Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection

Emily G Armbruster¹, Phoolwanti Rani², Jina Lee¹, Niklas Klusch², Joshua Hutchings², Lizbeth Y Hoffman², Hannah Buschkaemper³, Eray Enustun¹, Benjamin A Adler⁴, Koe Inlow¹, Arica R VanderWal², Madelynn Y Hoffman¹, Daksh Daksh⁵, Ann Aindow¹, Amar Deep⁶, Zaida K Rodriguez¹, Chase J Morgan¹, Majid Ghassemian⁷, Thomas G Laughlin¹, Emeric Charles⁸, Brady F Cress⁹, David F Savage¹⁰, Jennifer A Doudna¹¹, Kit Pogliano¹, Kevin D Corbett¹², Elizabeth Villa¹³, Joe Pogliano¹⁴

Affiliations

¹ School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
² School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
³ School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Gene Center and Department of Biochemistry, Ludwig Maximilian University of Munich, 80539 Munich, Germany.
⁴ California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
⁵ National Institute of Science, Education and Research (NISER), Bhubaneshwar 752050, Orissa, India.
⁶ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
⁷ Biomolecular and Proteomics Mass Spectrometry Facility, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
⁸ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
⁹ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
¹⁰ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
¹¹ California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, 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.
¹² School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
¹³ School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, San Diego, CA 92093, USA. Electronic address: evilla@ucsd.edu.
¹⁴ School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA. Electronic address: jpogliano@ucsd.edu.

PMID: 40168997
PMCID: PMC12256282 (available on 2026-03-31)
DOI: 10.1016/j.chom.2025.03.005

Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection

Emily G Armbruster et al. Cell Host Microbe. 2025.

. 2025 Apr 9;33(4):484-497.e6.

doi: 10.1016/j.chom.2025.03.005. Epub 2025 Mar 31.

Authors

Affiliations

¹ School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
² School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
³ School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Gene Center and Department of Biochemistry, Ludwig Maximilian University of Munich, 80539 Munich, Germany.
⁴ California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
⁵ National Institute of Science, Education and Research (NISER), Bhubaneshwar 752050, Orissa, India.
⁶ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
⁷ Biomolecular and Proteomics Mass Spectrometry Facility, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
⁸ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
⁹ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
¹⁰ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
¹¹ California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, 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.
¹² School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.
¹³ School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, San Diego, CA 92093, USA. Electronic address: evilla@ucsd.edu.
¹⁴ School of Biological Sciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA. Electronic address: jpogliano@ucsd.edu.

PMID: 40168997
PMCID: PMC12256282 (available on 2026-03-31)
DOI: 10.1016/j.chom.2025.03.005

Abstract

Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic viruses. Bacteriophages of the Chimalliviridae family sequester their genomes within a phage-generated organelle, the phage nucleus, which is enclosed by a lattice of the viral protein ChmA. We show that inhibiting phage nucleus formation arrests infections at an early stage in which the injected phage genome is enclosed within a membrane-bound early phage infection (EPI) vesicle. Early phage genes are expressed from the EPI vesicle, demonstrating its functionality as a prokaryotic, transcriptionally active, membrane-bound organelle. We also show that the phage nucleus is essential, with genome replication beginning after the injected DNA is transferred from the EPI vesicle to the phage nucleus. Our results show that Chimalliviridae require two sophisticated subcellular compartments of distinct compositions and functions that facilitate successive stages of the viral life cycle.

Keywords: EPI vesicle; bacterial cell biology; jumbo phage; phage; phage nucleus; viral organelle.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests K.P. and J.P. have an equity interest in Linnaeus Bioscience Incorporated and receive income. The terms of this arrangement have been reviewed and approved by the University of California, San Diego, in accordance with its conflict-of-interest policies. The regents of the University of California have patents issued and pending for CRISPR technologies on which J.A.D., B.F.C., B.A.A., D.F.S., E.C., J.P., K.P., E.G.A., and J.L. are inventors. J.A.D. is a cofounder of Azalea Therapeutics, Caribou Biosciences, Editas Medicine, Scribe Therapeutics, Intellia Therapeutics, and Mammoth Biosciences. J.A.D. is a scientific advisory board member of Vertex, Caribou Biosciences, Intellia Therapeutics, Scribe Therapeutics, Mammoth Biosciences, Algen Biotechnologies, Felix Biosciences, The Column Group, and Inari. J.A.D. is chief science advisor to Sixth Street; a director at Johnson & Johnson, Altos, and Tempus; and has research projects sponsored by Apple Tree Partners and Roche. D.F.S. is a cofounder and scientific advisory board member of Scribe Therapeutics.

References

1. Taxonomy Browser International Committee on Taxonomy of Viruses (ICTV). https://ictv.global/taxonomy.
1. Chaikeeratisak V, Nguyen K, Khanna K, Brilot AF, Erb ML, Coker JKC, Vavilina A, Newton GL, Buschauer R, Pogliano K, et al. (2017). Assembly of a nucleus-like structure during viral replication in bacteria. Science 355, 194–197. 10.1126/science.aal2130. - DOI - PMC - PubMed
1. Chaikeeratisak V, Birkholz EA, and Pogliano J. (2021). The Phage Nucleus and PhuZ Spindle: Defining Features of the Subcellular Organization and Speciation of Nucleus-Forming Jumbo Phages. Front. Microbiol 12, 641317. 10.3389/fmicb.2021.641317. - DOI - PMC - PubMed
1. Laughlin TG, Deep A, Prichard AM, Seitz C, Gu Y, Enustun E, Suslov S, Khanna K, Birkholz EA, Armbruster E, et al. (2022). Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature 608, 429–435. 10.1038/s41586-022-05013-4. - DOI - PMC - PubMed
1. Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, Spencer T, Asavavimol A, Cafferata A, Cameron M, et al. (2023). Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. Cell Rep. 42, 112432. 10.1016/j.celrep.2023.112432. - DOI - PMC - PubMed

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions

Grants and funding

LinkOut - more resources

Full Text Sources
- Elsevier Science
- eScholarship, University of California - Access Free Full Text

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection

Affiliations

Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection

Authors

Affiliations

Abstract

Conflict of interest statement

References

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources