. 92:1990;1-248.
29. Korsten K.H., Tomkiewicz C., Hausmann R. The strategy of infection as a criterion for phylogenetic relationships of non-coli phages morphologically similar to phage T7. J. Gen. Virol. 43:1979;57-73.
30. Kropinski A.M. Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J. Bacteriol. 182:2000;6066-6074.
31. Krylov V.N. Phagotherapy in terms of bacteriophage genetics hopes, perspectives, safety, limitations . Genetika. 37:2001;869-887.
32. Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227:1970;680-685.
33. Loessner M.J., Maier S.K., Daubek-Puza H., Wendlinger G., Scherer S. Three Bacillus cereus bacteriophage endolysins are unrelated but reveal high homology to cell wall hydrolases from different bacilli. J. Bacteriol. 179:1997;2845-2851.
34. Lowe T.M., Eddy S.R. tRNAscan-SE a program for improved detection of transfer RNA genes in genomic sequence . Nucleic Acids Res. 25:1997;955-964.
35. Merril C.R., Biswas B., Carlton R., Jensen N.C., Creed G.J., Zullo S., Adhya S. Long-circulating bacteriophage as antibacterial agents. Proc. Natl. Acad. Sci. USA. 93:1996;3188-3192.
36. Mesyanzhinov V.V., Robben J., Grymonprez B., Kostyuchenko V.A., Burkal'tseva M.V., Sykilinda N.N., Krylov V.N., Volckaert G. The Genome of Bacteriophage φKZ of Pseudomonas aeruginosa. J. Mol. Biol. 317:2002;1-19.
37. Moffatt B.A., Dunn J.J., Studier F.W. Nucleotide sequence of the gene for bacteriophage T7 RNA polymerase. J. Mol. Biol. 173:1984;265-269.
38. Moller S., Croning M.D., Apweiler R. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics. 18:2002;218.
39. Nakayama K., Kanaya S., Ohnishi M., Terawaki Y., Hayashi T. The complete nucleotide sequence of φ CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa implications for phage evolution and horizontal gene transfer via bacteriophages . Mol. Microbiol. 31:1999;399-419.
40. Pajunen M.I., Elizondo M.R., Skurnik M., Kieleczawa J., Molineux I.J. Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. J. Mol. Biol. 319:2002;1115-1132.
41. Pajunen M.I., Kiljunen S.J., Soderholm M.E., Skurnik M. Complete genomic sequence of the lytic bacteriophage φYeO3-12 of Yersinia enterocolitica serotype O:3. J. Bacteriol. 183:2001;1928-1937.
42. Raaijmakers H., Vix O., Toro I., Golz S., Kemper B., Suck D. X-ray structure of T4 endonuclease VII a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture . EMBO J. 18:1999;1447-1458.
43. Reese M.G. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 26:2001;51-56.
44. Rice P., Longden I., Bleasby A. EMBOSS the European Molecular Biology Open Software Suite . Trends Genet. 16:2000;276-277.
45. Rohwer F.L., Segall A.M., Steward G., Seguritan V., Breitbart M., Wolven F., Azam F. The complete genomic sequence of the marine phage Roseophage SIO1 shares homology with nonmarine phages. Limnol. Oceanogr. 45:2000;408-418.
46. Salzberg S.L., Delcher A.L., Kasif S., White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26:1998;544-548.
47. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning A Laboratory Manual . 2nd ed: 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
48. SantaLucia J. Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1998;1460-1465.
49. São-José C., Parreira R., Vieira G., Santos M.A. The N-terminal region of Oenococcus oeni bacteriophage fOg44 lysin behaves as a bona fide signal peptide in Escherichia coli and as a cis-inhibitory element, preventing lytic activity on oenoccocal cells. J. Bacteriol. 182:2000;5823-5831.
50. Sousa R., Chung Y.J., Rose J.P., Wang B.C. Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution. Nature. 364:1993;593-599.
51. Stahl S.J., Zinn K. Nucleotide sequence of the cloned gene for bacteriophage T7 RNA polymerase. J. Mol. Biol. 148:1981;481-485.
52. Stover C.K., Pham X.Q., Erwin A.L., Mizoguchi S.D., Warrener P., Hickey M.J., Brinkman F.S., Hufnagle W.O., Kowalik D.J., Lagrou M., Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y., Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R., Smith K., Spencer D., Wong G.K., Wu Z., Paulsen I.T. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature. 406:2000;959-964.
53. Tabor S., Richardson C.C. A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides. Proc. Natl. Acad. Sci. USA. 92:1995;6339-6343.
54. Valpuesta J.M., Carrascosa J.L. Structure of viral connectors and their function in bacteriophage assembly and DNA packaging. Q. Rev. Biophys. 27:1994;107-155.
55. Voet M., Defoor E., Verhasselt P., Riles L., Robben J., Volckaert G. The sequence of a nearly unclonable 22.8 kb segment on the left arm chromosome VII from Saccharomyces cerevisiae reveals ARO2, RPL9A, TIP1, MRF1 genes and six new open reading frames. Yeast. 13:1997;177-182.
56. Wang I.N., Smith D.L., Young R. Holins the protein clocks of bacteriophage infections . Annu. Rev. Microbiol. 54:2000;799-825.
57. Wikoff W.R., Liljas L., Duda R., Tsuruta H., Hendrix R.W., Johnson J.J. Topologically linked protein rings in the bacteriophage HK97 capsid. Science. 289:2000;2129-2133.
58. Young I., Wang I., Roof W.D. Phages will out strategies of host cell lysis . Trends Microbiol. 8:2000;120-128.
59. Young R. Bacteriophage lysis mechanism and regulation . Microbiol. Rev. 56:1992;430-481.
60. Young R., Blasi U. Holins form and function in bacteriophage lysis . FEMS Microbiol. Rev. 17:1995;191-205.