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Mozumdar D, Fossati A, Stevenson E, Guan J, Nieweglowska E, Rao S, Agard D, Swaney DL, Bondy-Denomy J. Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection. Cell Host Microbe 2024:S1931-3128(24)00188-4. [PMID: 38870941 DOI: 10.1016/j.chom.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/03/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Viral genomes are most vulnerable to cellular defenses at the start of the infection. A family of jumbo phages related to phage ΦKZ, which infects Pseudomonas aeruginosa, assembles a protein-based phage nucleus to protect replicating phage DNA, but how it is protected prior to phage nucleus assembly is unclear. We find that host proteins related to membrane and lipid biology interact with injected phage protein, clustering in an early phage infection (EPI) vesicle. The injected virion RNA polymerase (vRNAP) executes early gene expression until phage genome separation from the vRNAP and the EPI vesicle, moving into the nascent proteinaceous phage nucleus. Enzymes involved in DNA replication and CRISPR/restriction immune nucleases are excluded by the EPI vesicle. We propose that the EPI vesicle is rapidly constructed with injected phage proteins, phage DNA, host lipids, and host membrane proteins to enable genome protection, early transcription, localized translation, and to ensure faithful genome transfer to the proteinaceous nucleus.
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Affiliation(s)
- Deepto Mozumdar
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrea Fossati
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erica Stevenson
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jingwen Guan
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eliza Nieweglowska
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sanjana Rao
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Imaging Institute, Redwood City, CA 94065, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph Bondy-Denomy
- Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
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2
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Wu Q, An N, Fang Z, Li S, Xiang L, Liu Q, Tan L, Weng Q. Characteristics and whole-genome analysis of a novel Pseudomonas syringae pv. tomato bacteriophage D6 isolated from a karst cave. Virus Genes 2024; 60:295-308. [PMID: 38594490 PMCID: PMC11139720 DOI: 10.1007/s11262-024-02064-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6-10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases.
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Affiliation(s)
- Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Ni An
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Lan Xiang
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China.
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China.
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3
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Prichard A, Pogliano J. The intricate organizational strategy of nucleus-forming phages. Curr Opin Microbiol 2024; 79:102457. [PMID: 38581914 DOI: 10.1016/j.mib.2024.102457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 04/08/2024]
Abstract
Nucleus-forming phages (chimalliviruses) encode numerous genes responsible for creating intricate structures for viral replication. Research on this newly appreciated family of phages has begun to reveal the mechanisms underlying the subcellular organization of the nucleus-based phage replication cycle. These discoveries include the structure of the phage nuclear shell, the identification of a membrane-bound early phage infection intermediate, the dynamic localization of phage RNA polymerases, the phylogeny and core genome of chimalliviruses, and the variation in replication mechanisms across diverse nucleus-forming phages. This research is being propelled forward through the application of fluorescence microscopy and cryo-electron microscopy and the innovative use of new tools such as proximity labeling and RNA-targeting Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems.
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Affiliation(s)
- Amy Prichard
- 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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4
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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] [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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5
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Prichard A, Sy A, Meyer J, Villa E, Pogliano J. Asesino: a nucleus-forming phage that lacks PhuZ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593592. [PMID: 38766163 PMCID: PMC11100802 DOI: 10.1101/2024.05.10.593592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
As nucleus-forming phages become better characterized, understanding their unifying similarities and unique differences will help us understand how they occupy varied niches and infect diverse hosts. All identified nucleus-forming phages fall within the proposed Chimalliviridae family and share a core genome of 68 unique genes including chimallin, the major nuclear shell protein. A well-studied but non-essential protein encoded by many nucleus-forming phages is PhuZ, a tubulin homolog which aids in capsid migration, nucleus rotation, and nucleus positioning. One clade that represents 24% of all currently known chimalliviruses lacks a PhuZ homolog. Here we show that Erwinia phage Asesino, one member of this PhuZ-less clade, shares a common overall replication mechanism with other characterized nucleus-forming phages despite lacking PhuZ. We show that Asesino replicates via a phage nucleus that encloses phage DNA and partitions proteins in the nuclear compartment and cytoplasm in a manner similar to previously characterized nucleus-forming phages. Consistent with a lack of PhuZ, however, we did not observe active positioning or rotation of the phage nucleus within infected cells. These data show that some nucleus-forming phages have evolved to replicate efficiently without PhuZ, providing an example of a unique variation in the nucleus-based replication pathway.
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Affiliation(s)
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika Sy
- 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
| | - 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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6
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Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Malukhina K, Gu Y, Deep A, Naritomi J, Liang Q, Aigner S, Adler B, Cress B, Doudna J, Chaikeeratisak V, Cleveland D, Ghassemian M, Bintu B, Yeo G, Pogliano J, Corbett K. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection. Nucleic Acids Res 2024; 52:4440-4455. [PMID: 38554115 PMCID: PMC11077065 DOI: 10.1093/nar/gkae216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.
