Skip to main content
PMC home page
Applied and Environmental Microbiology logoLink to Applied and Environmental Microbiology
. 1995 Dec;61(12):4348–4356. doi: 10.1128/aem.61.12.4348-4356.1995

Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes.

M W Lubbers 1, N R Waterfield 1, T P Beresford 1, R W Le Page 1, A W Jarvis 1
PMCID: PMC167745  PMID: 8534101

Abstract

The 22,163-bp genome of the lactococcal prolate-headed phage c2 was sequenced. Thirty-nine open reading frames (ORFs), early and late promoters, and a putative transcription terminator were identified. Twenty-two ORFs were in the early gene region, and 17 were in the late gene region. Putative genes for a DNA polymerase, a recombination protein, a sigma factor protein, a transcription regulatory protein, holin proteins, and a terminase were identified. Transcription of the early and late genes proceeded divergently from a noncoding 611-bp region. A 521-bp fragment contained within the 611-bp intergenic region could act as an origin of replication in Lactococcus lactis. Three major structural proteins, with sizes of 175, 90, and 29 kDa, and eight minor proteins, with sizes of 143, 82, 66, 60, 44, 42, 32, and 28 kDa, were identified. Several of these proteins appeared to be posttranslationally modified by proteolytic cleavage. The 175- and 90-kDa proteins were identified as the major phage head proteins, and the 29- and 60-kDa proteins were identified as the major tail protein and (possibly) the tail adsorption protein, respectively. The head proteins appeared to be covalently linked multimers of the same 30-kDa gene product. Phage c2 and prolate-headed lactococcal phage bIL67 (C. Schouler, S. D. Ehrlich, and M.-C. Chopin, Microbiology 140:3061-3069, 1994) shared 80% nucleotide sequence identity. However, several DNA deletions or insertions which corresponded to the loss or acquisition of specific ORFs, respectively, were noted. The identification of direct nucleotide repeats flanking these sequences indicated that recombination may be important in the evolution of these phages.(ABSTRACT TRUNCATED AT 250 WORDS)

