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

Research output: Contribution to journalArticle

12 Citations (Scopus)

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 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
JournalMicrobiology
Volume154
Issue number6
DOIs
StatePublished - 2008
Externally publishedYes

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Virion
Proteomics
Proteins
Databases
Computational Biology
Bacteriophages
Open Reading Frames
Genome
Synechococcus
Search Engine
Bacteriophage T4
Protein S
Cyanobacteria
Proteome
Oceans and Seas
Polyacrylamide Gel Electrophoresis
Viruses

ASJC Scopus subject areas

  • Microbiology

Cite this

Clokie, M. R. J., Thalassinos, K., Boulanger, P., Slade, S. E., Stoilova-McPhie, S., Cane, M., ... 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

A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2. / Clokie, Martha R J; Thalassinos, Konstantinos; Boulanger, Pascale; Slade, Susan E.; Stoilova-McPhie, Svetla; Cane, Matt; Scrivens, James H.; Mann, Nicholas H.

In: Microbiology, Vol. 154, No. 6, 2008, p. 1775-1782.

Research output: Contribution to journalArticle

Clokie, MRJ, Thalassinos, K, Boulanger, P, Slade, SE, Stoilova-McPhie, S, Cane, M, Scrivens, JH & Mann, NH 2008, 'A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2', Microbiology, vol. 154, no. 6, pp. 1775-1782. https://doi.org/10.1099/mic.0.2007/016261-0
Clokie, Martha R J ; Thalassinos, Konstantinos ; Boulanger, Pascale ; Slade, Susan E. ; Stoilova-McPhie, Svetla ; Cane, Matt ; Scrivens, James H. ; Mann, Nicholas H. / A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2. In: Microbiology. 2008 ; Vol. 154, No. 6. pp. 1775-1782.
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