The prophages of Lactobacillus johnsonii NCC 533: Comparative genomics and transcription analysis

Virology

Volumn 320, Issue 2, 2004, Pages 229-242

  Ventura, Marco ^a,b   Canchaya, Carlos ^a   Pridmore, R David ^a   Brüssow, Harald ^a  

^a NESTLÉ RESEARCH CENTER   (Switzerland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Lactobacillus johnsonii; Prophages; Transcription

Indexed keywords

INTEGRASE; STRUCTURAL PROTEIN; TRANSFER RNA; VIRUS PROTEIN;

ARTICLE; BACTERIOPHAGE; DNA PACKAGING; DNA REPLICATION; DNA SEQUENCE; GENE INSERTION; GENE SEQUENCE; GENOME ANALYSIS; GENOMICS; LACTOBACILLUS DELBRUECKII; LACTOBACILLUS JOHNSONII; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROPHAGE; REPRESSOR GENE; RNA GENE; SEQUENCE HOMOLOGY; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS THERMOPHILUS; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS STRAIN; VIRUS TRANSCRIPTION;

ATTACHMENT SITES, MICROBIOLOGICAL; GENOME, VIRAL; GENOMICS; LACTOBACILLUS; MOLECULAR SEQUENCE DATA; PROPHAGES; SEQUENCE ANALYSIS, DNA; SIPHOVIRIDAE; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

LACTOBACILLUS; LACTOBACILLUS JOHNSONII; LACTOBACILLUS JOHNSONII NCC 533; LACTOCOCCUS; LACTOCOCCUS LACTIS; SIPHOVIRIDAE; STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS; STREPTOCOCCUS THERMOPHILUS;

EID: 1542375392     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virol.2003.11.034     Document Type: Article

References (54)

