The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice

Eliza S. Nieweglowska, Axel F. Brilot, Melissa Méndez-Moran, Claire Kokontis, Minkyung Baek, Junrui Li, Yifan Cheng, David Baker, Joseph Bondy-Denomy and David A. Agard ()
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Eliza S. Nieweglowska: University of California San Francisco
Axel F. Brilot: University of California San Francisco
Melissa Méndez-Moran: University of California San Francisco
Claire Kokontis: University of California San Francisco
Minkyung Baek: University of Washington
Junrui Li: University of California
Yifan Cheng: University of California San Francisco
David Baker: University of Washington
Joseph Bondy-Denomy: University of California San Francisco
David A. Agard: University of California San Francisco

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-36526-9

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