1
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Naknaen A, Samernate T, Saeju P, Nonejuie P, Chaikeeratisak V. Nucleus-forming jumbophage PhiKZ therapeutically outcompetes non-nucleus-forming jumbophage Callisto. iScience 2024; 27:109790. [PMID: 38726363 PMCID: PMC11079468 DOI: 10.1016/j.isci.2024.109790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/21/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
With the recent resurgence of phage therapy in modern medicine, jumbophages are currently under the spotlight due to their numerous advantages as anti-infective agents. However, most significant discoveries to date have primarily focused on nucleus-forming jumbophages, not their non-nucleus-forming counterparts. In this study, we compare the biological characteristics exhibited by two genetically diverse jumbophages: 1) the well-studied nucleus-forming jumbophage, PhiKZ; and 2) the newly discovered non-nucleus-forming jumbophage, Callisto. Single-cell infection studies further show that Callisto possesses different replication machinery, resulting in a delay in phage maturation compared to that of PhiKZ. The therapeutic potency of both phages was examined in vitro and in vivo, demonstrating that PhiKZ holds certain superior characteristics over Callisto. This research sheds light on the importance of the subcellular infection machinery and the organized progeny maturation process, which could potentially provide valuable insight in the future development of jumbophage-based therapeutics.
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Affiliation(s)
- Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Panida Saeju
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
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2
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Morgan CJ, Enustun E, Armbruster EG, Birkholz EA, Prichard A, Forman T, Aindow A, Wannasrichan W, Peters S, Inlow K, Shepherd IL, Razavilar A, Chaikeeratisak V, Adler BA, Cress BF, Doudna JA, Pogliano K, Villa E, Corbett KD, Pogliano J. An essential and highly selective protein import pathway encoded by nucleus-forming phage. Proc Natl Acad Sci U S A 2024; 121:e2321190121. [PMID: 38687783 PMCID: PMC11087766 DOI: 10.1073/pnas.2321190121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
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 protein import pathway: a species-specific surface-exposed region of a phage intranuclear protein required for nuclear entry and a conserved protein, PicA (Protein importer of chimalliviruses A), 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 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.
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Affiliation(s)
- Chase J Morgan
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Eray Enustun
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Emily G Armbruster
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Erica A Birkholz
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Amy Prichard
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Taylor Forman
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Ann Aindow
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Wichanan Wannasrichan
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand 10330
| | - Sela Peters
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Koe Inlow
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Isabelle L Shepherd
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Alma Razavilar
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand 10330
| | - Benjamin A Adler
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Jennifer A Doudna
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- HHMI, University of California, Berkeley, CA 94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Kit Pogliano
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth Villa
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Kevin D Corbett
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
| | - Joe Pogliano
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA 92093
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3
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Morgan CJ, Enustun E, Armbruster EG, Birkholz EA, Prichard A, Forman T, Aindow A, Wannasrichan W, Peters S, Inlow K, Shepherd IL, Razavilar A, Chaikeeratisak V, Adler BA, Cress BF, Doudna JA, Pogliano K, Villa E, Corbett KD, Pogliano J. An essential and highly selective protein import pathway encoded by nucleus-forming phage. bioRxiv 2024:2024.03.21.585822. [PMID: 38562762 PMCID: PMC10983916 DOI: 10.1101/2024.03.21.585822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
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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Cobián Güemes AG, Ghatbale P, Blanc AN, Morgan CJ, Garcia A, Leonard J, Huang L, Kovalick G, Proost M, Chiu M, Kuo P, Oh J, Karthikeyan S, Knight R, Pogliano J, Schooley RT, Pride DT. Jumbo phages are active against extensively drug-resistant eyedrop-associated Pseudomonas aeruginosa infections. Antimicrob Agents Chemother 2023; 67:e0065423. [PMID: 37931230 PMCID: PMC10720484 DOI: 10.1128/aac.00654-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/08/2023] [Indexed: 11/08/2023] Open
Abstract
Antibiotic-resistant bacteria present an emerging challenge to human health. Their prevalence has been increasing across the globe due in part to the liberal use of antibiotics that has pressured them to develop resistance. Those bacteria that acquire mobile genetic elements are especially concerning because those plasmids may be shared readily with other microbes that can then also become antibiotic resistant. Serious infections have recently been related to the contamination of preservative-free eyedrops with extensively drug-resistant (XDR) isolates of Pseudomonas aeruginosa, already resulting in three deaths. These drug-resistant isolates cannot be managed with most conventional antibiotics. We sought to identify alternatives to conventional antibiotics for the lysis of these XDR isolates and identified multiple bacteriophages (viruses that attack bacteria) that killed them efficiently. We found both jumbo phages (>200 kb in genome size) and non-jumbo phages that were active against these isolates, the former killing more efficiently. Jumbo phages effectively killed the three separate XDR P. aeruginosa isolates both on solid and liquid medium. Given the ongoing nature of the XDR P. aeruginosa eyedrop outbreak, the identification of phages active against them provides physicians with several novel potential alternatives for treatment.