1. Altschul S.F., Madden T.L., Shaffer 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. Aurvay F., Coddveville M., Espagno G., Ritzenthaler P. Integrative recombination of Lactobacillus delbrueckii bacteriophage mv4: functional analysis of the reaction and structure of the attP site. Mol. Gen. Genet. 262:1999;355-366.
3. Beres S.B., Sylva G.L., Barbian K.D., Lei B., Hoff J.S., Mammarella N.D., Liu M.Y., Smoot J.C., Porcella S.F., Parkins L.D., Campbell D.S., Smith T.M., McCormick J.K., Leung D.Y., Shlievert P.M., Musser J.M. Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc. Natl. Acad. Sci. U.S.A. 99:2002;10078-10083.
4. Boyce J.D., Davidson B.E., Hiller A.J. Identification of prophage genes expressed in lysogens of the Lactococcus lactis bacteriophage BK5-T. Appl. Environ. Microbiol. 61:1995;4099-4104.
5. Bronsted L., Ostergaard S., Pedersen M., Hammer K., 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.
6. Brüssow H. Phages of dairy bacteria. Annu. Rev. Microbiol. 55:2001;283-303.
7. Brüssow H., Bruttin A. Characterization of a temperate Streptococcus thermophilus bacteriophage and its genetic relationship with lytic phages. Virology. 212:1995;632-640.
8. Brüssow H., Desiere F. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol. Microbiol. 39:2001;213-222.
9. Bruttin A., Desiere F., Lucchini S., Foley S., Brüssow H. Characterization of the lysogeny DNA module from the temperate Streptococcus thermophilus bacteriophage phi Sfi21. Virology. 233:1997;136-148.
10. Bushman F. Lateral DNA Transfer-Mechanisms and Consequences. 2002;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
11. Campbell A.M. Chromosomal insertion sites for phages and plasmids. J. Bacteriol. 174:1992;7495-7499.
12. Campbell A.M. Preferential orientation of natural lambdoid prophages and bacterial chromosome organization. Theor. Popul. Biol. 61:2002;503-507.
13. Canchaya C., Proux C., Fournous G., Bruttin A., Brüssow H. Prophage genomics. Microbiol. Mol. Biol. Rev. 67:2003;238-276.
14. Casjens S. Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49:2003;277-300.
15. Casjens S., Hatfull G., Hendrix R. Evolution of dsDNA tailed-bacteriophage genomes. Semin. Virol. 3:1992;383-397.
16. Chopin A., Bolotin A., Sorokin A., Ehrlich S.D., Chopin M. Analysis of six prophages in Lactococcus lactis IL403: different genetic structure of temperate and virulent phage populations. Nucleic Acids Res. 29:2001;644-651.
17. Desiere F., Pridmore R.D., Brüssow H. Comparative genomics of the late gene cluster from Lactobacillus phages. Virology. 275:2000;294-305.
18. Doolittle W.F. Phylogenetic classification and the universal tree. Science. 284:1999;2124-2129.
19. Ferretti J.J., McShan W.M., Ajdic D., Savic D.J., Savic G., Lyon K., Primeaux C., Sezate S., Suvorov A.N., Kenton S., Lai H.S., Lin S.P., Qian Y., Jia H.G., Najar F.Z., Ren Q., Zhu H., Song L., White J., Yuan X., Clifton S.W., Roe B.A., McLaughlin R. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc. Natl. Acad. Sci. U.S.A. 98:2001;4658-4663.
20. Hendrix R.W., Smith M.C.M., Burns N., Ford M.E., Hatfull G.F. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc. Natl. Acad. Sci. U.S.A. 96:1999;2192-2197.
21. Henrich B., Binishofer B., Bläsi U. Primary structure and functional analysis of the lysis genes of Lactobacillus gasseri bacteriophage phi adh. J. Bacteriol. 177:1995;723-732.
22. Ikebe T., Wada A., Inagaki Y., Sugama K., Suzuki R., Tanaka D., Tamaru A., Fujinaga Y., Abe Y., Shimizu Y., Watanabe H. Dissemination of the phage-associated novel superantigen gene speL in recent invasive and noninvasive Streptococcus pyogenes M3/T3 isolates in Japan. Infect. Immun. 70:2002;3227-3233.
23. Iyer L.M., Koonin E.V., Aravind L. Extensive domain shuffling in transcription regulators of DNA viruses and implications of the origin of fungal APSES transcription factors. Genome Biol. 3:2002;1-11.
24. Jankovic I., Ventura M., Meylan V., Rouvet M., Elli M., Zink R. Contribution of aggregation-promoting factor to maintenance of cell shape in Lactobacillus gasseri 4B2. J. Bacteriol. 185:2003;3288-3296.
25. Johnson J.L., Phelps C.F., Cummins C.S., London J., Gasser F. Taxonomy of the Lactobacillus acidophilus group. Int. J. Syst. Bacteriol. 30:1980;53-68.
26. Johnson M.G., Neve H., Vogensen F.K., Hammer K. Virion positions and relationships of lactococcal temperate bacteriophage TP901-1 proteins. Virology. 212:1995;595-606.
27. Johnson M.G., Appel K.F., Madsen P.L., Vogensen F.K., Hammer K., Arnau J. A genomic region of lactococcal temperate bacteriophage TP901-1 encoding major virion proteins. Virology. 218:1996;306-315.
28. Kodaira K.I., Oki M., Kakikawa M., Watanabe N., Hirakawa M., Yamada K., Taketo A. Genome structure of the Lactobacillus temperate phage phi g1e: the whole genome sequence and the putative promoter/repressor system. Gene. 187:1997;45-53.