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Affiliation(s)
- Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Emily G Armbruster
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Sitao Zhang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kseniya Malukhina
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, 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
| | - Jack T Naritomi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Qishan Liang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, 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
| | - Brady F Cress
- Innovative Genomics 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
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, 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
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA
| | - Bogdan Bintu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Molecular Biology, 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
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
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7
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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] [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, CA92093
| | - Eray Enustun
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Emily G. Armbruster
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Erica A. Birkholz
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Amy Prichard
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Taylor Forman
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Ann Aindow
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Wichanan Wannasrichan
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
- 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, CA92093
| | - Koe Inlow
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Isabelle L. Shepherd
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Alma Razavilar
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - 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, CA94720
- Innovative Genomics Institute, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Brady F. Cress
- Innovative Genomics Institute, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jennifer A. Doudna
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Innovative Genomics Institute, University of California, Berkeley, CA94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Chemistry, University of California, Berkeley, CA94720
- HHMI, University of California, Berkeley, CA94720
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Kit Pogliano
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Elizabeth Villa
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
- HHMI, University of California San Diego, La Jolla, CA92093
| | - Kevin D. Corbett
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Joe Pogliano
- School of Biological Sciences, Division of Molecular Biology, University of California San Diego, La Jolla, CA92093
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8
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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9
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Kuzminov A. Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma. J Bacteriol 2024; 206:e0021123. [PMID: 38358278 PMCID: PMC10994824 DOI: 10.1128/jb.00211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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10
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Gerovac M, Chihara K, Wicke L, Böttcher B, Lavigne R, Vogel J. Phage proteins target and co-opt host ribosomes immediately upon infection. Nat Microbiol 2024; 9:787-800. [PMID: 38443577 PMCID: PMC10914614 DOI: 10.1038/s41564-024-01616-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024]
Abstract
Bacteriophages must seize control of the host gene expression machinery to replicate. To bypass bacterial anti-phage defence systems, this host takeover occurs immediately upon infection. A general understanding of phage mechanisms for immediate targeting of host transcription and translation processes is lacking. Here we introduce an integrative high-throughput approach to uncover phage-encoded proteins that target the gene expression machinery of Pseudomonas aeruginosa immediately upon infection with the jumbo phage ΦKZ. By integrating biochemical, genetic and structural analyses, we identify an abundant and conserved phage factor ΦKZ014 that targets the large ribosomal subunit by binding the 5S ribosomal RNA, and rapidly promotes replication in several clinical isolates. ΦKZ014 is among the earliest ΦKZ proteins expressed after infection and remains bound to ribosomes during the entire translation cycle. Our study provides a strategy to decipher molecular components of phage-mediated host takeover and argues that phage genomes represent an untapped discovery space for proteins that modulate the host gene expression machinery.
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Affiliation(s)
- Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Kotaro Chihara
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Laura Wicke
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Bettina Böttcher
- Biocenter and Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
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11
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Tuck OT, Adler BA, Armbruster EG, Lahiri A, Hu JJ, Zhou J, Pogliano J, Doudna JA. Hachiman is a genome integrity sensor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582594. [PMID: 38464307 PMCID: PMC10925250 DOI: 10.1101/2024.02.29.582594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman comprises a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact dsDNA. When the HamAB complex detects DNA damage, HamB helicase activity liberates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating 'phantom' cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and eukaryotic enzymes suggest this bacterial immune system has been repurposed for diverse functions across all domains of life.
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Affiliation(s)
- Owen T. Tuck
- Department of Chemistry, University of California, Berkeley, Berkeley, CA USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA USA
| | - Benjamin A. Adler
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA USA
| | - Emily G. Armbruster
- School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Arushi Lahiri
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
| | - Jason J. Hu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
| | - Julia Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Jennifer A. Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA USA
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12
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Costa AR, van den Berg DF, Esser JQ, Muralidharan A, van den Bossche H, Bonilla BE, van der Steen BA, Haagsma AC, Fluit AC, Nobrega FL, Haas PJ, Brouns SJJ. Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa. SCIENCE ADVANCES 2024; 10:eadj0341. [PMID: 38394193 PMCID: PMC10889362 DOI: 10.1126/sciadv.adj0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Prokaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains of Pseudomonas aeruginosa and a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems target specific phage genera and that defense systems with complementary phage specificities co-occur in P. aeruginosa genomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes of P. aeruginosa with at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistant P. aeruginosa strains.
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Affiliation(s)
- Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Daan F. van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Jelger Q. Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Aswin Muralidharan
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Halewijn van den Bossche
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Boris Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Baltus A. van der Steen
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Anna C. Haagsma
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Ad C. Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Stan J. J. Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
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13
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Putzeys L, Wicke L, Brandão A, Boon M, Pires DP, Azeredo J, Vogel J, Lavigne R, Gerovac M. Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches. Curr Opin Microbiol 2024; 77:102419. [PMID: 38271748 PMCID: PMC10884466 DOI: 10.1016/j.mib.2023.102419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
In the last decade, powerful high-throughput sequencing approaches have emerged to analyse microbial transcriptomes at a global scale. However, to date, applications of these approaches to microbial viruses such as phages remain scarce. Tailoring these techniques to virus-infected bacteria promises to obtain a detailed picture of the underexplored RNA biology and molecular processes during infection. In addition, transcriptome study of stress and perturbations induced by phages in their infected bacterial hosts is likely to reveal new fundamental mechanisms of bacterial metabolism and gene regulation. Here, we provide references and blueprints to implement emerging transcriptomic approaches towards addressing transcriptome architecture, RNA-RNA and RNA-protein interactions, RNA modifications, structures and heterogeneity of transcription profiles in infected cells that will provide guides for future directions in phage-centric therapeutic applications and microbial synthetic biology.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium; Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Ana Brandão
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Diana P Pires
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
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14
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Pozhydaieva N, Wolfram-Schauerte M, Keuthen H, Höfer K. The enigmatic epitranscriptome of bacteriophages: putative RNA modifications in viral infections. Curr Opin Microbiol 2024; 77:102417. [PMID: 38217927 DOI: 10.1016/j.mib.2023.102417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/15/2024]
Abstract
RNA modifications play essential roles in modulating RNA function, stability, and fate across all kingdoms of life. The entirety of the RNA modifications within a cell is defined as the epitranscriptome. While eukaryotic RNA modifications are intensively studied, understanding bacterial RNA modifications remains limited, and knowledge about bacteriophage RNA modifications is almost nonexistent. In this review, we shed light on known mechanisms of bacterial RNA modifications and propose how this knowledge might be extended to bacteriophages. We build hypotheses on enzymes potentially responsible for regulating the epitranscriptome of bacteriophages and their host. This review highlights the exciting prospects of uncovering the unexplored field of bacteriophage epitranscriptomics and its potential role to shape bacteriophage-host interactions.
