Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: Implications for phage evolution

Molecular Microbiology

Volumn 35, Issue 2, 2000, Pages 324-340

  Loessner, Martin J ^a   Inman, Ross B ^b   Lauer, Peter ^c   Calendar, Richard ^c  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DOUBLE STRANDED DNA; INTEGRASE; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; AUTOREGULATION; BACILLUS SUBTILIS; BACTERIAL GENETICS; BACTERIOPHAGE; CYTOLYSIS; DNA CROSS LINKING; DNA DENATURATION; DNA INTEGRATION; DNA MODIFICATION; DNA RECOMBINATION; DNA REPLICATION; ELECTRON MICROSCOPY; GENE MAPPING; GENE STRUCTURE; LISTERIA MONOCYTOGENES; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; PROPHAGE; REGULATOR GENE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BACTERIOPHAGES; BASE SEQUENCE; CAPSID; COMPUTATIONAL BIOLOGY; DNA, VIRAL; EVOLUTION, MOLECULAR; GENOME, VIRAL; LISTERIA MONOCYTOGENES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OPEN READING FRAMES; PROMOTER REGIONS (GENETICS); SEQUENCE ANALYSIS, DNA; TERMINATOR REGIONS (GENETICS); VIRAL PROTEINS; VIRAL STRUCTURAL PROTEINS; VIRUS INTEGRATION;

EID: 0033959106     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2000.01720.x     Document Type: Article

References (74)

1. Alonso, J.C., Luder, G., Stiege, A.C., Chai, S.H., Weise, F., and Trautner, T.A. (1997) The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1. Gene 204: 201-212.
2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
3. Baum, J.A., and Gilbert, M.P. (1991) Characterization and comparative sequence analysis of replication origins from three large Bacillus thuringiensis plasmids. J Bacteriol 173: 5280-5289.
4. Black, L.W. (1988) DNA packaging in dsDNA bacteriophages. In The Bacteriophages. Calendar, R. (ed.). New York: Plenum Press, pp. 321-373.
5. Botstein, D. (1980) A theory of modular evolution for bacteriophages. Ann NY Acad Sci 354: 484-491.
6. Bruttin, A., Desiere, F., Lucchini, S., Foley, S., and Brüssow, H. (1997) Characterization of the lysogeny DNA module from the temperate Streptococcus thermophilus bacteriophage ΦSfi21. Virology 233: 136-148.
7. Casjens, S., Huang, W.M., Hayden, M., and Parr, R. (1987) Initiation of bacteriophage P22 DNA packaging series. Analysis of a mutant that alters the DNA target specificity of the packaging apparatus. Mol Biol 194: 411-422.
8. Casjens, S., Hatfull, G., and Hendrix, R. (1992) Evolution of dsDNA tailed-bacteriophage genomes. Semin Virol 3: 383-397.
9. CDC (1998) Multistate outbreak of listeriosis - United States. Morbid Mortal Weekly Rep 47: 1085-1086.
10. Chai, S., Bravo, A., Luder, G., Nedlin, A., Trautner, T.A., and Alonso, J.C. (1992) Molecular analysis of the Bacillus subtilis bacteriophage SPP1 region encompassing genes 1-6. The products of gene 1 and gene 2 are required for pac cleavage. J Mol Biol 224: 87-102.
11. Chandry, P.S., Moore, S.C., Boyce, J.D., Davidson, B.E., and Hillier, A.J. (1997) Analysis of the DNA sequence, gene expression, origin of replication and modular structure of the Lactococcus lactis lytic bacteriophage sk1. Mol Microbiol 26: 49-64.
12. Chattoraj, D., and Inman, R.B. (1974) Location of DNA ends in P2, 186, P4 and lambda bacteriophage heads. J Mol Biol 87: 11-22.
13. Christiansen, B., Brondsted, L., Vogensen, F.K., and Hammer, K. (1996) A resolvase-like protein is required for the site-specific integration of the temperate lactococcal bacteriophage TP901-1. J Bacteriol 178: 5164-5173.
14. Dietrich, A., Bubert, A., Gentschev, I., Sokolovic, Z., Simm, A., Catic, A., et al. (1998) Delivery of antigen-encoding plasmid DNA into the cytosol of macrophages by attenuated suicide Listeria monocytogenes. Nature Biotechnol 16: 181-185.