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Affiliation(s)
| | - Pooja Ghatbale
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Alisha N. Blanc
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Chase J. Morgan
- Department of Biology, University of California San Diego, La Jolla, California, USA
| | - Andrew Garcia
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Jesse Leonard
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Lina Huang
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Grace Kovalick
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Marissa Proost
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Megan Chiu
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Joseph Oh
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Smruthi Karthikeyan
- Department of Environmental Science and Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Sciences & Engineering, University of California San Diego, La Jolla, California, USA
| | - Joe Pogliano
- Department of Biology, University of California San Diego, La Jolla, California, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, USA
| | - Robert T. Schooley
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - David T. Pride
- Department of Pathology, University of California San Diego, La Jolla, California, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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5
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Enustun E, Deep A, Gu Y, Nguyen KT, Chaikeeratisak V, Armbruster E, Ghassemian M, Villa E, Pogliano J, Corbett KD. Identification of the bacteriophage nucleus protein interaction network. Nat Struct Mol Biol 2023; 30:1653-1662. [PMID: 37667030 PMCID: PMC10643120 DOI: 10.1038/s41594-023-01094-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/11/2023] [Indexed: 09/06/2023]
Abstract
In the arms race between bacteria and bacteriophages (phages), some large-genome jumbo phages have evolved a protein shell that encloses their replicating genome to protect it against host immune factors. By segregating the genome from the host cytoplasm, however, the 'phage nucleus' introduces the need to specifically translocate messenger RNA and proteins through the nuclear shell and to dock capsids on the shell for genome packaging. Here, we use proximity labeling and localization mapping to systematically identify proteins associated with the major nuclear shell protein chimallin (ChmA) and other distinctive structures assembled by these phages. We identify six uncharacterized nuclear-shell-associated proteins, one of which directly interacts with self-assembled ChmA. The structure and protein-protein interaction network of this protein, which we term ChmB, suggest that it forms pores in the ChmA lattice that serve as docking sites for capsid genome packaging and may also participate in messenger RNA and/or protein translocation.
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Affiliation(s)
- Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Katrina T Nguyen
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Vorrapon Chaikeeratisak
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Emily Armbruster
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Villa
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
| | - Kevin D Corbett
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
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6
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Birkholz EA, Morgan CJ, Laughlin TG, Lau RK, Prichard A, Rangarajan S, Meza GN, Lee J, Armbruster EG, Suslov S, Pogliano K, Meyer JR, Villa E, Corbett KD, Pogliano J. A mobile intron facilitates interference competition between co-infecting viruses. bioRxiv 2023:2023.09.30.560319. [PMID: 37808663 PMCID: PMC10557746 DOI: 10.1101/2023.09.30.560319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Mobile introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in viruses, but whether they confer a selective advantage is unclear. Here we studied a mobile intron in bacteriophage ΦPA3 and found its homing endonuclease gp210 contributes to viral competition by interfering with the virogenesis of co-infecting phage ΦKZ. We show that gp210 targets a specific sequence in its competitor ΦKZ, preventing the assembly of progeny viruses. This work reports the first demonstration of how a mobile intron can be deployed to engage in interference competition and provide a reproductive advantage. Given the ubiquity of introns, this selective advantage likely has widespread evolutionary implications in nature.
