A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

Enustun, Eray; Armbruster, Emily G.; Lee, Jina; Zhang, Sitao; Yee, Brian A.; Malukhina, Kseniya; Gu, Yajie; Deep, Amar; Naritomi, Jack T.; Liang, Qishan; Aigner, Stefan; Adler, Benjamin A.; Cress, Brady F.; Doudna, Jennifer A.; Chaikeeratisak, Vorrapon; Cleveland, Don W.; Ghassemian, Majid; Bintu, Bogdan; Yeo, Gene W.; Pogliano, Joe; Corbett, Kevin D.

doi:10.1093/nar/gkae216

Title: A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

Journal Article · 29 March 2024 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkae216 · OSTI ID:2331352

Enustun, Eray;

; Lee, Jina; Zhang, Sitao; Yee, Brian A.; Malukhina, Kseniya; Gu, Yajie; Deep, Amar; Naritomi, Jack T.; Liang, Qishan; Aigner, Stefan;

;

; Doudna, Jennifer A.; Chaikeeratisak, Vorrapon; Cleveland, Don W.; Ghassemian, Majid; Bintu, Bogdan; Yeo, Gene W.; Pogliano, Joe more »

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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Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2331352

Alternate ID(s):: OSTI ID: 2448497

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 8 Vol. 52; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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