15. Dunn, J.J., and Studier, F.W. (1983) Complete nucleotide sequence of bacteriophage T7 DNA and the location of T7 genetic elements. J Mol Biol 166: 477-535.
16. Emond, E., Fliss, I, and Pandian, S. (1993) A ribosomal DNA fragment of Listeria monocytogenes and its use as a genus-specific probe in an aqueous-phase hybridization assay. Appl Environ Microbiol 59: 2690-2697.
17. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
18. Ford, M.E., Sarkis, G.J., Belanger, A.E., Hendrix, R.W., and Hatfull, G.F. (1998a) Genome structure of mycobacteriophage D29: implications for phage evolution. J Mol Biol 279: 143-164.
19. Ford, M.E., Stenstrom, C., Hendrix, R.W., and Hatfull, G.F. (1998b) Mycobacteriophage TM4: genome structure and gene expression. Tubercle Lung Dis 79: 63-73.
20. Funnell, B.E., and Inman, R.B. (1979) Comparison of partial denaturation maps with the known sequence of SV40 and ΦX174 RF DNA. J Mol Biol 131: 331-340.
21. Haggård-Ljungquist, E., Halling, C., and Calendar, R. (1992) DNA sequences of the tail fibre genes of bacteriophage P2: evidence for horizontal transfer of tail fibre genes among unrelated bacteriophages. J Bacteriol 174: 1462-1477.
22. Hall, S.D., Kane, M.F., and Kolodner, R.D. (1993) Identification and characterization of the Escherichia coli RecT protein, a protein encoded by the recE region that promotes renaturation of homologous single stranded DNA. J Bacteriol 175: 277-287.
23. Hansen, E.B. (1989) Structure and regulation of the lytic replicon of phage P1. J Mol Biol 207: 135-149.
24. Hatfull, G.F., and Sarkis, G.J. (1993) DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics. Mol Microbiol 7: 395-405.
25. Hendrix, R.W., and Duda, R.L. (1998) Bacteriophage HK97 head assembly: a protein ballet. Adv Virus Res 50: 235-288.
26. Hendrix, R.W., Smith, M.C.M., Burns, R.N., Ford, M.E., and Hatfull, G.F. (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci USA 96: 2192-2197.
27. Highton, P.J., Chang, Y., and Myers, R.J. (1990) Evidence for the exchange of segments between genomes during the evolution of lambdoid bacteriophages. Mol Microbiol 4: 1329-1340.
28. Hodgson, D.A. (2000) Generalized transduction of serotype 1/2 and serotype 4b strains of Listeria monocytogenes. Mol Microbiol 35: 312-323.
29. Hoshino, T., McKenzie, T., Schmidt, S., Tanaka, T., and Sueoka, N. (1987) Nucleotide sequence of Bacillus subtilis dnaB: a gene essential for DNA replication initiation and membrane attachment. Proc Natl Acad Sci USA 84: 653-657.
30. Inman, R.B., and Schnös, M. (1979) Partial denaturation of thymine-and BU-containing DNA in alkali. J Mol Biol 49: 93-98.
31. Ito, T., Katayama, Y., and Hiramatsu, K. (1999) Cloning and nucleotide sequence determination of the entire mec DNA of pre-methicillin-resistant Staphylococcus aureus N315. Antimicrob Agents Chemother 43: 1449-1458.
32. Kaneko, J., Kimura, T., Narita, S., Tomita, T., and Kamio, Y. (1998) Complete nucleotide sequence and molecular characterization of the temperate staphylococcal bacteriophage ΦPVL carrying panton-valentine leukocidin genes. Gene 215: 57-67.
33. Katsura, I. (1987) Determination of bacteriophage λ tail length by a protein ruler. Nature 327: 73-75.
34. Kodaira, K.I., Oki, M., Kakikawa, M., Watanabe, N., Hirakawa, M., Yamada, K., et al. (1997) Genome structure of the Lactobacillus temperate phage Φg1e: the whole genome sequence and the putative promoter/repressor system. Gene 187: 45-53.
35. Krogh, S., O'Reilly, M., Nolan, N., and Devine, K.M. (1996) The phage like element PBSX and part of the skin element, which are resident at different locations on the Bacillus subtilis chromosome, are highly homologous. Microbiology 142: 2031-2040.