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7
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Armbruster EG, Lee J, Hutchings J, VanderWal AR, Enustun E, Adler BA, Aindow A, Deep A, Rodriguez ZK, Morgan CJ, Ghassemian M, Charles E, Cress BF, Savage DF, Doudna JA, Pogliano K, Corbett KD, Villa E, Pogliano J. Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection. bioRxiv 2023:2023.09.20.558163. [PMID: 37781618 PMCID: PMC10541120 DOI: 10.1101/2023.09.20.558163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Eukaryotic viruses assemble compartments required for genome replication, but no such organelles are known to be essential for prokaryotic viruses. Bacteriophages of the family Chimalliviridae sequester their genomes within a phage-generated organelle, the phage nucleus, which is enclosed by a lattice of viral protein ChmA. Using the dRfxCas13d-based knockdown system CRISPRi-ART, we show that ChmA is essential for the E. coli phage Goslar life cycle. Without ChmA, infections are arrested at an early stage in which the injected phage genome is enclosed in a membrane-bound vesicle capable of gene expression but not DNA replication. Not only do we demonstrate that the phage nucleus is essential for genome replication, but we also show that the Chimalliviridae early phage infection (EPI) vesicle is a transcriptionally active, phage-generated organelle.
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Affiliation(s)
- Emily G. Armbruster
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Arica R. VanderWal
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Eray Enustun
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Benjamin A. Adler
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Ann Aindow
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Zaida K. Rodriguez
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Chase J. Morgan
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA
| | - Emeric Charles
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Brady F. Cress
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - David F. Savage
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Jennifer A. Doudna
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kit Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D. Corbett
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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8
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett KD, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. Cell Rep 2023; 42:112432. [PMID: 37120812 PMCID: PMC10299810 DOI: 10.1016/j.celrep.2023.112432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/28/2023] [Accepted: 04/08/2023] [Indexed: 05/01/2023] Open
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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Affiliation(s)
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas G Laughlin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Amber Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kyle P Thomas
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika E Sy
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tara Spencer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aileen Asavavimol
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Allison Cafferata
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Mia Cameron
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Chiu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Demyan Davydov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Isha Desai
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gabriel Diaz
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Melissa Guereca
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kiley Hearst
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Leyi Huang
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Emily Jacobs
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika Johnson
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Samuel Kahn
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ryan Koch
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adamari Martinez
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Meliné Norquist
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tyler Pau
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gino Prasad
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Katrina Saam
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Milan Sandhu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Angel Jose Sarabia
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Siena Schumaker
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aaron Sonin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ariya Uyeno
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alison Zhao
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin Meyer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel Dutton
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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9
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Enustun E, Deep A, Gu Y, Nguyen KT, Chaikeeratisak V, Armbruster E, Ghassemian M, Villa E, Pogliano J, Corbett KD. Identification of the bacteriophage nucleus protein interaction network. bioRxiv 2023:2023.05.18.541317. [PMID: 37292858 PMCID: PMC10245766 DOI: 10.1101/2023.05.18.541317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the arms race between bacteria and bacteriophages (phages), some large-genome jumbo phages have evolved a protein shell that encloses their replicating genome to protect it against DNA-targeting immune factors. By segregating the genome from the host cytoplasm, however, the "phage nucleus" introduces the need to specifically transport mRNA and proteins through the nuclear shell, and to dock capsids on the shell for genome packaging. Here, we use proximity labeling and localization mapping to systematically identify proteins associated with the major nuclear shell protein chimallin (ChmA) and other distinctive structures assembled by these phages. We identify six uncharacterized nuclear shell-associated proteins, one of which directly interacts with self-assembled ChmA. The structure and protein-protein interaction network of this protein, which we term ChmB, suggests that it forms pores in the ChmA lattice that serve as docking sites for capsid genome packaging, and may also participate in mRNA and/or protein transport.
