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Cited by 5Bacteriophages and microbial interactionsProtein Structure and DynamicsEnzyme Structure and Function

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Partial Atomic Model of the Tailed Lactococcal Phage TP901-1 as Predicted by AlphaFold2: Revelations and Limitations

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Mahony, Jennifer, Goulet, Adeline, van Sinderen, Douwe, Cambillau, Christian·2023·Viruses
DOI 10.3390/v15122440PMC PMC10747895

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Abstract

Bacteria are engaged in a constant battle against preying viruses, called bacteriophages (or phages). These remarkable nano-machines pack and store their genomes in a capsid and inject it into the cytoplasm of their bacterial prey following specific adhesion to the host cell surface. Tailed phages possessing dsDNA genomes are the most abundant phages in the bacterial virosphere, particularly those with long, non-contractile tails. All tailed phages possess a nano-device at their tail tip that specifically recognizes and adheres to a suitable host cell surface receptor, being proteinaceous and/or saccharidic. Adhesion devices of tailed phages infecting Gram-positive bacteria are highly diverse and, for the majority, remain poorly understood. Their long, flexible, multi-domain-encompassing tail limits experimental approaches to determine their complete structure. We have previously shown that the recently developed protein structure prediction program AlphaFold2 can overcome this limitation by predicting the structures of phage adhesion devices with confidence. Here, we extend this approach and employ AlphaFold2 to determine the structure of a complete phage, the lactococcal P335 phage TP901-1. Herein we report the structures of its capsid and neck, its extended tail, and the complete adhesion device, the baseplate, which was previously partially determined using X-ray crystallography.

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Metadata

Authors
Mahony, J., Goulet, A., van Sinderen, D., & Cambillau, C.
Affiliations
  • University College Cork (IE)
  • Centre National de la Recherche Scientifique (FR)
Corresponding author
Cambillau, Christian
ORCID
Venue
Viruses
Publisher
MDPI AG
Published
2023-12-15
Volume
15
Issue
12
Pages
2440
ISSN
1999-4915 (ISSN-L)
DOI
10.3390/v15122440
PMC
PMC10747895
OpenAlex
W4389781186
Cited by
5
References
1
Citations by year
2025: 3 · 2024: 1 · 2023: 1
FWCI
0.81
Type
journal article
Language
en
Open access
Licence
Locations
  • Viruses (publishedVersion, cc-by)
  • Preprints.org (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
Science Foundation Ireland (SFI/12/RC/2273-P2, SFI/20/FFP-P/8664)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
Lactococcus lactis, base plate, phage tail, capsid, neck, phage structure, AlphaFold2, protein structure prediction, tailed phages
MeSH terms
Bacteriophages, Lactococcus lactis, Siphoviridae, Crystallography, X-Ray, Capsid Proteins

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