Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids

Oliver W. Bayfield, Evgeny Klimuk, Dennis C. Winkler, Emma L. Hesketh, Maria Chechik, Naiqian Cheng, Eric C. Dykeman, Leonid Minakhin, Neil A. Ranson, Konstantin Severinov, Alasdair C. Steven, Alfred A. Antson

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermo-stable bacteriophage, P23-45 of Thermus thermophilus. Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-Å and 4.4-Å resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-Å resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.

Original languageEnglish (US)
Pages (from-to)3556-3561
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume116
Issue number9
DOIs
StatePublished - Feb 26 2019

Fingerprint

DNA Packaging
Capsid
Viruses
DNA
Product Packaging
Bacteriophages
T-Phages
In Vitro Techniques
Genome
Thermus thermophilus
Protein Conformation
Proteins
DNA Viruses
Herpesviridae
Adenosine Triphosphatases
Adenosine Triphosphate

All Science Journal Classification (ASJC) codes

  • General

Keywords

  • Capsid
  • Cryo-EM
  • DNA packaging
  • Portal protein
  • Virus assembly

Cite this

Bayfield, Oliver W. ; Klimuk, Evgeny ; Winkler, Dennis C. ; Hesketh, Emma L. ; Chechik, Maria ; Cheng, Naiqian ; Dykeman, Eric C. ; Minakhin, Leonid ; Ranson, Neil A. ; Severinov, Konstantin ; Steven, Alasdair C. ; Antson, Alfred A. / Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids. In: Proceedings of the National Academy of Sciences of the United States of America. 2019 ; Vol. 116, No. 9. pp. 3556-3561.
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abstract = "Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermo-stable bacteriophage, P23-45 of Thermus thermophilus. Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-{\AA} and 4.4-{\AA} resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-{\AA} resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.",
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author = "Bayfield, {Oliver W.} and Evgeny Klimuk and Winkler, {Dennis C.} and Hesketh, {Emma L.} and Maria Chechik and Naiqian Cheng and Dykeman, {Eric C.} and Leonid Minakhin and Ranson, {Neil A.} and Konstantin Severinov and Steven, {Alasdair C.} and Antson, {Alfred A.}",
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Bayfield, OW, Klimuk, E, Winkler, DC, Hesketh, EL, Chechik, M, Cheng, N, Dykeman, EC, Minakhin, L, Ranson, NA, Severinov, K, Steven, AC & Antson, AA 2019, 'Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 9, pp. 3556-3561. https://doi.org/10.1073/pnas.1813204116

Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids. / Bayfield, Oliver W.; Klimuk, Evgeny; Winkler, Dennis C.; Hesketh, Emma L.; Chechik, Maria; Cheng, Naiqian; Dykeman, Eric C.; Minakhin, Leonid; Ranson, Neil A.; Severinov, Konstantin; Steven, Alasdair C.; Antson, Alfred A.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 116, No. 9, 26.02.2019, p. 3556-3561.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids

AU - Bayfield, Oliver W.

AU - Klimuk, Evgeny

AU - Winkler, Dennis C.

AU - Hesketh, Emma L.

AU - Chechik, Maria

AU - Cheng, Naiqian

AU - Dykeman, Eric C.

AU - Minakhin, Leonid

AU - Ranson, Neil A.

AU - Severinov, Konstantin

AU - Steven, Alasdair C.

AU - Antson, Alfred A.

PY - 2019/2/26

Y1 - 2019/2/26

N2 - Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermo-stable bacteriophage, P23-45 of Thermus thermophilus. Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-Å and 4.4-Å resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-Å resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.

AB - Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermo-stable bacteriophage, P23-45 of Thermus thermophilus. Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 °C to 70 °C temperature range, with optimum activity at 50 °C to 65 °C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-Å and 4.4-Å resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit β-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-Å resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.

KW - Capsid

KW - Cryo-EM

KW - DNA packaging

KW - Portal protein

KW - Virus assembly

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VL - 116

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JO - Proceedings of the National Academy of Sciences of the United States of America

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