A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2.
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.
Department of Infection, Immunity and Inflammation, Maurice Shock Medical Sciences Building, University of Leicester, Leicester LE1 9HN, UK.
Martha R J
MRJ
Clokie
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Konstantinos
K
Thalassinos
U IBBMC-CNRS UMR 8619, Bât. 430 - Université de Paris-Sud, F-91405 Orsay, Paris, France.
Pascale
P
Boulanger
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Susan E
SE
Slade
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Svetla
S
Stoilova-McPhie
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Matt
M
Cane
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
James H
JH
Scrivens
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Nicholas H
NH
Mann
D017122:Bacteriophage T4 / Q000235:genetics / Q000378:metabolism; D001435:Bacteriophages / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020285:Cryoelectron Microscopy; D030562:Databases, Protein; D008386:Marine Biology; D040901:Proteomics; D046940:Synechococcus / Q000821:virology; D015678:Viral Structural Proteins / Q000235:genetics / Q000378:metabolism*
D015678:Viral Structural Proteins