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Affiliation(s)
- Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Katrina T. Nguyen
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Vorrapon Chaikeeratisak
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Emily Armbruster
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Villa
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, La Jolla, California, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Kevin D. Corbett
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
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10
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy A, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett K, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. bioRxiv 2023:2023.02.24.529968. [PMID: 36865095 PMCID: PMC9980170 DOI: 10.1101/2023.02.24.529968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication encoded in the core genome are conserved among diverse chimalliviruses, and reveal that non-core components can confer intriguing variations on this replication mechanism. For instance, unlike previously studied nucleus-forming phages, RAY doesn't degrade the host genome, and its PhuZ homolog appears to form a five-stranded filament with a lumen. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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11
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Liu Z, Xiang Y. Structural studies of the nucleus-like assembly of jumbo bacteriophage 201φ2-1. Front Microbiol 2023; 14:1170112. [PMID: 37138628 PMCID: PMC10149743 DOI: 10.3389/fmicb.2023.1170112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
The jumbo phages encode proteins that assemble to form a nucleus-like compartment in infected cells. Here we report the cryo-EM structure and biochemistry characterization of gp105, a protein that is encoded by the jumbo phage 201φ2-1 and is involved in the formation of the nucleus-like compartment in phage 201φ2-1 infected Pseudomonas chlororaphis. We found that, although most gp105 molecules are in the monomeric state in solution, a small portion of gp105 assemble to form large sheet-like assemblies and small cube-like particles. Reconstruction of the cube-like particles showed that the particle consists of six flat head-to-tail tetramers arranged into an octahedral cube. The four molecules at the contact interface of two head-to-tail tetramers are 2-fold symmetry-related and constitute a concave tetramer. Further reconstructions without applying symmetry showed that molecules in the particles around the distal ends of a 3-fold axis are highly dynamic and have the tendency to open up the assembly. Local classifications and refinements of the concave tetramers in the cube-like particle resulted in a map of the concave tetramer at a resolution of 4.09 Å. Structural analysis of the concave tetramer indicates that the N and C terminal fragments of gp105 are important for mediating the intermolecular interactions, which was further confirmed by mutagenesis studies. Biochemistry assays showed that, in solution, the cube-like particles of gp105 are liable to either disassemble to form the monomers or recruit more molecules to form the high molecular weight lattice-like assembly. We also found that monomeric gp105s can self-assemble to form large sheet-like assemblies in vitro, and the assembly of gp105 in vitro is a reversible dynamic process and temperature-dependent. Taken together, our results revealed the dynamic assembly of gp105, which helps to understand the development and function of the nucleus-like compartment assembled by phage-encoded proteins.
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12
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Knipe DM, Prichard A, Sharma S, Pogliano J. Replication Compartments of Eukaryotic and Bacterial DNA Viruses: Common Themes Between Different Domains of Host Cells. Annu Rev Virol 2022; 9:307-327. [PMID: 36173697 DOI: 10.1146/annurev-virology-012822-125828] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Subcellular organization is essential for life. Cells organize their functions into organelles to concentrate their machinery and supplies for optimal efficiency. Likewise, viruses organize their replication machinery into compartments or factories within their host cells for optimal replicative efficiency. In this review, we discuss how DNA viruses that infect both eukaryotic cells and bacteria assemble replication compartments for synthesis of progeny viral DNA and transcription of the viral genome. Eukaryotic DNA viruses assemble replication compartments in the nucleus of the host cell while DNA bacteriophages assemble compartments called phage nuclei in the bacterial cytoplasm. Thus, DNA viruses infecting host cells from different domains of life share common replication strategies.