29. Kurland C.G., Canback B., Berg O.G. Horizontal gene transfer: a critical view. Proc. Natl. Acad. Sci. U.S.A. 100:2003;9658-9662.
30. Kuroda M., Otha T., Uchiyama I., Baba T., Yuzawa H., Kobayashi I., Cui L., Oguchi A., Aoki K., Nagai Y., Lian J., Ito T., Kanamori M., Matsumara H., Maruyama A., Murakami H., Hosoyama A., Mizutami Y., Takahashi N., Sawano T., Inoue R., Kaito C., Sekimizu K., Hirakawa H., Kuhara S., Goto S., Yabuzaki J., Kanehisa M., Yamashita A., Oshima K., Furuya K., Yoshino C., Shiba T., Hattori M., Ogasawara N., Hayashi H., Hiramatsu K. Whole genome sequencing of meticillin-resistant Staphyloccus aureus. Lancet. 357:2001;1225-1240.
31. Lawrence J.G., Hendrix R.W., Casjens S. Where are the pseudogenes in bacterial genomes? Trends Microbiol. 9:2001;535-540.
32. Lipman D.J., Pearson W.R. Rapid and sensitive protein similarity searches. Science. 227:1985;1435-1441.
33. 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.
34. Lucchini S., Desiere F., Brüssow H. Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram-positive bacteria. Virology. 263:1999;427-435.
35. Luo Y., Pfister P., Leisinger T., Wasserfallen A. The genome of archaeal prophage PsiM100 encodes the lytic enzyme responsible for autolysis of Methanothermobacter wolfeii. J. Bacteriol. 183:2001;5788-5792.
36. Madsen P.L., Hammer K. Temporal transcription of the lactococcal temperate phage TP901-1 and DNA sequence of the early promoter region. Microbiology. 144:1998;2203-2215.
37. Madsen P.L., Johansen A.H., Hammer K., Bronsted L. The genetic switch activity of early promoters of the temperate lactococcal bacteriophage TP901-1. J. Bacteriol. 181:1999;7430-7438.
38. McGrath S., Seegers J., Fitzgerald G.F., van Sinderen D. Molecular characterization of a phage-encoded resistance system in Lactococcus lactis. Appl. Environ. Microbiol. 65:1999;1891-1899.
39. McGrath S., Fitzgerald G.F., van Sinderen D. Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages. Mol. Microbiol. 43:2002;509-520.
40. Moineau S., Tremblay D., Labrie S. Phages of lactic acid bacteria: from genomics to industrial applications. ASM News. 68:2002;388-393.
41. Neve H., Zenz K.I., Desiere F., Koch A., Heller K.J., Brüssow H. Comparison of the lysogeny modules from the temperate Streptococcus thermophillus bacteriophages TP-J34 and Sfi21: implications for the modular theory of phage evolution. Virology. 241:1998;61-72.
42. Nilsen T., Nes I.F., Holo H. Enterolysin A, a cell wall-degrading bacteriocin from Enterococcus faecalis LMG 2333. Appl. Environ. Microbiol. 69:2003;2975-2984.
43. Ohnishi M., Kurokowa K., Hayashi T. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 9:2002;481-485.
44. Ostergaard S., Bronsted L., Vogensen F.K. Identification of a replication protein and repeats essential for DNA replication of the temperate lactococcal bacteriophage TP901-1. Appl. Environ. Microbiol. 67:2001;774-781.
45. Pedersen M., Ostergaard S., Bresciani J., 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.
46. Pedulla M.L., Ford M.E., Houtz J.M., Karthikeyan T., Wadsworth C., Lewis J.A., Jacobs-sera D., Falbo J., Gross J., Pannunzio N., Brucker W., Kumar V., Kandasamy J., Keenan L., Bardarov S., Kriakov J., Lawrence J., Jacobs W., Hendrix R., Hatfull G. Origin of highly mosaic mycobacteriophage genomes. Cell. 113:2003;171-182.
47. Pfister P., Wasserfallen A., Stettler R., Leisinger T. Molecular analysis of Methanobacterium phage psiM2. Mol. Microbiol. 30:1998;233-244.
48. Pridmore R.D., Berger B., Desiere F., Vilanova D., Barreto C., Pittet A.-C., Zwahlen M.-C., Rouvet M., Barrangou R., Altermann E., Mollet B., Mercenier A., Klaenhammer T., Arigoni F., Schell M.A. The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc. Natl. Acad. Sci. (USA). 2004;. in press.
49. Sambrook J., Maniatis T., Fritsch E.F. Molecular Cloning a Laboratory Manual. 1989;Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
50. Smoot J.C., Barbian K.D., Van Gompel J.J., Smoot L.M., Chaussee M.S., Sylva G.L., Sturdevant D.E., Ricklefs S.M., Porcella S.F., Parkins L.D., Beres S.B., Campbell D.S., Smith T.M., Zhang Q., Kapur V., Daly J.A., Veasy L.G., Musser J.M. Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc. Natl. Acad. Sci. U.S.A. 99:2002;4668-4673.
51. Ventura M., Foley S., Bruttin A., Chennoufi S.C., Canchaya C., Brüssow H. Transcription mapping as a tool in phage genomics: the case of temperate Streptococcus thermophilus phage Sfi21. Virology. 296:2002;62-76.
52. Ventura M., Bruttin A., Canchaya C., Brüssow H. Transcription analysis of Streptococcus thermophilus phages in the lysogenic state. Virology. 302:2002;21-32.
53. Ventura M., Canchaya C., Brüssow H. Integration and distribution of Lactobacillus johnsonii prophages. J. Bacteriol. 185:2003a;4603-4608.
54. Ventura M., Canchaya C., Kleerebezem M., de Vos W.M., Siezen R., Brüssow H. The prophage sequences of Lactobacillus plantarum strain WCFS1. Virology. 2003b;. (in press).