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An essential and highly selective protein import pathway encoded by nucleus-forming phage
Open accessPreprint — published as 10.1073/pnas.2321190121 · Paper page
Abstract
Targeting proteins to specific subcellular destinations is essential in prokaryotes, eukaryotes, and the viruses that infect them. Chimalliviridae phages encapsulate their genomes in a nucleus-like replication compartment composed of the protein chimallin (ChmA) that excludes ribosomes and decouples transcription from translation. These phages selectively partition proteins between the phage nucleus and the bacterial cytoplasm. Currently, the genes and signals that govern selective protein import into the phage nucleus are unknown. Here we identify two components of this novel protein import pathway: a species-specific surface-exposed region of a phage intranuclear protein required for nuclear entry and a conserved protein, PicA, that facilitates cargo protein trafficking across the phage nuclear shell. We also identify a defective cargo protein that is targeted to PicA on the nuclear periphery but fails to enter the nucleus, providing insight into the mechanism of nuclear protein trafficking. Using CRISPRi-ART protein expression knockdown of PicA, we show that PicA is essential early in the chimallivirus replication cycle. Together our results allow us to propose a multistep model for the Protein Import Chimallivirus (PIC) pathway, where proteins are targeted to PicA by amino acids on their surface, and then licensed by PicA for nuclear entry. The divergence in the selectivity of this pathway between closely-related chimalliviruses implicates its role as a key player in the evolutionary arms race between competing phages and their hosts. Significance Statement: The phage nucleus is an enclosed replication compartment built by Chimalliviridae phages that, similar to the eukaryotic nucleus, separates transcription from translation and selectively imports certain proteins. This allows the phage to concentrate proteins required for DNA replication and transcription while excluding DNA-targeting host defense proteins. However, the mechanism of selective trafficking into the phage nucleus is currently unknown. Here we determine the region of a phage nuclear protein that targets it for nuclear import and identify a conserved, essential nuclear shell-associated protein that plays a key role in this process. This work provides the first mechanistic model of selective import into the phage nucleus.
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Highly accurate protein structure prediction with AlphaFold
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Metadata
- Authors
- Morgan, C. J., Enustun, E., Armbruster, E. G., Birkholz, E. A., Prichard, A., Forman, T., Aindow, A., Wannasrichan, W., Peters, S., Inlow, K., Shepherd, I. L., Razavilar, A., Chaikeeratisak, V., Adler, B. A., Cress, B. F., Doudna, J. A., Pogliano, K., Villa, E., Corbett, K. D., & Pogliano, J.
- Affiliations
- University of California San Diego (US)
- Chulalongkorn University (TH)
- QB3 (US)
- Innovative Genomics Institute (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Pogliano, Joe
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- openRxiv
- Published
- 2024-03-21
- Volume
- 121
- Issue
- 19
- Pages
- e2321190121-e2321190121
- ISSN
- 0027-8424 (ISSN-L)
- PMC
- PMC11087766
- OpenAlex
- W4396508065
- Cited by
- 25
- References
- 1
- Citations by year
- 2026: 10 · 2025: 10 · 2024: 4
- FWCI
- 6.58
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- PubMed Central (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Greater South Information System
- Funders
- Howard Hughes Medical Institute (DE-AC02-05CH11231)
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- California Institute for Quantitative Biosciences
- Innovative Genomics Institute
- Chulalongkorn University (10330)
- National Institutes of Health (GM133351)
- Directorate for Biological Sciences
- Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02)
- University of California, San Diego
- Faculty of Science, Chulalongkorn University
- National Institute of General Medical Sciences (T32GM007198, R35GM144121, T32GM133351, R01GM129245)
- National Institute of Allergy and Infectious Diseases (F30AI176696)
- Biological and Environmental Research (05CH11231, DE-AC02 − 05CH11231, AC02-05CH11231)
- Lawrence Berkeley National Laboratory (AC02‐05CH11231, DE-AC02-05CH11231, 05CH11231)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- protein import, pica, nuclear localization signal, phage evolution
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