36. Lazarevic, V., Düsterhöft, A., Soldo, B., Hilbert, H., Mauël, C., and Karamata, D. (1999) Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPβc2. Microbiology 145: 1055-1067.
37. Lebrun, M., Audurier, A., and Cossart, P. (1994) Plasmidborne cadmium resistance genes in Listeria monocytogenes are present on Tn5422, a novel transposon closely related to Tn917. J Bacteriol 176: 3049-3061.
38. Lee, C.S., Davis, R.W., and Davidson, N. (1970) A physical study by electron microscopy of the terminally repetitious circularly permuted DNA from the coliphage particles of Escherichia coli 15. J Mol Biol 48: 1-22.
39. Littlewood, R.K., and Inman, R.B. (1982) Computer-assisted DNA length measurements from electron micrographs with special reference to partial denaturation mapping. Nucleic Acids Res 10: 1691-1706.
40. Loessner, M.J., and Busse, M. (1990) Bacteriophage typing of Listeria species. Appl Environ Microbiol 56: 1912-1918.
41. Loessner, M.J., Goeppl, S., and Busse, M. (1991) The phagovar variability of Listeria strains under the influence of virulent and temperate bacteriophages. Lett Appl Microbiol 12: 192-195.
42. Loessner, M.J., Krause, I.B., Henle, T., and Scherer, S. (1994) Structural proteins and DNA characteristics of 14 Listeria typing bacteriophages. J Gen Virol 75: 701-710.
43. Loessner, M.J., Wendlinger, G., and Scherer, S. (1995a) Heterogeneous endolysins in Listeria monocytogenes bacteriophages: a new class of enzymes and evidence for conserved holin genes within the siphoviral lysis cassettes. Mol Microbiol 16: 1231-1241.
44. Loessner, M.J., Schneider, A., and Scherer, S. (1995b) A new procedure for efficient recovery of DNA, RNA, and proteins from Listeria cells by rapid lysis with a recombinant bacteriophage endolysin. Appl Environ Microbiol 61: 1150-1152.
45. Loessner, M.J., Maier, S.K., Daubek-Puza, H., Wendlinger, G., and Scherer, S. (1997) Three Bacillus cereus bacteriophage endolysins are unrelated but reveal high homology to cell wall hydrolases from different bacilli. J Bacteriol 179: 2845-2851.
46. Löfdahl, S., Zabielski, J., and Phitipson, L. (1981) Structure and restriction maps of the circularly permuted DNA of staphylococcal bacteriophage Φ11. J Virol 37: 784-794.
47. Lucchini, S., Desiere, F., and Brüssow, H. (1998) The structural gene module in Streptococcus thermophilus bacteriophage ΦSfi11 shows a hierarchy of relatedness to Siphoviridae from a wide range of bacterial hosts. Virology 246: 63-73.
48. McDonnell, G.E., Wood, H., Devine, K.M., and McConnell, D.J. (1994) Genetic control of bacterial suicide: regulation of the induction of PBSX in Bacillus subtilis. J Bacteriol 176: 5820-5830.
49. Marvik, O.J., Dokland, T., Nokling, R.H., Jacobsen, E., Larsen, T., and Lindqvist, B.H. (1995) The capsid size-determining protein Sid forms an external scaffold on phage P4 procapsids. J Mol Biol 251: 59-75.
50. Mikkonen, M., and Alatossava, T. (1994) Characterization of the genome region encoding structural proteins of Lactobacillus delbrueckii supsp. lactis bacteriophage LL-H. Gene 151: 53-59.
51. Mikkonen, M., and Alatossava, T. (1995) A group 1 intron in the terminase gene of Lactobacillus delbrueckii supsp. lactis phage LL-H. Microbiology 141: 2183-2190.
52. Mouw, A.R., Beachey, E.H., and Burdett, V. (1988) Molecular evolution of streptococcal M protein: cloning and nucleotide sequence of the type 24 M protein gene and relation to other genes of Streptococcus pyogenes. J Bacteriol 170: 676-684.
53. Nakayama, K., Kanaya, S., Ohnishi, M., Terawaki, Y., and Hayashi, T. (1999) The complete nucleotide sequence of phi CTX, a cytotoxin converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. Mol Microbiol 31: 399-419.