Full Text

The Full Text of this article is available as a PDF (600.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adamski F. M., Donly B. C., Tate W. P. Competition between frameshifting, termination and suppression at the frameshift site in the Escherichia coli release factor-2 mRNA. Nucleic Acids Res. 1993 Nov 11;21(22):5074–5078. doi: 10.1093/nar/21.22.5074. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  3. Arendt E. K., Daly C., Fitzgerald G. F., van de Guchte M. Molecular characterization of lactococcal bacteriophage Tuc2009 and identification and analysis of genes encoding lysin, a putative holin, and two structural proteins. Appl Environ Microbiol. 1994 Jun;60(6):1875–1883. doi: 10.1128/aem.60.6.1875-1883.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Atkins J. F., Weiss R. B., Gesteland R. F. Ribosome gymnastics--degree of difficulty 9.5, style 10.0. Cell. 1990 Aug 10;62(3):413–423. doi: 10.1016/0092-8674(90)90007-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Beresford T. P., Ward L. J., Jarvis A. W. Temporally Regulated Transcriptional Expression of the Genomes of Lactococcal Bacteriophages c2 and sk1. Appl Environ Microbiol. 1993 Nov;59(11):3708–3712. doi: 10.1128/aem.59.11.3708-3712.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Botstein D. A theory of modular evolution for bacteriophages. Ann N Y Acad Sci. 1980;354:484–490. doi: 10.1111/j.1749-6632.1980.tb27987.x. [DOI] [PubMed] [Google Scholar]
  7. Brennan R. G., Matthews B. W. Structural basis of DNA-protein recognition. Trends Biochem Sci. 1989 Jul;14(7):286–290. doi: 10.1016/0968-0004(89)90066-2. [DOI] [PubMed] [Google Scholar]
  8. Chopin A. Organization and regulation of genes for amino acid biosynthesis in lactic acid bacteria. FEMS Microbiol Rev. 1993 Sep;12(1-3):21–37. doi: 10.1111/j.1574-6976.1993.tb00011.x. [DOI] [PubMed] [Google Scholar]
  9. Chung D. K., Kim J. H., Batt C. A. Cloning and nucleotide sequence of the major capsid protein from Lactococcus lactis ssp. cremoris bacteriophage F4-1. Gene. 1991 May 15;101(1):121–125. doi: 10.1016/0378-1119(91)90233-2. [DOI] [PubMed] [Google Scholar]
  10. Coveney J. A., Fitzgerald G. F., Daly C. Detailed characterization and comparison of four lactic streptococcal bacteriophages based on morphology, restriction mapping, DNA homology, and structural protein analysis. Appl Environ Microbiol. 1987 Jul;53(7):1439–1447. doi: 10.1128/aem.53.7.1439-1447.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dao M. L., Ferretti J. J. Streptococcus-Escherichia coli shuttle vector pSA3 and its use in the cloning of streptococcal genes. Appl Environ Microbiol. 1985 Jan;49(1):115–119. doi: 10.1128/aem.49.1.115-119.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dodd I. B., Egan J. B. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 1990 Sep 11;18(17):5019–5026. doi: 10.1093/nar/18.17.5019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gribskov M., Burgess R. R. Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. Nucleic Acids Res. 1986 Aug 26;14(16):6745–6763. doi: 10.1093/nar/14.16.6745. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hatfull G. F., Sarkis G. J. DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics. Mol Microbiol. 1993 Feb;7(3):395–405. doi: 10.1111/j.1365-2958.1993.tb01131.x. [DOI] [PubMed] [Google Scholar]
  15. He M., Wilde A., Kaderbhai M. A. A simple single-step procedure for small-scale preparation of Escherichia coli plasmids. Nucleic Acids Res. 1990 Mar 25;18(6):1660–1660. doi: 10.1093/nar/18.6.1660. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Helmann J. D., Chamberlin M. J. Structure and function of bacterial sigma factors. Annu Rev Biochem. 1988;57:839–872. doi: 10.1146/annurev.bi.57.070188.004203. [DOI] [PubMed] [Google Scholar]
  17. Henikoff S., Henikoff J. G. Automated assembly of protein blocks for database searching. Nucleic Acids Res. 1991 Dec 11;19(23):6565–6572. doi: 10.1093/nar/19.23.6565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Holmes D. S., Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem. 1981 Jun;114(1):193–197. doi: 10.1016/0003-2697(81)90473-5. [DOI] [PubMed] [Google Scholar]
  19. Ish-Horowicz D., Burke J. F. Rapid and efficient cosmid cloning. Nucleic Acids Res. 1981 Jul 10;9(13):2989–2998. doi: 10.1093/nar/9.13.2989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jarvis A. W. Differentiation of lactic streptococcal phages into phage species by DNA-DNA homology. Appl Environ Microbiol. 1984 Feb;47(2):343–349. doi: 10.1128/aem.47.2.343-349.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Jarvis A. W., Fitzgerald G. F., Mata M., Mercenier A., Neve H., Powell I. B., Ronda C., Saxelin M., Teuber M. Species and type phages of lactococcal bacteriophages. Intervirology. 1991;32(1):2–9. doi: 10.1159/000150179. [DOI] [PubMed] [Google Scholar]