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Affiliation(s)
| | | | - Helene Keuthen
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
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15
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Nichiporenko A, Antonova D, Kurdyumova I, Khodorkovskii M, Yakunina MV. Assembly of phiKZ bacteriophage Inner Body during infection. Biochem Biophys Res Commun 2024; 693:149372. [PMID: 38128246 DOI: 10.1016/j.bbrc.2023.149372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
The giant myovirus phiKZ is characterised by an Inner Body (IB) structure within its capsid, crucial for orderly DNA packaging. The IB is composed of six phiKZ-specific proteins. Notably, four of these IB proteins are co-injected with DNA into the host cell, where they potentially play a role in attacking the bacterial cell. The dynamics of IB assembling within the phiKZ capsid during infection remain poorly understood. In this study, we used fluorescent microscopy to track the localisation of IB proteins fused to fluorescent proteins within the cell throughout the infection process. Our findings reveal that the proteins Gp97 and Gp162 are incorporated into new virion heads during phage head maturation. In contrast, proteins Gp90, Gp93, and Gp95 are likely integrated into the virion shortly before the DNA packaging.
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Affiliation(s)
- Anna Nichiporenko
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Daria Antonova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Inna Kurdyumova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Maria V Yakunina
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia.
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16
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Sharma P, Maklashina E, Voehler M, Balintova S, Dvorakova S, Kraus M, Hadrava Vanova K, Nahacka Z, Zobalova R, Boukalova S, Cunatova K, Mracek T, Ghayee HK, Pacak K, Rohlena J, Neuzil J, Cecchini G, Iverson TM. Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners. Nat Commun 2024; 15:473. [PMID: 38212624 PMCID: PMC10784507 DOI: 10.1038/s41467-023-44563-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/19/2023] [Indexed: 01/13/2024] Open
Abstract
Complex II (CII) activity controls phenomena that require crosstalk between metabolism and signaling, including neurodegeneration, cancer metabolism, immune activation, and ischemia-reperfusion injury. CII activity can be regulated at the level of assembly, a process that leverages metastable assembly intermediates. The nature of these intermediates and how CII subunits transfer between metastable complexes remains unclear. In this work, we identify metastable species containing the SDHA subunit and its assembly factors, and we assign a preferred temporal sequence of appearance of these species during CII assembly. Structures of two species show that the assembly factors undergo disordered-to-ordered transitions without the appearance of significant secondary structure. The findings identify that intrinsically disordered regions are critical in regulating CII assembly, an observation that has implications for the control of assembly in other biomolecular complexes.
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Affiliation(s)
- Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Markus Voehler
- Department of Chemistry Vanderbilt University, Nashville, TN, 37232, USA
- Center for Structural Biology Vanderbilt University, Nashville, TN, 37232, USA
| | - Sona Balintova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
- Faculty of Science, Charles University, 128 00, Prague 2, Czech Republic
| | - Sarka Dvorakova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Michal Kraus
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Katerina Hadrava Vanova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Zuzana Nahacka
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Renata Zobalova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Stepana Boukalova
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Kristyna Cunatova
- Institute of Physiology, Czech Academy of Sciences, Prague 4, 142 20, Prague, Czech Republic
| | - Tomas Mracek
- Institute of Physiology, Czech Academy of Sciences, Prague 4, 142 20, Prague, Czech Republic
| | - Hans K Ghayee
- Department of Medicine, Division of Endocrinology & Metabolism, University of Florida College of Medicine and Malcom Randall, VA Medical Center, Gainesville, FL, 32608, USA
| | - Karel Pacak
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Jakub Rohlena
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic
| | - Jiri Neuzil
- Institute of Biotechnology, Czech Academy of Sciences, 252 50, Prague-West, Czech Republic.
- Faculty of Science, Charles University, 128 00, Prague 2, Czech Republic.
- School of Pharmacy and Medical Science, Griffith University, Southport, QLD, 4222, Australia.
- 1st Faculty of Medicine, Charles University, 128 00, Prague 2, Czech Republic.
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA.
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.
- Center for Structural Biology Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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17
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Gios E, Mosley OE, Hoggard M, Handley KM. High niche specificity and host genetic diversity of groundwater viruses. THE ISME JOURNAL 2024; 18:wrae035. [PMID: 38452204 PMCID: PMC10980836 DOI: 10.1093/ismejo/wrae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.
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Affiliation(s)
- Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- NINA, Norwegian Institute for Nature Research, Trondheim 7034, Norway
| | - Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- NatureMetrics Ltd, Surrey Research Park, Guildford GU2 7HJ, United Kingdom
| | - Michael Hoggard
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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18
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Muzyukina P, Shkaruta A, Guzman NM, Andreani J, Borges AL, Bondy-Denomy J, Maikova A, Semenova E, Severinov K, Soutourina O. Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile. mSphere 2023; 8:e0040123. [PMID: 38009936 PMCID: PMC10732046 DOI: 10.1128/msphere.00401-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/10/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Clostridioides difficile is the widespread anaerobic spore-forming bacterium that is a major cause of potentially lethal nosocomial infections associated with antibiotic therapy worldwide. Due to the increase in severe forms associated with a strong inflammatory response and higher recurrence rates, a current imperative is to develop synergistic and alternative treatments for C. difficile infections. In particular, phage therapy is regarded as a potential substitute for existing antimicrobial treatments. However, it faces challenges because C. difficile has highly active CRISPR-Cas immunity, which may be a specific adaptation to phage-rich and highly crowded gut environment. To overcome this defense, C. difficile phages must employ anti-CRISPR mechanisms. Here, we present the first anti-CRISPR protein that inhibits the CRISPR-Cas defense system in this pathogen. Our work offers insights into the interactions between C. difficile and its phages, paving the way for future CRISPR-based applications and development of effective phage therapy strategies combined with the engineering of virulent C. difficile infecting phages.
