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GSE243675

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

Organism: 287
Platform: GPL24583
Samples: 8
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Sep 20 2023
Last Updated: Jun 11 2024
Status: Public on Mar 12 2024
Contact: Brian,,Yee (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1019367

Summary

Large-genome bacteriophages (jumbo phages) of the Chimalliviriadae family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and 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. Targeted knockdown of ChmC using mRNA-targeting Cas13d halts infections at an early stage. Taken together, our data suggest that the conserved ChmC protein acts as a chaperone for phage mRNAs, potentially stabilizing these mRNAs and driving their translocation through the nuclear shell to promote translation and infection progression.

Overall Design

eCLIP-seq (enhanced UV crosslinking and immunoprecipitation, followed by deep sequencing) in PhiPA3-infected P. aeruginosa cells expressing GFP-tagged ChmC.

Analysis (9 steps)

View Data Processing
Processing steps for GSE243675
  1. R1 data was processed using the single ended eCLIP pipeline and available at: http://github.com/yeolab/eclip.
  2. Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with umi_tools extract
  3. Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
  4. Trimmed reads were mapped against RepBase with STAR to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 30 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
  5. Remaining reads were mapped to the appropriate genome build (Pa_P01 + PhiPA3) using STAR aligner (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
  6. Uniquely mapped reads were removed of PCR duplicates with umi_tools
  7. Peak clusters were identified with CLIPper, available at: https://github.com/YeoLab/clipper
  8. Clusters enriched over corresponding size-matched input (SMInput) were identified using a custom Perl script, available in the main eCLIP repository as: overlap_peakfi_with_bam.pl
Showing first 8 steps.

Supplementary Files (3)

GSE243675_RAW.tar Download
GSE243675_SA_gp61-sfGFP_rep1.vs.SA_gp61-sfGFP_rep2.bed.gz Download
GSE243675_SA_sfGFP_rep1.vs.SA_sfGFP_rep2.bed.gz Download
GEO Samples (8)
GSM7793995 GSM7793996 GSM7793997 GSM7793998 GSM7793999 GSM7794000 GSM7794001 GSM7794002

Dataset Citations (1)

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.
PMID 38554115 · 2024 · Nucleic acids research
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

SRA Experiments (8) and Runs (8)

