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PreprintCited by 32Bacteriophages and microbial interactionsEnzyme Structure and FunctionAdvanced Electron Microscopy Techniques and Applications

A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability

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Podgorski, Jennifer M., Freeman, Krista, Gosselin, Sophia, Huet, Alexis, Conway, James F., Bird, Mary, Grecco, John, Patel, Shreya, Jacobs-Sera, Deborah, Hatfull, Graham, Gogarten, Johann Peter, Ravantti, Janne, White, Simon·2022·Structure
DOI 10.1101/2022.09.09.507160PMC PMC10071307

Preprint — published as 10.1016/j.str.2022.12.012 · Paper page

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Abstract

Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. Following the genome packaging at near-crystalline densities, the capsid is subjected to a major expansion and stabilization step that allows it to withstand environmental stresses and internal high pressure. Several different mechanisms for stabilizing the capsid have been structurally characterized, but how these mechanisms have evolved is still not understood. Using cryo-EM structure determination, structural comparisons, phylogenetic analyses, and Alphafold predictions, we have constructed a detailed structural dendrogram describing the evolution of capsid structural stability within the actinobacteriophages. The cryo-EM reconstructions of ten capsids solved to resolutions between 2.2 and 4 Ångstroms revealed that eight of them exhibit major capsid proteins that are linked by a covalent cross-linking (isopeptide bond) between subunits that was first described in the HK97 phage. Those covalent interactions ultimately lead to the formation of mutually interlinked capsomers that has been compared to the structure of chain mail. However, three of the closely related phages do not exhibit such an isopeptide bond as demonstrated by both our cryo-EM maps and the lack of the required residue. This work raises questions about the importance of previously described capsid stabilization mechanisms.

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Authors
Podgorski, J. M., Freeman, K., Gosselin, S., Huet, A., Conway, J. F., Bird, M., Grecco, J., Patel, S., Jacobs-Sera, D., Hatfull, G., Gogarten, J. P., Ravantti, J., & White, S.
Affiliations
  • University of Connecticut (US)
  • University of Pittsburgh (US)
  • University of Helsinki (FI)
Corresponding author
White, Simon
ORCID
Venue
Structure
Publisher
openRxiv
Published
2022-09-09
Volume
31
Issue
3
Pages
282-294.e5
ISSN
0969-2126 (ISSN-L)
DOI
10.1101/2022.09.09.507160
PMC
PMC10071307
OpenAlex
W4316495397
Cited by
32
References
1
Citations by year
2026: 9 · 2025: 18 · 2024: 2 · 2023: 3
FWCI
5.17
Type
journal article
Language
en
Open access
Locations
  • Structure (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Työväentutkimus Vuosikirja (submittedVersion)
Funders
  • Howard Hughes Medical Institute (GT12053)
  • U.S. Department of Energy
  • Purdue University
  • Oregon Health and Science University (436923)
  • University of Connecticut
  • University of Pittsburgh
  • University of North Texas
  • Inyuvesi Yakwazulu-Natali
  • National Institutes of Health (1s10od019995-01, 1s10od025009-01, GT12053)
  • Office of Science
  • National Institute of General Medical Sciences (U24GM129547, R35GM131729)
  • Biological and Environmental Research
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
Keywords
capsid stability, icosahedral capsid, tailed bacteriophages, herpesvirus
MeSH terms
Bacteriophages, Capsid, Phylogeny, Virus Assembly, Cryoelectron Microscopy, Capsid Proteins

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