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Affiliation(s)
- Polina Muzyukina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anton Shkaruta
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Noemi M. Guzman
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Adair L. Borges
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Anna Maikova
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ekaterina Semenova
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Konstantin Severinov
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
- Institute of Molecular Genetics, Kurchatov National Research Center, Moscow, Russia
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Institut Universitaire de France (IUF), Paris, France
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19
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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] [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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20
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Soonthonsrima T, Htoo HH, Thiennimitr P, Srisuknimit V, Nonejuie P, Chaikeeratisak V. Phage-induced bacterial morphological changes reveal a phage-derived antimicrobial affecting cell wall integrity. Antimicrob Agents Chemother 2023; 67:e0076423. [PMID: 37843261 PMCID: PMC10648931 DOI: 10.1128/aac.00764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/24/2023] [Indexed: 10/17/2023] Open
Abstract
In a looming post-antibiotic era, antibiotic alternatives have become key players in the combat against pathogens. Although recent advances in genomic research allow scientists to fully explore an organism's genome in the search for novel antibacterial molecules, laborious work is still needed in order to dissect each individual gene product for its antibacterial activity. Here, we exploited phage-induced bacterial morphological changes as anchors to explore and discover a potential phage-derived antimicrobial embedded in the phage genome. We found that, upon vibriophage KVP40 infection, Vibrio parahaemolyticus exhibited morphological changes similar to those observed when treated with mecillinam, a cell wall synthesis inhibitor, suggesting the mechanism of pre-killing that KVP40 exerts inside the bacterial cell upon sieging the host. Genome analysis revealed that, of all the annotated gene products in the KVP40 genome that are involved in cell wall degradation, lytic transglycosylase (LT) is of particular interest for subsequent functional studies. A single-cell morphological analysis revealed that heterologous expression of wild-type KVP40-LT induced similar bacterial morphological changes to those treated with the whole phage or mecillinam, prior to cell burst. On the contrary, neither the morphology nor the viability of the bacteria expressing signal-peptide truncated- or catalytic mutant E80A- KVP40-LT was affected, suggesting the necessity of these domains for the antibacterial activities. Altogether, this research paves the way for the future development of the discovery of phage-derived antimicrobials that is guided through phage-induced morphological changes.
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Affiliation(s)
- Tanapon Soonthonsrima
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Veerasak Srisuknimit
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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21
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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] [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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22
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Thammatinna K, Sinprasertporn A, Naknaen A, Samernate T, Nuanpirom J, Chanwong P, Somboonwiwat K, Pogliano J, Sathapondecha P, Thawonsuwan J, Nonejuie P, Chaikeeratisak V. Nucleus-forming vibriophage cocktail reduces shrimp mortality in the presence of pathogenic bacteria. Sci Rep 2023; 13:17844. [PMID: 37857653 PMCID: PMC10587174 DOI: 10.1038/s41598-023-44840-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023] Open
Abstract
The global aquaculture industry has suffered significant losses due to the outbreak of Acute Hepatopancreatic Necrosis Disease (AHPND) caused by Vibrio parahaemolyticus. Since the use of antibiotics as control agents has not been shown to be effective, an alternative anti-infective regimen, such as phage therapy, has been proposed. Here, we employed high-throughput screening for potential phages from 98 seawater samples and obtained 14 phages exhibiting diverse host specificity patterns against pathogenic VPAHPND strains. Among others, two Chimallinviridae phages, designated Eric and Ariel, exhibited the widest host spectrum against vibrios. In vitro and in vivo studies revealed that a cocktail derived from these two nucleus-forming vibriophages prolonged the bacterial regrowth of various pathogenic VPAHPND strains and reduced shrimp mortality from VPAHPND infection. This research highlights the use of high-throughput phage screening that leads to the formulation of a nucleus-forming phage cocktail applicable for bacterial infection treatment in aquaculture.
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Affiliation(s)
- Khrongkhwan Thammatinna
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ammara Sinprasertporn
- Songkhla Aquatic Animal Health Research and Development Center (SAAHRDC), Department of Fisheries, Songkhla, Thailand
| | - Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Jiratchaya Nuanpirom
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Parinda Chanwong
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ponsit Sathapondecha
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Jumroensri Thawonsuwan
- Songkhla Aquatic Animal Health Research and Development Center (SAAHRDC), Department of Fisheries, Songkhla, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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23
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Antonova D, Belousova VV, Zhivkoplias E, Sobinina M, Artamonova T, Vishnyakov IE, Kurdyumova I, Arseniev A, Morozova N, Severinov K, Khodorkovskii M, Yakunina MV. The Dynamics of Synthesis and Localization of Jumbo Phage RNA Polymerases inside Infected Cells. Viruses 2023; 15:2096. [PMID: 37896872 PMCID: PMC10612078 DOI: 10.3390/v15102096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
A nucleus-like structure composed of phage-encoded proteins and containing replicating viral DNA is formed in Pseudomonas aeruginosa cells infected by jumbo bacteriophage phiKZ. The PhiKZ genes are transcribed independently from host RNA polymerase (RNAP) by two RNAPs encoded by the phage. The virion RNAP (vRNAP) transcribes early viral genes and must be injected into the cell with phage DNA. The non-virion RNAP (nvRNAP) is composed of early gene products and transcribes late viral genes. In this work, the dynamics of phage RNAPs localization during phage phiKZ infection were studied. We provide direct evidence of PhiKZ vRNAP injection in infected cells and show that it is excluded from the phage nucleus. The nvRNAP is synthesized shortly after the onset of infection and localizes in the nucleus. We propose that spatial separation of two phage RNAPs allows coordinated expression of phage genes belonging to different temporal classes.
