KSY1, a lactococcal phage with a T7-like transcription

Virology

Volumn 365, Issue 1, 2007, Pages 1-9

  Chopin, Alain ^a   Deveau, Hélène ^b   Ehrlich, S Dusko ^a   Moineau, Sylvain ^b   Chopin, Marie Christine ^a  

^a CEMAGREF   (France)

^b UNIVERSITÉ LAVAL   (Canada)

Author keywords

Bacteriophage; Genome sequence; Lactococcus; Podoviridae; T7 like RNA polymerase

Indexed keywords

BACTERIAL PROTEIN; DNA; PROTEIN KSY1; RIFAMPICIN; RNA POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIOPHAGE T7; GENE STRUCTURE; GENE TRANSFER; GENETIC TRANSCRIPTION; LACTOCOCCUS; MORPHOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

BACTERIOPHAGE T7; GENOME, VIRAL; LACTOCOCCUS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PODOVIRIDAE; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

LACTOCOCCUS; MIRIDAE; PODOVIRIDAE;

EID: 34250189879     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2007.03.044     Document Type: Article

References (63)

1. Ackermann H.W. Tailed bacteriophages: the order Caudovirales. Adv. Virus Res. 51 (1999) 135-201
2. Ackermann H.W. Frequency of morphological phage descriptions in the year 2000. Arch. Virol. 146 (2001) 843-857
3. Ackermann H.W., and Eisenstark A. The present state of phage taxonomy. Intervirology 3 (1974) 201-219
4. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
5. Bailey T.L., and Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (1994), AAAI Press, Menlo Park, California 28-36
6. Bamford D.H. Do viruses form lineages across different domains of life?. Res. Microbiol. 154 (2003) 231-236
7. Besemer J., and Borodovsky M. Heuristic approach to deriving models for gene finding. Nucleic Acids Res. 27 (1999) 3911-3920
8. Bidnenko E., Ehrlich S.D., and Chopin M.C. Phage operon involved in sensitivity to the Lactococcus lactis abortive infection mechanism AbiD1. J. Bacteriol. 177 (1995) 3824-3829
9. Bouchard J.D., and Moineau S. Homologous recombination between a lactococcal bacteriophage and the chromosome of its host strain. Virology 270 (2000) 65-75
10. Brondsted L., Ostergaard S., Pedersen M., Hammern K., and Vogensen F.K. Analysis of the complete DNA sequence of the temperate bacteriophage TP901-1: evolution, structure, and genome organization of lactococcal bacteriophages. Virology 283 (2001) 93-109
11. Brüssow H., and Desiere F. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol. Microbiol. 39 (2001) 213-222
12. Brüssow H., and Hendrix R.W. Phage genomics: small is beautiful. Cell 108 (2002) 13-16
13. Casjens S., Hatfull G., and Hendrix R. Evolution of dsDNA-tailed bacteriophage genomes. Sem. Virol. 3 (1992) 383-397
14. Cermakian N., Ikeda T.M., Miramontes P., Lang B.F., Gray M.W., and Cedergren R. On the evolution of the single-subunit RNA polymerases. J. Mol. Evol. 45 (1997) 671-681
15. Chibani Azaiez S.R., Fliss I., Simard R.E., and Moineau S. Monoclonal antibodies raised against native major capsid proteins of lactococcal c2-like bacteriophages. Appl. Environ. Microbiol. 64 (1998) 4255-4259
16. Chopin A. Organization and regulation of genes for amino acid biosynthesis in lactic acid bacteria. FEMS Microbiol. Rev. 12 (1993) 21-37
17. Deveau H., Labrie S.J., Chopin M.C., and Moineau S. Biodiversity and classification of lactococcal phages. Appl. Environ. Microbiol. 72 (2006) 4338-4346
18. Dunn J.J., and Studier F.W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166 (1983) 477-535
19. Dupont K., Vogensen F.K., Neve H., Bresciani J., and Josephsen J. Identification of the receptor-binding protein in 936-species lactococcal bacteriophages. Appl. Environ. Microbiol. 70 (2004) 5818-5824
20. Fortier L.-C., Bransi A., and Moineau S. Genome sequence and global gene expression of Q54, a new phage species linking the 936 and c2 phage species of Lactococcus lactis. J. Bacteriol. 188 (2006) 6101-6114
