A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2 Free

Abstract

In this study, an MS-based proteomics approach to characterizing the virion structural proteins of the novel marine ‘photosynthetic’ phage S-PM2 is presented. The virus infects ecologically important cyanobacteria of the genus that make a substantial contribution to primary production in the oceans. The S-PM2 genome encodes 236 ORFs, some of which exhibit similarity to known phage virion structural proteins, but the majority (54 %) show no detectable homology to known proteins from other organisms. Using public and in-house bioinformatics tools the proteome of S-PM2 was predicted and a database compatible with MS-based search engines was constructed. S-PM2 virion proteins were resolved by SDS-PAGE, excised, tryptically digested and analysed by LC-ESI-MS/MS. The resulting MS data were searched against the database. A parallel control study was undertaken on the well-characterized coliphage T4 in order to assess the sensitivity and efficiency of this approach. In total, 11 of the 15 S-PM2 proteins, predicted to be virion proteins by bioinformatics approaches, were confirmed as such, together with the identification of a further 12 novel structural proteins. In the case of T4, 24 of the 39 known virion structural proteins were identified, including the major tail-fibre proteins. This approach has wide-ranging applicability and can be applied to any novel organism whose genome encodes ORFs with few detectable homologies in the public databases.

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2008-06-01
2024-03-29
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References

  1. Akhter T., Zhao L., Kohda A., Mio K., Kanamaru S., Arisaka F. 2007 The neck of bacteriophage T4 is a ring-like structure formed by a hetero-oligomer of gp13 and gp14 Biochim Biophys Acta ; 17741036–1043
    [Google Scholar]
  2. Black L. W., Showe M. K., Steven A. C. others 1994; Morphogenesis of the T4 head. In Molecular Biology of Bacteriophage T4 pp 218–258 Edited by Karam J. D., Drake J. W., Kreuzer K. N. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  3. Field C. B., Behrenfeld M. J., Randerson J. T., Falkowski P. 1998; Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281:237–240
    [Google Scholar]
  4. Frank J. 2006 Three Dimensional Electron Microscopy of Macromolecular Assemblies Oxford: Oxford University Press;
    [Google Scholar]
  5. Fuhrman J. A. 1999; Marine viruses and their biogeochemical and ecological effects. Nature 399:541–548
    [Google Scholar]
  6. Hambly E., Tétart F., Desplats C., Wilson W. H., Krisch H. M., Mann N. H. 2001; A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2. Proc Natl Acad Sci U S A 98:11411–11416
    [Google Scholar]
  7. Konopa G., Taylor K. 1979; Coliphage lambda ghosts obtained by osmotic shock or LiCl treatment are devoid of J- and H-gene products. J Gen Virol 43:729–733
    [Google Scholar]
  8. Kostyuchenko V. A., Leiman P. G., Chipman P. R., Kanamaru S., van Raaij M. J., Arisaka F., Mesyanzhinov V. V., Rossmann M. 2003; Three-dimensional structure of bacteriophage T4 baseplate. Nat Struct Biol 10:688–693
    [Google Scholar]
  9. Kostyuchenko V. A., Chipman P. R., Leiman P. G., Arisaka F., Mesyanzhinov V. V., Rossmann M. G. 2005; The tail structure of bacteriophage T4 and its mechanism of contraction. Nat Struct Mol Biol 12:810–813
    [Google Scholar]
  10. Leiman P. G., Kanamaru S., Mesyanzhinov V. V., Arisaka F., Rossmann M. G. 2003; Structure and morphogenesis of bacteriophage T4. Cell Mol Life Sci 60:2356–2370
    [Google Scholar]
  11. Leiman P. G., Chipman P. R., Kostyuchenko V. A., Mesyanzhinov V. V., Rossmann M. G. 2004; Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host. Cell 118:419–429
    [Google Scholar]
  12. Mann N. H., Clokie M. R. J., Millard A., Cook A., Wilson W. H., Wheatley P. J., Letarov A., Krisch H. M. 2005; The genome of S-PM2, a ‘photosynthetic’ T4-type bacteriophage that infects marine Synechococcus strains. J Bacteriol 187:3188–3200
    [Google Scholar]
  13. Miller E. S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Rüger W. 2003a; Bacteriophage T4 genome. Microbiol Mol Biol Rev 67:86–156
    [Google Scholar]
  14. Miller E. S., Heidelberg J. F., Eisen J. A., Nelson W. C., Durkin A. S., Ciecko A., Feldblyum T. V., White O., Paulsen I. T. other authors 2003b; Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J Bacteriol 185:5220–5233
    [Google Scholar]
  15. Pope W. H., Weigele P. R., Chang J., Pedulla M. L., Ford M. E., Houtz J. M., Jiang W., Chiu W., Hatfull G. F. other authors 2007; Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a ‘horned’ bacteriophage of marine Synechococcus . J Mol Biol 368:966–981
    [Google Scholar]
  16. Prangishvili D., Garrett R. J. 2004; Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses. Biochem Soc Trans 32:204–208
    [Google Scholar]
  17. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  18. Speicher K. D., Kolbas O., Harper S., Speicher D. W. 2000; Systematic analysis of peptide recoveries from in-gel digestions for protein identifications in proteome studies. J Biomol Tech 11:74–86
    [Google Scholar]
  19. Suttle C. A. 2007; Marine viruses – major players in the global ecosystem. Nat Rev Microbiol 5:801–812
    [Google Scholar]
  20. Van Raaij M. J., Schoehn G., Burda M. R., Miller S. 2001; Crystal structure of a heat and protease-stable part of the bacteriophage T4 short tail fibre. J Mol Biol 314:1137–1146
    [Google Scholar]
  21. Weigele P. R., Pope W. H., Pedulla M. L., Houtz J. M., Smith A. L., Conway J. F., King J., Hatfull G. F., Lawrence J. G., Hendrix R. W. 2007; Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus . Environ Microbiol 9:1675–1695
    [Google Scholar]
  22. Wilson W. H., Joint I. R., Carr N. G., Mann N. H. 1993; Isolation and molecular characterization of 5 marine cyanophages propagated on Synechococcus sp. strain WH7803. Appl Environ Microbiol 59:3736–3743
    [Google Scholar]
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