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MBE Advance Access published online on April 7, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn080
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

The Capsid of the T4 Phage Superfamily: The Evolution, Diversity, and Structure of Some of the Most Prevalent Proteins in the Biosphere

André M. Comeau and Henry M. Krisch*

Laboratoire de Microbiologie et Génétique Moléculaires, CNRS – Université Paul Sabatier-Toulouse III UMR5100, 31062 Toulouse Cedex 9, FRANCE

* Corresponding author: H. M. Krisch, Laboratoire de Microbiologie et Génétique Moléculaires, CNRS – Université Paul Sabatier Toulouse III UMR 5100, 31062 Toulouse Cedex 9, FRANCE, Phone: ++33.5.61.33.58.81, Fax: ++33.5.61.33.58.86, Email: krisch{at}ibcg.biotoul.fr

Received for publication December 9, 2007. Revision received March 6, 2008. Accepted for publication March 21, 2008.

The Escherichia coli bacteriophage T4 has served as a classic system in phage biology for more than 60 years. Only recently have phylogenetic analyses and genomic comparisons demonstrated the existence of a large, diverse and widespread superfamily of T4-like phages in the environment. We report here on the T4-like Major Capsid Protein (MCP) sequences that were obtained by targeted PCR of marine environmental samples. This analysis was then expanded to include 1000s of new sequences of T4-like capsid genes from the metagenomic data obtained during the Sorcerer II Global Ocean Sampling (GOS) expedition. This data compilation reveals that the diversity of the major and minor capsid proteins from the GOS metagenome follows the same general patterns as the sequences from cultured phage genomes. Interestingly, the new MCP sequences obtained by PCR targeted to MCP sequences in environmental samples are more divergent (deeper-branching) than the vast majority of the MCP sequences coming from the other sources. The marine T4-like phage population appears to be largely dominated by the T4-like cyanophages. Using ~1400 T4-like MCP sequences from various sources, we mapped the degree of sequence conservation on a structural model of the T4-like MCP. The results indicate that within the T4 superfamily there are some clear phylogenetic groups with regard to the more conserved and more variable domains of the MCP. Such differences can be correlated with variations in capsid morphology, the arrangement of the MCP lattice and the presence of different capsid accessory proteins between the subgroups of the T4 superfamily.

Key Words: bacteriophage T4 • major capsid protein • evolution • structure • diversity • metagenomics


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