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

Martha R. J. Clokie^1,

Konstantinos Thalassinos^2,

¹ Department of Infection, Immunity and Inflammation, Maurice Shock Medical Sciences Building, University of Leicester, Leicester LE1 9HN, UK
² Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
³ U IBBMC-CNRS UMR 8619, Bât. 430 – Université de Paris-Sud, F-91405 Orsay, Paris, France

Correspondence
Martha R. J. Clokie
mrjc1{at}le.ac.uk

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 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.