Three-dimensional architecture of the bacteriophage φ29 packaged genome and elucidation of its packaging process

Luis R. Comolli; Andrew J. Spakowitz; Cristina E. Siegerist; Paul J. Jardine; Shelley Grimes; Dwight L. Anderson; Carlos Bustamante; Kenneth H. Downing

doi:10.1016/j.virol.2007.07.035

Three-dimensional architecture of the bacteriophage φ29 packaged genome and elucidation of its packaging process

Luis R. Comolli, Andrew J. Spakowitz, Cristina E. Siegerist, Paul J. Jardine, Shelley Grimes, Dwight L. Anderson, Carlos Bustamante, Kenneth H. Downing

Basic Sciences

Research output: Contribution to journal › Article › peer-review

76 Scopus citations

Abstract

The goal of the work reported here is to understand the precise molecular mechanism of the process of DNA packaging in dsDNA bacteriophages. Cryo-EM was used to directly visualize the architecture of the DNA inside the capsid and thus to measure fundamental physical parameters such as inter-strand distances, local curvatures, and the degree of order. We obtained cryo-EM images of bacteriophage that had packaged defined fragments of the genome as well as particles that had partially completed the packaging process. The resulting comparison of structures observed at intermediate and final stages shows that there is no unique, deterministic DNA packaging pathway. Monte Carlo simulations of the packaging process provide insights on the forces involved and the resultant structures.

Original language	English (US)
Pages (from-to)	267-277
Number of pages	11
Journal	Virology
Volume	371
Issue number	2
DOIs	https://doi.org/10.1016/j.virol.2007.07.035
State	Published - Feb 20 2008

Bibliographical note

Funding Information:
This work was supported by the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy, also under Contract No. DE-AC02-05CH11231. Support was also provided via NIH grants # DE03606 (DLA) and GM051487 (CB).

Keywords

Bacteriophage structure
Cryo-electron microscopy
DNA packaging
Monte Carlo
φ29

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title = "Three-dimensional architecture of the bacteriophage φ29 packaged genome and elucidation of its packaging process",

abstract = "The goal of the work reported here is to understand the precise molecular mechanism of the process of DNA packaging in dsDNA bacteriophages. Cryo-EM was used to directly visualize the architecture of the DNA inside the capsid and thus to measure fundamental physical parameters such as inter-strand distances, local curvatures, and the degree of order. We obtained cryo-EM images of bacteriophage that had packaged defined fragments of the genome as well as particles that had partially completed the packaging process. The resulting comparison of structures observed at intermediate and final stages shows that there is no unique, deterministic DNA packaging pathway. Monte Carlo simulations of the packaging process provide insights on the forces involved and the resultant structures.",

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author = "Comolli, {Luis R.} and Spakowitz, {Andrew J.} and Siegerist, {Cristina E.} and Jardine, {Paul J.} and Shelley Grimes and Anderson, {Dwight L.} and Carlos Bustamante and Downing, {Kenneth H.}",

note = "Funding Information: This work was supported by the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy, also under Contract No. DE-AC02-05CH11231. Support was also provided via NIH grants # DE03606 (DLA) and GM051487 (CB). ",

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doi = "10.1016/j.virol.2007.07.035",

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AU - Comolli, Luis R.

AU - Spakowitz, Andrew J.

AU - Siegerist, Cristina E.

AU - Jardine, Paul J.

AU - Grimes, Shelley

AU - Anderson, Dwight L.

AU - Bustamante, Carlos

AU - Downing, Kenneth H.

N1 - Funding Information: This work was supported by the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy, also under Contract No. DE-AC02-05CH11231. Support was also provided via NIH grants # DE03606 (DLA) and GM051487 (CB).

PY - 2008/2/20

Y1 - 2008/2/20

N2 - The goal of the work reported here is to understand the precise molecular mechanism of the process of DNA packaging in dsDNA bacteriophages. Cryo-EM was used to directly visualize the architecture of the DNA inside the capsid and thus to measure fundamental physical parameters such as inter-strand distances, local curvatures, and the degree of order. We obtained cryo-EM images of bacteriophage that had packaged defined fragments of the genome as well as particles that had partially completed the packaging process. The resulting comparison of structures observed at intermediate and final stages shows that there is no unique, deterministic DNA packaging pathway. Monte Carlo simulations of the packaging process provide insights on the forces involved and the resultant structures.

AB - The goal of the work reported here is to understand the precise molecular mechanism of the process of DNA packaging in dsDNA bacteriophages. Cryo-EM was used to directly visualize the architecture of the DNA inside the capsid and thus to measure fundamental physical parameters such as inter-strand distances, local curvatures, and the degree of order. We obtained cryo-EM images of bacteriophage that had packaged defined fragments of the genome as well as particles that had partially completed the packaging process. The resulting comparison of structures observed at intermediate and final stages shows that there is no unique, deterministic DNA packaging pathway. Monte Carlo simulations of the packaging process provide insights on the forces involved and the resultant structures.

KW - Bacteriophage structure

KW - Cryo-electron microscopy

KW - DNA packaging

KW - Monte Carlo

KW - φ29

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Three-dimensional architecture of the bacteriophage φ29 packaged genome and elucidation of its packaging process

Abstract

Bibliographical note

Keywords

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