54. Nauta, A., van Sinderen, D., Karsens, H., Smit, E., Venema, G., and Kok, J. (1996) Inducible gene expression mediated by a repressor-operator system isolated from Lactococcus lactis bacteriophage r1t. Mol Microbiol 19: 1331-1341.
55. Neve, H., Zenz, K.I., Desiere, F., Koch, A., Heller, K.J., and Brüssow, H. (1998) Comparison of the lysogeny modules from the temperate Streptococcus thermophilus bacteriophages TP-J34 and Sfi21: implications for the modular theory of phage evolution. Virology 241: 61-72.
56. Pedre, X., Weise, F., Chai, S., Lüder, G., and Alonso, J. (1994) Analysis of eis and Irans elements required for the initiation of DNA replication in the Bacillus subtilis bacteriophage SPP1. J Mol Biol 236: 1324-1340.
57. Plasterk, R.H., and van de Putte, P. (1985) The invertible P-DNA segment in the chromosome of Escherichia coli. EMBO J 4: 237-242.
58. Radlinska, M., and Piekarowicz, A. (1998) Cloning and characterization of a gene encoding a new methyltransferase from Neisseria gonorrhoeae. Biol Chem 379: 1391-1395.
59. Rausch, H., and Lehmann, M. (1991) Structural analysis of the actinophage ΦC31 attachment site. Nucleic Acids Res 19: 5187-5189.
60. Sambrook, J., Maniatis, T., and Fritsch, E.F. (1989) Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
61. Schäferkordt, S., and Chakraborty, T. (1997) Identification, cloning, and characterization of the Ima operon, whose gene products are unique to Listeria monocytogenes. J Bacteriol 179: 2707-2716.
62. Slutsker, L, and Schuchat, A. (1999) Listeriosis in humans. In Listeria, Listeriosis, and Food Safety. Ryser, E.T., and Marth, E.H. (eds). New York, NY: Marcel Dekker, pp. 75-95.
63. Stanley, E., Fitzgerald, G.F., Le Marrec, C., Fayard, B., and van Sinderen, D. (1997) Sequence analysis and characterization of ΦO1205, a temperate bacteriophage infecting Streptococcus thermophilus CNRZ 1205. Microbiology 143: 3417-3429.
64. Streisinger, G., Emrich, J., and Stahl, M.M. (1967) Chromosome structure in the phage T4. III. Terminal redundancy and length determination. Proc Natl Acad Sci USA 57: 292-295.
65. Stuart, S.E., and Welshimer, H.J. (1973) Intrageneric relatedness of Listeria Pirie. Int J Syst Bacteriol 23: 8-14.
66. Takemaru, K., Mizuno, M., Sato, T., Takeuchi, M., and Kobayashi, Y. (1995) Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis. Microbiology 141: 323-327.
67. Thorpe, H.M., and Smith, M.C.M. (1998) In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family. Proc Natl Acad Sci USA 95: 5505-5510.
68. Tye, B.K., Huberman, J.A., and Botstein, D. (1974) Non-random circular permutation of phage P22 DNA. J Mol Biol 85: 501-532.
69. Van Sinderen, D., Luttinger, A., Kong, L, Dubnau, D., Venema, G., and Hamoen, L. (1995) comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis. Mol Microbiol 15: 455-462.
70. Wendlinger, G., Loessner, M.J., and Scherer, S. (1996) Bacteriophage receptors on Listeria monocytogenes cells are the N-acetylglucosamine and rhamnose substituents of teichoic acids or the peptidoglycan itself. Microbiology 142: 985-992.
71. Wood, D.O., and Waite, R.T. (1994) Sequence analysis of the Rickettsia prowazekii gyrA gene. Gene 151: 191-196.
72. Yung, D.L., and Hollingshead, S.K. (1996) DNA sequencing and gene expression of the emm gene cluster in a M50 group A Streptococcus strain virulent for mice. Infect Immun 64: 2193-2200.
73. Zink, R., and Loessner, M.J. (1992) Classification of virulent and temperate bacteriophages of Listeria spp. on the basis of morphology and protein analysis. Appl Environ Microbiol 58: 296-302.
74. Zink, R., Loessner, M.J., and Scherer, S. (1995) Characterization of cryptic prophages (monocins) in Listeria and sequence analysis of a holin/endolysin gene. Microbiology 141: 2577-2584.