21. Huggins A.R., and Sandine W.E. Incidence and properties of temperate bacteriophages induced from lactic streptococci. Appl. Environ. Microbiol. 33 (1977) 184-191
22. Imburgio D., Rong M., Ma K., and McAllister W.T. Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants. Biochemistry 39 (2000) 10419-10430
23. Imburgio D., Anikin M., and McAllister W.T. Effects of substitutions in a conserved DX(2)GR sequence motif, found in many DNA-dependent nucleotide polymerases, on transcription by T7 RNA polymerase. J. Mol. Biol. 319 (2002) 37-51
24. Jarvis A.W., Fitzgerald G.F., Mata M., Mercenier A., Neve H., Powell I.B., Ronda C., Saxelin M., and Teuber M. Species and type phages of lactococcal bacteriophages. Intervirology 32 (1991) 2-9
25. Kenny J.G., McGrath S., Fitzgerald G.F., and van Sinderen D. Bacteriophage Tuc2009 encodes a tail-associated cell wall-degrading activity. J. Bacteriol. 186 (2004) 3480-3491
26. Kumar A., Malloch R.A., Fujita N., Smillie D.A., Ishihama A., and Hayward R.S. The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "extended minus 10" promoter. J. Mol. Biol. 232 (1993) 406-418
27. Labrie S.J., and Moineau S. Abortive infection mechanisms and prophage sequences significantly influence the genetic make-up of emerging lytic lactococcal phages. J. Bacteriol. 189 (2007) 1482-1487
28. Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227 (1970) 680-685
29. Lillehaug D. An improved plaque assay for poor plaque-producing temperate lactococcal bacteriophages. J. Appl. Microbiol. 83 (1997) 85-90
30. Loessner M.J., Gaeng S., and Scherer S. Evidence for a holin-like protein gene fully embedded out of frame in the endolysin gene of Staphylococcus aureus bacteriophage 187. J. Bacteriol. 181 (1999) 4452-4460
31. Lowe T.M., and Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (1997) 955-964
32. Lubbers M.W., Waterfield N.R., Beresford T.P., Le Page R.W., and Jarvis A.W. Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes. Appl. Environ. Microbiol. 61 (1995) 4348-4356
33. Lukashin A.V., and Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26 (1998) 1107-1115
34. Mahony J., Deveau H., McGrath S., Ventura M., Canchaya C., Moineau S., Fitzgerald G.F., and van Sinderen D. Sequence and comparative genomic analysis of lactococcal bacteriophages jj50, 712, and P008: evolutionary insights into the 936 phage species. FEMS Microbiol. Lett. 261 (2006) 253-261
35. Mann N.H., Clokie M.R., Millard A., Cook A., Wilson W.H., Wheatley P.J., Letarov A., and Krisch H.M. The genome of S-PM2, a "photosynthetic" T4-type bacteriophage that infects marine Synechococcus strains. J. Bacteriol. 187 (2005) 3188-3200
36. Marchler G.H., Mullokandov M., Shoemaker B.A., Simonyan V., Song J.S., Thiessen P.A., Yamashita R.A., Yin J.J., Zhang D., and Bryant S.H. CDD: a conserved domain database for protein classification. Nucleic Acids Res. 33 (2005) D192-D196
37. McAllister W.T., and Raskin C.A. The phage RNA polymerases are related to DNA polymerases and reverse transcriptases. Mol. Microbiol. 10 (1993) 1-6
38. Miller J.F. Bacteriophage and the evolution of epidemic cholera. Infect. Immun. 71 (2003) 2981-2982
39. Moak M., and Molineux I.J. Peptidoglycan hydrolytic activities associated with bacteriophage virions. Mol. Microbiol. 51 (2004) 1169-1183
40. Moineau S., Pandian S., and Klaenhammer T.R. Restriction/modification systems and restriction endonucleases are more effective on lactococcal bacteriophages that have emerged recently in the dairy industry. Appl. Environ. Microbiol. 59 (1993) 197-202
41. Pajunen M.I., Elizondo M.R., Skurnik M., Kieleczawa J., and Molineux I.J. Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. J. Mol. Biol. 319 (2002) 1115-1132
