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

Emily G Armbruster; Phoolwanti Rani; Jina Lee; Niklas Klusch; Joshua Hutchings; Lizbeth Y Hoffman; Hannah Buschkaemper; Eray Enustun; Benjamin A Adler; Koe Inlow; Arica R VanderWal; Madelynn Y Hoffman; Daksh Daksh; Ann Aindow; Amar Deep; Zaida K Rodriguez; Chase J Morgan; Majid Ghassemian; Thomas G Laughlin; Emeric Charles; Brady F Cress; David F Savage; Jennifer A Doudna; Kit Pogliano; Kevin D Corbett; Elizabeth Villa; Joe Pogliano

doi:10.1016/j.chom.2025.03.005

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

Cell Host Microbe. 2025 Apr 9;33(4):484-497.e6. doi: 10.1016/j.chom.2025.03.005. Epub 2025 Mar 31.

Authors

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

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.

MeSH terms

Bacteriophages* / genetics
Bacteriophages* / physiology
Cell Nucleus / virology
Genome, Viral*
Organelles* / metabolism
Organelles* / virology
Viral Proteins / genetics
Viral Proteins / metabolism
Virus Replication

Substances

Viral Proteins

Abstract

MeSH terms

Substances

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