  22. Jarvis A. W., Meyer J. Electron microscopic heteroduplex study and restriction endonuclease cleavage analysis of the DNA genomes of three lactic streptococcal bacteriophages. Appl Environ Microbiol. 1986 Mar;51(3):566–571. doi: 10.1128/aem.51.3.566-571.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  24. 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 Nov 5;234(1):124–139. doi: 10.1006/jmbi.1993.1568. [DOI] [PubMed] [Google Scholar]
  25. Ludwig W., Seewaldt E., Kilpper-Bälz R., Schleifer K. H., Magrum L., Woese C. R., Fox G. E., Stackebrandt E. The phylogenetic position of Streptococcus and Enterococcus. J Gen Microbiol. 1985 Mar;131(3):543–551. doi: 10.1099/00221287-131-3-543. [DOI] [PubMed] [Google Scholar]
  26. Moineau S., Bernier D., Jobin M., Hébert J., Klaenhammer T. R., Pandian S. Production of Monoclonal Antibodies against the Major Capsid Protein of the Lactococcus Bacteriophage ul36 and Development of an Enzyme-Linked Immunosorbent Assay for Direct Phage Detection in Whey and Milk. Appl Environ Microbiol. 1993 Jul;59(7):2034–2040. doi: 10.1128/aem.59.7.2034-2040.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Moineau S., Pandian S., Klaenhammer T. R. Evolution of a Lytic Bacteriophage via DNA Acquisition from the Lactococcus lactis Chromosome. Appl Environ Microbiol. 1994 Jun;60(6):1832–1841. doi: 10.1128/aem.60.6.1832-1841.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Normark S., Bergström S., Edlund T., Grundström T., Jaurin B., Lindberg F. P., Olsson O. Overlapping genes. Annu Rev Genet. 1983;17:499–525. doi: 10.1146/annurev.ge.17.120183.002435. [DOI] [PubMed] [Google Scholar]
  29. O'sullivan D. J., Klaenhammer T. R. Rapid Mini-Prep Isolation of High-Quality Plasmid DNA from Lactococcus and Lactobacillus spp. Appl Environ Microbiol. 1993 Aug;59(8):2730–2733. doi: 10.1128/aem.59.8.2730-2733.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Popa M. P., McKelvey T. A., Hempel J., Hendrix R. W. Bacteriophage HK97 structure: wholesale covalent cross-linking between the major head shell subunits. J Virol. 1991 Jun;65(6):3227–3237. doi: 10.1128/jvi.65.6.3227-3237.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Schouler C., Bouet C., Ritzenthaler P., Drouet X., Mata M. Characterization of Lactococcus lactis phage antigens. Appl Environ Microbiol. 1992 Aug;58(8):2479–2484. doi: 10.1128/aem.58.8.2479-2484.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Schouler C., Ehrlich S. D., Chopin M. C. Sequence and organization of the lactococcal prolate-headed bIL67 phage genome. Microbiology. 1994 Nov;140(Pt 11):3061–3069. doi: 10.1099/13500872-140-11-3061. [DOI] [PubMed] [Google Scholar]
  33. Shearman C. A., Jury K. L., Gasson M. J. Controlled expression and structural organization of a Lactococcus lactis bacteriophage lysin encoded by two overlapping genes. Appl Environ Microbiol. 1994 Sep;60(9):3063–3073. doi: 10.1128/aem.60.9.3063-3073.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Tinoco I., Jr, Borer P. N., Dengler B., Levin M. D., Uhlenbeck O. C., Crothers D. M., Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. doi: 10.1038/newbio246040a0. [DOI] [PubMed] [Google Scholar]
  35. Ward L. J., Beresford T. P., Lubbers M. W., Jarvis B. D., Jarvis A. W. Sequence analysis of the lysin gene region of the prolate lactococcal bacteriophage c2. Can J Microbiol. 1993 Aug;39(8):767–774. doi: 10.1139/m93-113. [DOI] [PubMed] [Google Scholar]
  36. Wurtz M. Bacteriophage structure. Electron Microsc Rev. 1992;5(2):283–309. doi: 10.1016/0892-0354(92)90013-g. [DOI] [PubMed] [Google Scholar]
  37. Xu F. F., Pearce L. E., Yu P. L. Construction of a family of lactococcal vectors for gene cloning and translational fusion. FEMS Microbiol Lett. 1991 Jan 1;61(1):55–59. doi: 10.1111/j.1574-6968.1991.tb04321.x. [DOI] [PubMed] [Google Scholar]
  38. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  39. Young R. Bacteriophage lysis: mechanism and regulation. Microbiol Rev. 1992 Sep;56(3):430–481. doi: 10.1128/mr.56.3.430-481.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. van de Guchte M., Kok J., Venema G. Gene expression in Lactococcus lactis. FEMS Microbiol Rev. 1992 Feb;8(2):73–92. doi: 10.1111/j.1574-6968.1992.tb04958.x. [DOI] [PubMed] [Google Scholar]

Articles from Applied and Environmental Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES