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

Martha R.J. Clokie, Konstantinos Thalassinos, Pascale Boulanger, Susan E. Slade, Svetla Stoilova-McPhie, Matt Cane, James H. Scrivens, Nicholas H. Mann

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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 Synechococcus 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 tails-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.

Original languageEnglish (US)
Pages (from-to)1775-1782
Number of pages8
Issue number6
StatePublished - Sep 11 2008


ASJC Scopus subject areas

  • Microbiology

Cite this

Clokie, M. R. J., Thalassinos, K., Boulanger, P., Slade, S. E., Stoilova-McPhie, S., Cane, M., Scrivens, J. H., & Mann, N. H. (2008). A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2. Microbiology, 154(6), 1775-1782. https://doi.org/10.1099/mic.0.2007/016261-0