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.
Clokie
Martha R J
MRJ
Department of Infection, Immunity and Inflammation, Maurice Shock Medical Sciences Building, University of Leicester, Leicester LE1 9HN, UK.
Thalassinos
Konstantinos
K
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Boulanger
Pascale
P
U IBBMC-CNRS UMR 8619, Bât. 430 - Université de Paris-Sud, F-91405 Orsay, Paris, France.
Slade
Susan E
SE
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Stoilova-McPhie
Svetla
S
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Cane
Matt
M
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Scrivens
James H
JH
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
Mann
Nicholas H
NH
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.
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