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PMID:18524932
| Citation |
Clokie, MR, Thalassinos, K, Boulanger, P, Slade, SE, Stoilova-McPhie, S, Cane, M, Scrivens, JH and Mann, NH (2008) A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2. Microbiology (Reading, Engl.) 154:1775-82 |
|---|---|
| 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 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. |
| Links |
PubMed Online version:10.1099/mic.0.2007/016261-0 |
| Keywords |
Bacteriophage T4/genetics; Bacteriophage T4/metabolism; Bacteriophages/chemistry; Bacteriophages/genetics; Bacteriophages/metabolism; Cryoelectron Microscopy; Databases, Protein; Marine Biology; Proteomics; Synechococcus/virology; Viral Structural Proteins/genetics; Viral Structural Proteins/metabolism |
| edit table |
Significance
Annotations
| Gene product | Qualifier | GO Term | Evidence Code | with/from | Aspect | Extension | Notes | Status |
|---|---|---|---|---|---|---|---|---|
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
| GO:0019012: virion |
ECO:0000314: |
C |
Figure 3. |
complete | ||||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0019012: virion |
ECO:0000314: direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
See also
References
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