Abstract
Marine phages have an astounding global abundance and ecological impact. However, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. To infer potential functional and ecological relevance of sequenced marine Pseudoalteromonas phage H105/1, two strategies were used. First, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. This approach revealed ‘ecogenomic’ patterns of Pseudoalteromonas phage H105/1, such as its estuarine origin. Second, intrinsic genome signatures (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies) were evaluated on a resolved intra-genomic level to shed light on the evolution of phage functional modules. On the basis of differential codon adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas spp., regions of the phage genome with the most ‘host’-adapted proteins also have the strongest bacterial tetra signature, whereas the least ‘host’-adapted proteins have the strongest phage tetra signature. Such a pattern may reflect the evolutionary history of the respective phage proteins and functional modules. Finally, analysis of the structural proteome identified seven proteins that make up the mature virion, four of which were previously unknown. This integrated approach combines both novel and classical strategies and serves as a model to elucidate ecological inferences and evolutionary relationships from phage genomes that typically abound with unknown gene content.
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Acknowledgements
MBD is grateful to Amelia Rotaru for SDS-PAGE assistance, Marianne Jacob for contributions to tetra analysis, Matthew B Sullivan and Vincent Denef for critically reading the paper, and Matthias Ullrich, Renzo Kottmann and Ivaylo Kostadinov for fruitful discussions and support. A Marie Curie Early Stage Training Fellowship to MBD supports funding for this project (MEST-CT-2004-007776) through the MarMic program of the MPI for Marine Microbiology. Further acknowledgement goes to two anonymous reviewers who offered useful suggestions, strengthening this analysis and paper.
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Duhaime, M., Wichels, A., Waldmann, J. et al. Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1. ISME J 5, 107–121 (2011). https://doi.org/10.1038/ismej.2010.94
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DOI: https://doi.org/10.1038/ismej.2010.94
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