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Affiliation(s)
- Daria Antonova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Viktoriia V. Belousova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Erik Zhivkoplias
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Mariia Sobinina
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Tatyana Artamonova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Innokentii E. Vishnyakov
- Group of Molecular Cytology of Prokaryotes and Bacterial Invasion, Institute of Cytology of the Russian Academy of Science, St. Petersburg 194064, Russia;
| | - Inna Kurdyumova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Anatoly Arseniev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia Morozova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Konstantin Severinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow 119334, Russia
- Institute of Molecular Genetics National Kurchatov Center, Moscow 123182, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Mikhail Khodorkovskii
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Maria V. Yakunina
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
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24
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Seoane LF, Solé R. How Turing parasites expand the computational landscape of digital life. Phys Rev E 2023; 108:044407. [PMID: 37978635 DOI: 10.1103/physreve.108.044407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 09/19/2023] [Indexed: 11/19/2023]
Abstract
Why are living systems complex? Why does the biosphere contain living beings with complexity features beyond those of the simplest replicators? What kind of evolutionary pressures result in more complex life forms? These are key questions that pervade the problem of how complexity arises in evolution. One particular way of tackling this is grounded in an algorithmic description of life: living organisms can be seen as systems that extract and process information from their surroundings to reduce uncertainty. Here we take this computational approach using a simple bit string model of coevolving agents and their parasites. While agents try to predict their worlds, parasites do the same with their hosts. The result of this process is that, to escape their parasites, the host agents expand their computational complexity despite the cost of maintaining it. This, in turn, is followed by increasingly complex parasitic counterparts. Such arms races display several qualitative phases, from monotonous to punctuated evolution or even ecological collapse. Our minimal model illustrates the relevance of parasites in providing an active mechanism for expanding living complexity beyond simple replicators, suggesting that parasitic agents are likely to be a major evolutionary driver for biological complexity.
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Affiliation(s)
- Luís F Seoane
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología (CSIC), C/Darwin 3, 28049 Madrid, Spain
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra (GRIB), Dr Aiguader 80, 08003 Barcelona, Spain
- Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA
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25
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Banas I, Esser SP, Turzynski V, Soares A, Novikova P, May P, Moraru C, Hasenberg M, Rahlff J, Wilmes P, Klingl A, Probst AJ. Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere. THE ISME JOURNAL 2023; 17:1789-1792. [PMID: 37468677 PMCID: PMC10504349 DOI: 10.1038/s41396-023-01474-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023]
Abstract
Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.
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Affiliation(s)
- Indra Banas
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Sarah P Esser
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Victoria Turzynski
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - André Soares
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Polina Novikova
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Cristina Moraru
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Oldenburg, Germany
| | | | - Janina Rahlff
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Andreas Klingl
- Plant Development & Electron Microscopy, Biocenter LMU Munich, Planegg-Martinsried, Planegg, Germany.
| | - Alexander J Probst
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
- Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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26
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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27
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Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Gu Y, Deep A, Naritomi JT, Liang Q, Aigner S, Adler BA, Cress BF, Doudna JA, Chaikeeratisak V, Cleveland DW, Ghassemian M, Yeo GW, Pogliano J, Corbett KD. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559000. [PMID: 37790334 PMCID: PMC10542519 DOI: 10.1101/2023.09.22.559000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Large-genome bacteriophages (jumbo phages) of the Chimalliviridae family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d halts infections at an early stage. Taken together, our data suggest that the conserved ChmC protein acts as a chaperone for phage mRNAs, potentially stabilizing these mRNAs and driving their translocation through the nuclear shell to promote translation and infection progression.
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Affiliation(s)
- Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Emily G. Armbruster
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Jina Lee
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Sitao Zhang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian A. Yee
- 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
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jack T. Naritomi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qishan Liang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Benjamin A. Adler
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Brady F. Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A. Doudna
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Don W. Cleveland
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, 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
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
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28
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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Graham M, Zhang P. Cryo-electron tomography to study viral infection. Biochem Soc Trans 2023; 51:1701-1711. [PMID: 37560901 PMCID: PMC10578967 DOI: 10.1042/bst20230103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023]
Abstract
Developments in cryo-electron microscopy (cryo-EM) have been interwoven with the study of viruses ever since its first applications to biological systems. Following the success of single particle cryo-EM in the last decade, cryo-electron tomography (cryo-ET) is now rapidly maturing as a technology and catalysing great advancement in structural virology as its application broadens. In this review, we provide an overview of the use of cryo-ET to study viral infection biology, discussing the key workflows and strategies used in the field. We highlight the vast body of studies performed on purified viruses and virus-like particles (VLPs), as well as discussing how cryo-ET can characterise host-virus interactions and membrane fusion events. We further discuss the importance of in situ cellular imaging in revealing previously unattainable details of infection and highlight the need for validation of high-resolution findings from purified ex situ systems. We give perspectives for future developments to achieve the full potential of cryo-ET to characterise the molecular processes of viral infection.
