A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.
Eray Enustun, Emily G Armbruster, Jina Lee, Sitao Zhang, Brian A Yee, Kseniya Malukhina, Yajie Gu, Amar Deep, Jack T Naritomi, Qishan Liang, Stefan Aigner, Benjamin A Adler, Brady F Cress, Jennifer A Doudna, Vorrapon Chaikeeratisak, Don W Cleveland, Majid Ghassemian, Bogdan Bintu, Gene W Yeo, Joe Pogliano, Kevin D Corbett
Nucleic acids research · 2024 · Vol. 52 (8) · pp. 4440-4455
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.
Linked datasets 1
A phage nucleus-associated RNA-binding protein required for jumbo phage infection
287
16 data files
| File | Type | Size |
|---|---|---|
| SA_gp61-sfGFP_IN_1_S7_L002_R1_001.fastq.gz | RNA-Seq | 682.9 MB |
| SA_gp61-sfGFP_IN_2_S5_L002_R1_001.fastq.gz | RNA-Seq | 640.0 MB |
| SA_gp61-sfGFP_IP_1_S11_L002_R1_001.fastq.gz | RIP-Seq | 588.1 MB |
| SA_gp61-sfGFP_IP_2_S9_L002_R1_001.fastq.gz | RIP-Seq | 392.2 MB |
| SA_sfGFP_IN_1_S4_L002_R1_001.fastq.gz | RNA-Seq | 476.7 MB |
| SA_sfGFP_IN_2_S6_L002_R1_001.fastq.gz | RNA-Seq | 551.8 MB |
| SA_sfGFP_IP_1_S8_L002_R1_001.fastq.gz | RIP-Seq | 272.2 MB |
| SA_sfGFP_IP_2_S10_L002_R1_001.fastq.gz | RIP-Seq | 604.7 MB |
| SRR26130299_GSM7794002 | RNA-Seq | 639.0 MB |
| SRR26130300_GSM7794001 | RNA-Seq | 682.0 MB |
| SRR26130301_GSM7794000 | RIP-Seq | 392.0 MB |
| SRR26130302_GSM7793999 | RIP-Seq | 588.0 MB |
| SRR26130303_GSM7793998 | RNA-Seq | 551.0 MB |
| SRR26130304_GSM7793997 | RNA-Seq | 476.0 MB |
| SRR26130305_GSM7793996 | RIP-Seq | 604.0 MB |
| SRR26130306_GSM7793995 | RIP-Seq | 272.0 MB |
Potentially related datasets 2
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.
Analysis pipelines 1
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE243675 eCLIP Data Processing geo_data_processing | eCLIP | 9 | GSE243675 |
Funding 5 grants
| Grant | Funder |
|---|---|
| R35 GM144121 | NIGMS NIH HHS (United States) |
| R01 GM129245 | NIH HHS (United States) |
| S10 OD021724 | NIH HHS (United States) |
| Howard Hughes Medical Institute (United States) | |
| R01 GM129245 | NIGMS NIH HHS (United States) |