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. and Mann, Nicholas H.. (2008) A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2. Microbiology, Vol.154 (Part 6). pp. 1775-1782. ISSN 1350-0872Full text not available from this repository.
Official URL: http://dx.doi.org/10.1099/mic.0.2007/016261-0
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 SIDS-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.
|Item Type:||Journal Article|
|Subjects:||Q Science > QP Physiology
Q Science > QR Microbiology
|Divisions:||Faculty of Science > Life Sciences (2010- ) > Biological Sciences ( -2010)|
|Library of Congress Subject Headings (LCSH):||Proteomics, Viral proteins, Bacteriophages, Marine microbiology|
|Journal or Publication Title:||Microbiology|
|Publisher:||Society for General Microbiology|
|Number of Pages:||8|
|Page Range:||pp. 1775-1782|
|Access rights to Published version:||Restricted or Subscription Access|
|References:||Akhter, T., Zhao, L., Kohda, A., Mio, K., Kanamaru, S. & Arisaka, F. (2007). The neck of bacteriophage T4 is a ring-like structure formed by a hetero-oligomer of gp13 and gp14. Biochim Biophys Acta 1774, 1036–1043. Black, L. W., Showe, M. K. & Steven, A. C. (1994). Morphogenesis of the T4 head. In Molecular Biology of Bacteriophage T4, pp. 218–258. Edited by J. D. Karam, J. W. Drake, K. N. Kreuzer and others. Washington, DC: American Society for Microbiology. Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. (1998). Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237–240. Frank, J. (2006). Three Dimensional Electron Microscopy of Macromolecular Assemblies. Oxford: Oxford University Press. Fuhrman, J. A. (1999). Marine viruses and their biogeochemical and ecological effects. Nature 399, 541–548. Hambly, E., Te´ tart, F., Desplats, C., Wilson, W. H., Krisch, H. M. & Mann, N. H. (2001). A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2. Proc Natl Acad Sci U S A 98, 11411–11416. Konopa, G. & Taylor, K. (1979). Coliphage lambda ghosts obtained by osmotic shock or LiCl treatment are devoid of J- and H-gene products. J Gen Virol 43, 729–733. Kostyuchenko, V. A., Leiman, P. G., Chipman, P. R., Kanamaru, S., van Raaij, M. J., Arisaka, F., Mesyanzhinov, V. V. & Rossmann, M. (2003). Three-dimensional structure of bacteriophage T4 baseplate. Nat Struct Biol 10, 688–693. Kostyuchenko, V. A., Chipman, P. R., Leiman, P. G., Arisaka, F., Mesyanzhinov, V. V. & Rossmann, M. G. (2005). The tail structure of bacteriophage T4 and its mechanism of contraction. Nat Struct Mol Biol 12, 810–813. Leiman, P. G., Kanamaru, S., Mesyanzhinov, V. V., Arisaka, F. & Rossmann, M. G. (2003). Structure and morphogenesis of bacteriophage T4. Cell Mol Life Sci 60, 2356–2370. Leiman, P. G., Chipman, P. R., Kostyuchenko, V. A., Mesyanzhinov, V. V. & Rossmann, M. G. (2004). Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host. Cell 118, 419–429. Mann, N. H., Clokie, M. R. J., Millard, A., Cook, A., Wilson, W. H., Wheatley, P. J., Letarov, A. & Krisch, H. M. (2005). The genome of S-PM2, a ‘photosynthetic’ T4-type bacteriophage that infects marine Synechococcus strains. J Bacteriol 187, 3188–3200. Miller, E. S., Kutter, E., Mosig, G., Arisaka, F., Kunisawa, T. & Ru¨ ger,W. (2003a). Bacteriophage T4 genome. Microbiol Mol Biol Rev 67, 86–156. Miller, E. S., Heidelberg, J. F., Eisen, J. A., Nelson, W. C., Durkin, A. S., Ciecko, A., Feldblyum, T. V., White, O., Paulsen, I. T. & other authors (2003b). Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J Bacteriol 185, 5220–5233. Pope, W. H., Weigele, P. R., Chang, J., Pedulla, M. L., Ford, M. E., Houtz, J. M., Jiang, W., Chiu, W., Hatfull, G. F. & other authors (2007). Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a ‘horned’ bacteriophage of marine Synechococcus. J Mol Biol 368, 966–981. Prangishvili, D. & Garrett, R. J. (2004). Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses. Biochem Soc Trans 32, 204–208. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory. Speicher, K. D., Kolbas, O., Harper, S. & Speicher, D. W. (2000). Systematic analysis of peptide recoveries from in-gel digestions for protein identifications in proteome studies. J Biomol Tech 11, 74–86. Suttle, C. A. (2007). Marine viruses – major players in the global ecosystem. Nat Rev Microbiol 5, 801–812. Van Raaij, M. J., Schoehn, G., Burda, M. R. & Miller, S. (2001). Crystal structure of a heat and protease-stable part of the bacteriophage T4 short tail fibre. J Mol Biol 314, 1137–1146. Weigele, P. R., Pope, W. H., Pedulla, M. L., Houtz, J. M., Smith, A. L., Conway, J. F., King, J., Hatfull, G. F., Lawrence, J. G. & Hendrix, R. W. (2007). Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. EnvironMicrobiol 9, 1675–1695. Wilson, W. H., Joint, I. R., Carr, N. G. & Mann, N. H. (1993). Isolation and molecular characterization of 5 marine cyanophages propagated on Synechococcus sp. strainWH7803. Appl EnvironMicrobiol 59, 3736–3743.|
Actions (login required)