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Affiliation(s)
- Miles Graham
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, U.K
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30
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Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping. Nat Commun 2023; 14:5156. [PMID: 37620325 PMCID: PMC10449902 DOI: 10.1038/s41467-023-40724-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Host-pathogen interactions are pivotal in regulating establishment, progression, and outcome of an infection. While affinity-purification mass spectrometry has become instrumental in characterizing such interactions, it suffers from limitations in scalability and biological authenticity. Here we present the use of co-fractionation mass spectrometry for high throughput analysis of host-pathogen interactions from native viral infections of two jumbophages (ϕKZ and ϕPA3) in Pseudomonas aeruginosa. This approach enabled the detection of > 6000 unique host-pathogen interactions for each phage, encompassing > 50% of their respective proteomes. This deep coverage provided evidence for interactions between KZ-like phage proteins and the host ribosome, and revealed protein complexes for previously undescribed phage ORFs, including a ϕPA3 complex showing strong structural and sequence similarity to ϕKZ non-virion RNA polymerase. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction ( https://phagemap.ucsf.edu/ ). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of host-pathogen interactomes and protein complex dynamics upon infection.
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Affiliation(s)
- Andrea Fossati
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Deepto Mozumdar
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Claire Kokontis
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Melissa Mèndez-Moran
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Eliza Nieweglowska
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Adrian Pelin
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Yuping Li
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Baron Guo
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - David A Agard
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Joseph Bondy-Denomy
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA.
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA.
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31
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Gaïa M, Forterre P. From Mimivirus to Mirusvirus: The Quest for Hidden Giants. Viruses 2023; 15:1758. [PMID: 37632100 PMCID: PMC10458455 DOI: 10.3390/v15081758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Our perception of viruses has been drastically evolving since the inception of the field of virology over a century ago. In particular, the discovery of giant viruses from the Nucleocytoviricota phylum marked a pivotal moment. Their previously concealed diversity and abundance unearthed an unprecedented complexity in the virus world, a complexity that called for new definitions and concepts. These giant viruses underscore the intricate interactions that unfold over time between viruses and their hosts, and are themselves suspected to have played a significant role as a driving force in the evolution of eukaryotes since the dawn of this cellular domain. Whether they possess exceptional relationships with their hosts or whether they unveil the actual depths of evolutionary connections between viruses and cells otherwise hidden in smaller viruses, the attraction giant viruses exert on the scientific community and beyond continues to grow. Yet, they still hold surprises. Indeed, the recent identification of mirusviruses connects giant viruses to herpesviruses, each belonging to distinct viral realms. This discovery substantially broadens the evolutionary landscape of Nucleocytoviricota. Undoubtedly, the years to come will reveal their share of surprises.
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Affiliation(s)
- Morgan Gaïa
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75012 Paris, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- Département de Microbiologie, Institut Pasteur, 75015 Paris, France
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32
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Caetano-Anollés G, Claverie JM, Nasir A. A critical analysis of the current state of virus taxonomy. Front Microbiol 2023; 14:1240993. [PMID: 37601376 PMCID: PMC10435761 DOI: 10.3389/fmicb.2023.1240993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and C.R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), IM2B, IOM, Aix Marseille University, CNRS, Marseille, France
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33
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Harding KR, Kyte N, Fineran PC. Jumbo phages. Curr Biol 2023; 33:R750-R751. [PMID: 37490856 DOI: 10.1016/j.cub.2023.05.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
In this Quick guide, Harding et al. introduce jumbo phages - the overlooked giants of the phage universe.
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Affiliation(s)
- Kate R Harding
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin 9054, New Zealand
| | - Natalie Kyte
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin 9054, New Zealand.
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34
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Tsunemoto H, Sugie J, Enustun E, Pogliano K, Pogliano J. Bacterial cytological profiling reveals interactions between jumbo phage φKZ infection and cell wall active antibiotics in Pseudomonas aeruginosa. PLoS One 2023; 18:e0280070. [PMID: 37418366 PMCID: PMC10328376 DOI: 10.1371/journal.pone.0280070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/20/2022] [Indexed: 07/09/2023] Open
Abstract
The emergence of antibiotic resistance in bacteria has led to the investigation of alternative treatments, such as phage therapy. In this study, we examined the interactions between the nucleus-forming jumbo phage ФKZ and antibiotic treatment against Pseudomonas aeruginosa. Using the fluorescence microscopy technique of bacterial cytological profiling, we identified mechanism-of-action-specific interactions between antibiotics that target different biosynthetic pathways and ФKZ infection. We found that certain classes of antibiotics strongly inhibited phage replication, while others had no effect or only mildly affected progression through the lytic cycle. Antibiotics that caused an increase in host cell length, such as the cell wall active antibiotic ceftazidime, prevented proper centering of the ФKZ nucleus via the PhuZ spindle at midcell, leading us to hypothesize that the kinetic parameters of the PhuZ spindle evolved to match the average length of the host cell. To test this, we developed a computational model explaining how the dynamic properties of the PhuZ spindle contribute to phage nucleus centering and why some antibiotics affect nucleus positioning while others do not. These findings provide an understanding of the molecular mechanisms underlying the interactions between antibiotics and jumbo phage replication.
