The Capsid of the T4 Phage Superfamily: The Evolution, Diversity, and Structure of Some of the Most Prevalent Proteins in the Biosphere
| Autor: | Henry M. Krisch, André M. Comeau |
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| Rok vydání: | 2008 |
| Předmět: |
Models
Molecular Protein Conformation Molecular Sequence Data Population Genomics Sequence alignment Genome Viral Genome Bacteriophage 03 medical and health sciences Capsid Phylogenetics Genetics Animals Bacteriophage T4 Amino Acid Sequence 14. Life underwater education Molecular Biology Phylogeny Ecology Evolution Behavior and Systematics 030304 developmental biology 0303 health sciences education.field_of_study Sequence Homology Amino Acid biology Phylogenetic tree 030306 microbiology Genetic Variation biology.organism_classification Biological Evolution Capsid Proteins Sequence Alignment |
| Zdroj: | Molecular Biology and Evolution. 25:1321-1332 |
| ISSN: | 1537-1719 0737-4038 |
| Popis: | 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 polymerase chain reaction (PCR) of marine environmental samples. This analysis was then expanded to include 1,000 s 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 approximately 1,400 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. |
| Databáze: | OpenAIRE |
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