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Energy landscape for DNA rotation and sliding through a phage portal.

ABSTRACT: Molecular motors involved in the packaging of DNA in tailed viruses are among the strongest known. The mechanism by which the motors operate has long been speculated to involve a coupling between rotation of the portal pore (the gate through which DNA passes upon its packaging or ejection), and translation of DNA. Recent experimental evidence rules out portal rotation with a substantial degree of certainty. We have created an atomistic model for the interaction between DNA and the portal of the bacteriophage SPP1, on the basis of cryo-electron microscopy images and of a recently solved crystal structure. A free energy surface describing the interaction is calculated using molecular dynamics simulations, and found to be inconsistent with a mechanism in which portal rotation drives DNA import. The low-energy pathways on the surface are used to advance a hypothesis on DNA import compatible with all available experiments. Additionally, temperature-dependent kinetic data are used to validate computed barriers to DNA ejection.

SUBMITTER: Nummela J

PROVIDER: S-EPMC2717235 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

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Energy landscape for DNA rotation and sliding through a phage portal.

Nummela Jeremiah J Andricioaei Ioan I

Biophysical journal 20090201 4

Molecular motors involved in the packaging of DNA in tailed viruses are among the strongest known. The mechanism by which the motors operate has long been speculated to involve a coupling between rotation of the portal pore (the gate through which DNA passes upon its packaging or ejection), and translation of DNA. Recent experimental evidence rules out portal rotation with a substantial degree of certainty. We have created an atomistic model for the interaction between DNA and the portal of the ...[more]

PMID: 19217842

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Project description:Oceanic phages are critical components of the global ecosystem, where they play a role in microbial mortality and evolution. Our understanding of phage diversity is greatly limited by the lack of useful genetic diversity measures. Previous studies, focusing on myophages that infect the marine cyanobacterium Synechococcus, have used the coliphage T4 portal-protein-encoding homologue, gene 20 (g20), as a diversity marker. These studies revealed 10 sequence clusters, 9 oceanic and 1 freshwater, where only 3 contained cultured representatives. We sequenced g20 from 38 marine myophages isolated using a diversity of Synechococcus and Prochlorococcus hosts to see if any would fall into the clusters that lacked cultured representatives. On the contrary, all fell into the three clusters that already contained sequences from cultured phages. Further, there was no obvious relationship between host of isolation, or host range, and g20 sequence similarity. We next expanded our analyses to all available g20 sequences (769 sequences), which include PCR amplicons from wild uncultured phages, non-PCR amplified sequences identified in the Global Ocean Survey (GOS) metagenomic database, as well as sequences from cultured phages, to evaluate the relationship between g20 sequence clusters and habitat features from which the phage sequences were isolated. Even in this meta-data set, very few sequences fell into the sequence clusters without cultured representatives, suggesting that the latter are very rare, or sequencing artefacts. In contrast, sequences most similar to the culture-containing clusters, the freshwater cluster and two novel clusters, were more highly represented, with one particular culture-containing cluster representing the dominant g20 genotype in the unamplified GOS sequence data. Finally, while some g20 sequences were non-randomly distributed with respect to habitat, there were always numerous exceptions to general patterns, indicating that phage portal proteins are not good predictors of a phage's host or the habitat in which a particular phage may thrive.

Dataset Information

Energy landscape for DNA rotation and sliding through a phage portal.

Publications

Energy landscape for DNA rotation and sliding through a phage portal.

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