42. Pedersen M., Ostergaard S., Bresciani J., and Vogensen F.K. Mutational analysis of two structural genes of the temperate lactococcal bacteriophage TP901-1 involved in tail length determination and baseplate assembly. Virology 276 (2000) 315-328
43. Perler F.B., Olsen G.J., and Adam E. Compilation and analysis of intein sequences. Nucleic Acids Res. 25 (1997) 1087-1093
44. Proux C., van Sinderen D., Suarez J., Garcia P., Ladero V., Fitzgerald G.F., Desiere F., and Brussow H. The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria. J. Bacteriol. 184 (2002) 6026-6036
45. Reese M.G. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 26 (2001) 51-56
46. Rohwer F. Global phage diversity. Cell 113 (2003) 141
47. Rohwer F., Seguritan V., Choi D.H., Segall A.M., and Azam F. Production of shotgun libraries using random amplification. Biotechniques 31 (2001) 108-118
48. Sambrook J., and Russell D.W. Molecular Cloning: A Laboratory Manual. 3rd ed. (2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
49. Sandmeier H. Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibers. Mol. Microbiol. 12 (1994) 343-350
50. Saxelin M.L., Nurmiaho E.L., Korhola M.P., and Sundman V. Partial characterization of a new C3-type capsule-dissolving phage of Streptococcus cremoris. Can. J. Microbiol. 25 (1979) 1182-1187
51. Saxelin M.L., Nurmiaho-Lassila E.V., Merilaïnen V.T., and Forsen R.I. Ultrastructure and host specificity of bacteriophages of Streptococcus cremoris, Streptococcus lactis subsp. diacetylactis, and Leuconostoc cremoris from Finnish fermented milk "Viili". Appl. Environ. Microbiol. 52 (1986) 771-777
52. Schouler C., Ehrlich S.D., and Chopin M.C. Sequence and organization of the lactococcal prolate-headed bIL67 phage genome. Microbiology 140 (1994) 3061-3069
53. Sousa R., Chung Y.J., Rose J.P., and Wang B.C. Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution. Nature 364 (1993) 593-599
54. Spinelli S., Campanacci V., Blangy S., Moineau S., Tegoni M., and Cambillau C. Modular structure of the receptor binding proteins of Lactococcus lactis phages: the RBP structure of the temperate phage TP901-1. J. Biol. Chem. 281 (2006) 14256-14262
55. Spinelli S., Desmyter A., Verrips C.T., de Haard H.J.W., Moineau S., and Cambillau C. Lactococcal bacteriophage p2 receptor binding protein structure suggests a common ancestor gene with bacterial and mammalian viruses. Nat. Struct. Mol. Biol. 13 (2006) 85-89
56. Staden R., Beal K.F., and Bonfield J.K. The Staden package, 1998. Methods Mol. Biol. 132 (2000) 115-130
57. Stuer-Lauridsen B., Janzen T., Schnabl J., and Johansen E. Identification of the host determinant of two prolate-headed phages infecting Lactococcus lactis. Virology 309 (2003) 10-17
58. Terzaghi B.E., and Sandine W.E. Improved medium for lactic streptococci and their bacteriophages. Appl. Microbiol. 29 (1975) 807-813
59. Tétart F., Desplats C., and Krisch H.M. Genome plasticity in the distal tail fiber locus of the T-even bacteriophage: recombination between conserved motifs swaps adhesin specificity. J. Mol. Biol. 282 (1998) 543-556
60. Tock M.R., and Dryden D.T. The biology of restriction and anti-restriction. Curr. Opin. Microbiol. 8 (2005) 466-472
61. Vegge C.S., Brondsted L., Neve H., Mc Grath S., van Sinderen D., and Vogensen F.K. Structural characterization and assembly of the distal tail structure of the temperate lactococcal bacteriophage TP901-1. J. Bacteriol. 187 (2005) 4187-4197
62. Vegge C.S., Vogensen F.K., Mc Grath S., Neve H., van Sinderen D., and Brondsted L. Identification of the lower baseplate protein as the antireceptor of the temperate lactococcal bacteriophages TP901-1 and Tuc2009. J. Bacteriol. 188 (2006) 55-63
63. Wang I.N., Smith D.L., and Young R. Holins: the protein clocks of bacteriophage infections. Annu. Rev. Microbiol. 54 (2000) 799-825