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Affiliation(s)
- Hannah Tsunemoto
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
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35
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Naknaen A, Samernate T, Wannasrichan W, Surachat K, Nonejuie P, Chaikeeratisak V. Combination of genetically diverse Pseudomonas phages enhances the cocktail efficiency against bacteria. Sci Rep 2023; 13:8921. [PMID: 37264114 DOI: 10.1038/s41598-023-36034-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023] Open
Abstract
Phage treatment has been used as an alternative to antibiotics since the early 1900s. However, bacteria may acquire phage resistance quickly, limiting the use of phage treatment. The combination of genetically diverse phages displaying distinct replication machinery in phage cocktails has therefore become a novel strategy to improve therapeutic outcomes. Here, we isolated and studied lytic phages (SPA01 and SPA05) that infect a wide range of clinical Pseudomonas aeruginosa isolates. These relatively small myophages have around 93 kbp genomes with no undesirable genes, have a 30-min latent period, and reproduce a relatively high number of progenies, ranging from 218 to 240 PFU per infected cell. Even though both phages lyse their hosts within 4 h, phage-resistant bacteria emerge during the treatment. Considering SPA01-resistant bacteria cross-resist phage SPA05 and vice versa, combining SPA01 and SPA05 for a cocktail would be ineffective. According to the decreased adsorption rate of the phages in the resistant isolates, one of the anti-phage mechanisms may occur through modification of phage receptors on the target cells. All resistant isolates, however, are susceptible to nucleus-forming jumbophages (PhiKZ and PhiPA3), which are genetically distinct from phages SPA01 and SPA05, suggesting that the jumbophages recognize a different receptor during phage entry. The combination of these phages with the jumbophage PhiKZ outperforms other tested combinations in terms of bactericidal activity and effectively suppresses the emergence of phage resistance. This finding reveals the effectiveness of the diverse phage-composed cocktail for reducing bacterial growth and prolonging the evolution of phage resistance.
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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
| | - Wichanan Wannasrichan
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
- Cell and Biomolecular Imaging Research Unit (CBIRU), Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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36
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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] [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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37
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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38
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Abstract
Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.
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Affiliation(s)
- Lindsey N Young
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth Villa
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA
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39
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Berger C, Premaraj N, Ravelli RBG, Knoops K, López-Iglesias C, Peters PJ. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat Methods 2023; 20:499-511. [PMID: 36914814 DOI: 10.1038/s41592-023-01783-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.
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Affiliation(s)
- Casper Berger
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Navya Premaraj
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Kèvin Knoops
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Carmen López-Iglesias
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
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40
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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41
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Dulberger CL, Guerrero-Bustamante CA, Owen SV, Wilson S, Wuo MG, Garlena RA, Serpa LA, Russell DA, Zhu J, Braunecker BJ, Squyres GR, Baym M, Kiessling LL, Garner EC, Rubin EJ, Hatfull GF. Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection. Nat Microbiol 2023; 8:695-710. [PMID: 36823286 PMCID: PMC10066036 DOI: 10.1038/s41564-023-01333-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/23/2023] [Indexed: 02/25/2023]
Abstract
Mycobacteriophages are a diverse group of viruses infecting Mycobacterium with substantial therapeutic potential. However, as this potential becomes realized, the molecular details of phage infection and mechanisms of resistance remain ill-defined. Here we use live-cell fluorescence microscopy to visualize the spatiotemporal dynamics of mycobacteriophage infection in single cells and populations, showing that infection is dependent on the host nucleoid-associated Lsr2 protein. Mycobacteriophages preferentially adsorb at Mycobacterium smegmatis sites of new cell wall synthesis and following DNA injection, Lsr2 reorganizes away from host replication foci to establish zones of phage DNA replication (ZOPR). Cells lacking Lsr2 proceed through to cell lysis when infected but fail to generate consecutive phage bursts that trigger epidemic spread of phage particles to neighbouring cells. Many mycobacteriophages code for their own Lsr2-related proteins, and although their roles are unknown, they do not rescue the loss of host Lsr2.
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Affiliation(s)
- Charles L Dulberger
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sean Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael G Wuo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lexi A Serpa
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ben J Braunecker
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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42
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Nieweglowska ES, Brilot AF, Méndez-Moran M, Kokontis C, Baek M, Li J, Cheng Y, Baker D, Bondy-Denomy J, Agard DA. The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nat Commun 2023; 14:927. [PMID: 36807264 PMCID: PMC9938867 DOI: 10.1038/s41467-023-36526-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 02/03/2023] [Indexed: 02/20/2023] Open
Abstract
To protect themselves from host attack, numerous jumbo bacteriophages establish a phage nucleus-a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host proteins associated with replication and transcription are concentrated inside the phage nucleus while other phage and host proteins are excluded, including CRISPR-Cas and restriction endonuclease host defense systems. Here, we show that nucleus fragments isolated from ϕPA3 infected Pseudomonas aeruginosa form a 2-dimensional lattice, having p2 or p4 symmetry. We further demonstrate that recombinantly purified primary Phage Nuclear Enclosure (PhuN) protein spontaneously assembles into similar 2D sheets with p2 and p4 symmetry. We resolve the dominant p2 symmetric state to 3.9 Å by cryo-EM. Our structure reveals a two-domain core, organized into quasi-symmetric tetramers. Flexible loops and termini mediate adaptable inter-tetramer contacts that drive subunit assembly into a lattice and enable the adoption of different symmetric states. While the interfaces between subunits are mostly well packed, two are open, forming channels that likely have functional implications for the transport of proteins, mRNA, and small molecules.
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Affiliation(s)
- Eliza S Nieweglowska
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Axel F Brilot
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
- Sauer Structural Biology Laboratory, Center for Biomedical Research Support, University of Texas at Austin, Austin, TX, USA
| | - Melissa Méndez-Moran
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Claire Kokontis
- Department of Microbiology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Minkyung Baek
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Junrui Li
- Howard Hughes Medical Institute, University of California, San Francisco, CA, 94143, USA
| | - Yifan Cheng
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, 94143, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David A Agard
- Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA.
