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

Emily G Armbruster; Jina Lee; Joshua Hutchings; Arica R VanderWal; Eray Enustun; Benjamin A Adler; Ann Aindow; Amar Deep; Zaida K Rodriguez; Chase J Morgan; Majid Ghassemian; Emeric Charles; Brady F Cress; David F Savage; Jennifer A Doudna; Kit Pogliano; Kevin D Corbett; Elizabeth Villa; Joe Pogliano

doi:10.1101/2023.09.20.558163

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

bioRxiv [Preprint]. 2023 Sep 21:2023.09.20.558163. doi: 10.1101/2023.09.20.558163.

Authors

Emily G Armbruster¹, Jina Lee¹, Joshua Hutchings^{1

2}, Arica R VanderWal^{1

2}, Eray Enustun¹, Benjamin A Adler^{3

4}, Ann Aindow¹, Amar Deep⁵, Zaida K Rodriguez¹, Chase J Morgan¹, Majid Ghassemian⁶, Emeric Charles^{4

7}, Brady F Cress⁴, David F Savage^{3

4

7

8}, Jennifer A Doudna^{3

4

7

8

9

10

11}, Kit Pogliano¹, Kevin D Corbett^{1

5}, Elizabeth Villa^{1

2}, Joe Pogliano¹

Affiliations

¹ School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
² Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA.
³ California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
⁴ Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
⁵ Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA.
⁶ Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA.
⁷ Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
⁸ Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.
⁹ Department of Chemistry, University of California, Berkeley, CA 94720, USA.
¹⁰ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
¹¹ MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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.

Publication types

Preprint

Abstract

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