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Affiliation(s)
- David M Knipe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA;
| | - Amy Prichard
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
| | - Surendra Sharma
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA;
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
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13
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Birkholz EA, Laughlin TG, Armbruster E, Suslov S, Lee J, Wittmann J, Corbett KD, Villa E, Pogliano J. A cytoskeletal vortex drives phage nucleus rotation during jumbo phage replication in E. coli. Cell Rep 2022; 40:111179. [PMID: 35977483 DOI: 10.1016/j.celrep.2022.111179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/29/2022] [Accepted: 07/19/2022] [Indexed: 02/03/2023] Open
Abstract
Nucleus-forming jumbo phages establish an intricate subcellular organization, enclosing phage genomes within a proteinaceous shell called the phage nucleus. During infection in Pseudomonas, some jumbo phages assemble a bipolar spindle of tubulin-like PhuZ filaments that positions the phage nucleus at midcell and drives its intracellular rotation. This facilitates the distribution of capsids on its surface for genome packaging. Here we show that the Escherichia coli jumbo phage Goslar assembles a phage nucleus surrounded by an array of PhuZ filaments resembling a vortex instead of a bipolar spindle. Expression of a mutant PhuZ protein strongly reduces Goslar phage nucleus rotation, demonstrating that the PhuZ cytoskeletal vortex is necessary for rotating the phage nucleus. While vortex-like cytoskeletal arrays are important in eukaryotes for cytoplasmic streaming and nucleus alignment, this work identifies a coherent assembly of filaments into a vortex-like structure driving intracellular rotation within the prokaryotic cytoplasm.
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14
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Chaikeeratisak V, Khanna K, Nguyen KT, Egan ME, Enustun E, Armbruster E, Lee J, Pogliano K, Villa E, Pogliano J. Subcellular organization of viral particles during maturation of nucleus-forming jumbo phage. Sci Adv 2022; 8:eabj9670. [PMID: 35507660 PMCID: PMC9067925 DOI: 10.1126/sciadv.abj9670] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 03/16/2022] [Indexed: 06/03/2023]
Abstract
Many eukaryotic viruses assemble mature particles within distinct subcellular compartments, but bacteriophages are generally assumed to assemble randomly throughout the host cell cytoplasm. Here, we show that viral particles of Pseudomonas nucleus-forming jumbo phage PhiPA3 assemble into a unique structure inside cells we term phage bouquets. We show that after capsids complete DNA packaging at the surface of the phage nucleus, tails assemble and attach to capsids, and these particles accumulate over time in a spherical pattern, with tails oriented inward and the heads outward to form bouquets at specific subcellular locations. Bouquets localize at the same fixed distance from the phage nucleus even when it is mispositioned, suggesting an active mechanism for positioning. These results mark the discovery of a pathway for organizing mature viral particles inside bacteria and demonstrate that nucleus-forming jumbo phages, like most eukaryotic viruses, are highly spatially organized during all stages of their lytic cycle.
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Affiliation(s)
- Vorrapon Chaikeeratisak
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katrina T Nguyen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - MacKennon E Egan
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily Armbruster
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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15
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Laughlin TG, Deep A, Prichard AM, Seitz C, Gu Y, Enustun E, Suslov S, Khanna K, Birkholz EA, Armbruster E, McCammon JA, Amaro RE, Pogliano J, Corbett KD, Villa E. Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature 2022; 608:429-435. [PMID: 35922510 PMCID: PMC9365700 DOI: 10.1038/s41586-022-05013-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/22/2022] [Indexed: 12/26/2022]
Abstract
Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems1. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors2-4. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
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Affiliation(s)
- Thomas G. Laughlin
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Amar Deep
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Amy M. Prichard
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Christian Seitz
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Yajie Gu
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Eray Enustun
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Sergey Suslov
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Kanika Khanna
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA ,grid.47840.3f0000 0001 2181 7878Present Address: Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Erica A. Birkholz
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Emily Armbruster
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - J. Andrew McCammon
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pharmacology, University of California San Diego, La Jolla, CA USA
| | - Rommie E. Amaro
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Joe Pogliano
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Kevin D. Corbett
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Elizabeth Villa
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA. .,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA.
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