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43
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Villarreal L, Witzany G. Self-empowerment of life through RNA networks, cells and viruses. F1000Res 2023; 12:138. [PMID: 36785664 PMCID: PMC9918806 DOI: 10.12688/f1000research.130300.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 01/05/2024] Open
Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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44
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Villarreal L, Witzany G. Self-empowerment of life through RNA networks, cells and viruses. F1000Res 2023; 12:138. [PMID: 36785664 PMCID: PMC9918806 DOI: 10.12688/f1000research.130300.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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45
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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] [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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46
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Abstract
CRISPR-Cas is a widespread adaptive immune system in bacteria and archaea that protects against viral infection by targeting specific invading nucleic acid sequences. Whereas some CRISPR-Cas systems sense and cleave viral DNA, type III and type VI CRISPR-Cas systems sense RNA that results from viral transcription and perhaps invasion by RNA viruses. The sequence-specific detection of viral RNA evokes a cell-wide response that typically involves global damage to halt the infection. How can one make sense of an immune strategy that encompasses broad, collateral effects rather than specific, targeted destruction? In this Review, we summarize the current understanding of RNA-targeting CRISPR-Cas systems. We detail the composition and properties of type III and type VI systems, outline the cellular defence processes that are instigated upon viral RNA sensing and describe the biological rationale behind the broad RNA-activated immune responses as an effective strategy to combat viral infection.
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47
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When bacteria are phage playgrounds: interactions between viruses, cells, and mobile genetic elements. Curr Opin Microbiol 2022; 70:102230. [PMID: 36335712 DOI: 10.1016/j.mib.2022.102230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/23/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and other mobile genetic elements are determinant to the success of infections. These interactions are often associated with antagonism and competition, but sometimes involve cooperation or parasitism. We describe two key types of interactions - defense systems and genetic regulation - that allow the partners of the interaction to destroy or control the others. These interactions evolve rapidly by genetic exchanges, including among competing partners. They are sometimes followed by functional diversification. Gene exchanges also facilitate the emergence of cross-talk between elements in the same bacterium. In the end, these processes produce multilayered networks of interactions that shape the outcome of viral infections.
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48
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Bacteriophage genome engineering with CRISPR-Cas13a. Nat Microbiol 2022; 7:1956-1966. [PMID: 36316452 PMCID: PMC9722621 DOI: 10.1038/s41564-022-01243-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/02/2022] [Indexed: 12/05/2022]
Abstract
Jumbo phages such as Pseudomonas aeruginosa ФKZ have potential as antimicrobials and as a model for uncovering basic phage biology. Both pursuits are currently limited by a lack of genetic engineering tools due to a proteinaceous 'phage nucleus' structure that protects from DNA-targeting CRISPR-Cas tools. To provide reverse-genetics tools for DNA jumbo phages from this family, we combined homologous recombination with an RNA-targeting CRISPR-Cas13a enzyme and used an anti-CRISPR gene (acrVIA1) as a selectable marker. We showed that this process can insert foreign genes, delete genes and add fluorescent tags to genes in the ФKZ genome. Fluorescent tagging of endogenous gp93 revealed that it is ejected with the phage DNA while deletion of the tubulin-like protein PhuZ surprisingly had only a modest impact on phage burst size. Editing of two other phages that resist DNA-targeting CRISPR-Cas systems was also achieved. RNA-targeting Cas13a holds great promise for becoming a universal genetic editing tool for intractable phages, enabling the systematic study of phage genes of unknown function.
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49
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Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection. Mol Cell 2022; 82:4471-4486.e9. [PMID: 36395770 DOI: 10.1016/j.molcel.2022.10.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/13/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
Bacteria have diverse defenses against phages. In response, jumbo phages evade multiple DNA-targeting defenses by protecting their DNA inside a nucleus-like structure. We previously demonstrated that RNA-targeting type III CRISPR-Cas systems provide jumbo phage immunity by recognizing viral mRNA exported from the nucleus for translation. Here, we demonstrate that recognition of phage mRNA by the type III system activates a cyclic triadenylate-dependent accessory nuclease, NucC. Although unable to access phage DNA in the nucleus, NucC degrades the bacterial chromosome, triggers cell death, and disrupts phage replication and maturation. Hence, type-III-mediated jumbo phage immunity occurs via abortive infection, with suppression of the viral epidemic protecting the population. We further show that type III systems targeting jumbo phages have diverse accessory nucleases, including RNases that provide immunity. Our study demonstrates how type III CRISPR-Cas systems overcome the inaccessibility of jumbo phage DNA to provide robust immunity.
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50
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Forterre P, Gaïa M. [Viruses and the evolution of modern eukaryotic cells]. Med Sci (Paris) 2022; 38:990-998. [PMID: 36692278 DOI: 10.1051/medsci/2022164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
It is now well accepted that viruses have played an important role in the evolution of modern eukaryotes. In this review, we suggest that interactions between ancient eukaryoviruses and proto-eukaryotes also played a major role in eukaryogenesis. We discuss phylogenetic analyses that highlight the viral origin of several key proteins in the molecular biology of eukaryotes. We also discuss recent observations that, by analogy, could suggest a viral origin of the cellular nucleus. Finally, we hypothesize that mechanisms of cell differentiation in multicellular organisms might have originated from mechanisms implemented by viruses to transform infected cells into virocells.
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Affiliation(s)
- Patrick Forterre
- Département de microbiologie, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France - Institut de biologie intégrative de la cellule (I2BC), Département de microbiologie, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Morgan Gaïa
- Génomique métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057 Évry, France
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