Total: 4209 MB
SRX21843715 SRP462252 RIP-Seq PAIRED
GSM7793995: sfGFP-1 IP; Pseudomonas aeruginosa; RIP-Seq
Sample: SRS18941732
BioProject: PRJNA1019367
BioSample: SAMN37485529
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Pseudomonas aeruginosa
Sample attributes
source_name: K2733
cell line: K2733
genotype: sfGFP
geo_loc_name: missing
collection_date: missing
Original files (1)
K2733
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR26130306 4311996 871023192 272.25 SA_sfGFP_IP_1_S8_L002_R1_001.fastq.gz, SA_sfGFP_IP_1_S8_L002_R2_001.f… SRA
SRX21843716 SRP462252 RIP-Seq PAIRED
GSM7793996: sfGFP-2 IP; Pseudomonas aeruginosa; RIP-Seq
Sample: SRS18941733
BioProject: PRJNA1019367
BioSample: SAMN37485528
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Pseudomonas aeruginosa
Sample attributes
source_name: K2733
cell line: K2733
genotype: sfGFP
geo_loc_name: missing
collection_date: missing
Original files (1)
K2733
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR26130305 9899726 1999744652 604.72 SA_sfGFP_IP_2_S10_L002_R1_001.fastq.gz, SA_sfGFP_IP_2_S10_L002_R2_001… SRA
SRX21843717 SRP462252 RNA-Seq PAIRED
GSM7793997: sfGFP-1 IN; Pseudomonas aeruginosa; RNA-Seq
Sample: SRS18941735
BioProject: PRJNA1019367
BioSample: SAMN37485527
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Pseudomonas aeruginosa
Sample attributes
source_name: K2733
cell line: K2733
genotype: sfGFP
geo_loc_name: missing
collection_date: missing
Original files (1)
K2733
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR26130304 7835367 1582744134 476.68 SA_sfGFP_IN_1_S4_L002_R1_001.fastq.gz, SA_sfGFP_IN_1_S4_L002_R2_001.f… SRA
SRX21843718 SRP462252 RNA-Seq PAIRED
GSM7793998: sfGFP-2 IN; Pseudomonas aeruginosa; RNA-Seq
Sample: SRS18941734
BioProject: PRJNA1019367
BioSample: SAMN37485526
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Pseudomonas aeruginosa
Sample attributes
source_name: K2733
cell line: K2733
genotype: sfGFP
geo_loc_name: missing
collection_date: missing
Original files (1)
K2733
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR26130303 9081679 1834499158 551.83 SA_sfGFP_IN_2_S6_L002_R1_001.fastq.gz, SA_sfGFP_IN_2_S6_L002_R2_001.f… SRA
SRX21843719 SRP462252 RIP-Seq PAIRED
GSM7793999: gp61-sfGFP-1 IP; Pseudomonas aeruginosa; RIP-Seq
Sample: SRS18941737
BioProject: PRJNA1019367
BioSample: SAMN37485525
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Pseudomonas aeruginosa
Sample attributes
source_name: K2733
cell line: K2733
genotype: gp61-sfGFP
geo_loc_name: missing
collection_date: missing
Original files (1)
K2733
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR26130302 9609466 1941112132 588.11 SA_gp61-sfGFP_IP_1_S11_L002_R1_001.fastq.gz, SA_gp61-sfGFP_IP_1_S11_L… SRA
SRX21843720 SRP462252 RIP-Seq PAIRED
GSM7794000: gp61-sfGFP-2 IP; Pseudomonas aeruginosa; RIP-Seq
Sample: SRS18941736
BioProject: PRJNA1019367
BioSample: SAMN37485524
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Pseudomonas aeruginosa
Sample attributes
source_name: K2733
cell line: K2733
genotype: gp61-sfGFP
geo_loc_name: missing
collection_date: missing
Original files (1)
K2733
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR26130301 6429884 1298836568 392.19 SA_gp61-sfGFP_IP_2_S9_L002_R1_001.fastq.gz, SA_gp61-sfGFP_IP_2_S9_L00… SRA
SRX21843721 SRP462252 RNA-Seq PAIRED
GSM7794001: gp61-sfGFP-1 IN; Pseudomonas aeruginosa; RNA-Seq
Sample: SRS18941738
BioProject: PRJNA1019367
BioSample: SAMN37485523
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Pseudomonas aeruginosa
Sample attributes
source_name: K2733
cell line: K2733
genotype: gp61-sfGFP
geo_loc_name: missing
collection_date: missing
Original files (1)
K2733
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR26130300 11335132 2289696664 682.9 SA_gp61-sfGFP_IN_1_S7_L002_R1_001.fastq.gz, SA_gp61-sfGFP_IN_1_S7_L00… SRA
SRX21843722 SRP462252 RNA-Seq PAIRED
GSM7794002: gp61-sfGFP-2 IN; Pseudomonas aeruginosa; RNA-Seq
Sample: SRS18941739
BioProject: PRJNA1019367
BioSample: SAMN37485522
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Pseudomonas aeruginosa
Sample attributes
source_name: K2733
cell line: K2733
genotype: gp61-sfGFP
geo_loc_name: missing
collection_date: missing
Original files (1)
K2733
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR26130299 10442969 2109479738 639.97 SA_gp61-sfGFP_IN_2_S5_L002_R1_001.fastq.gz, SA_gp61-sfGFP_IN_2_S5_L00… SRA

Linked Publications (1)

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.
Nucleic acids research · 2024

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.
Nucleic acids research · 2024

Data Files (16)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— SA_gp61-sfGFP_IP_1_S11_L002_R1_001.fastq.gz RIP-Seq 588.1 MB link
— SA_gp61-sfGFP_IP_2_S9_L002_R1_001.fastq.gz RIP-Seq 392.2 MB link
— SA_sfGFP_IP_1_S8_L002_R1_001.fastq.gz RIP-Seq 272.2 MB link
— SA_sfGFP_IP_2_S10_L002_R1_001.fastq.gz RIP-Seq 604.7 MB link
— SRR26130301_GSM7794000 RIP-Seq 392.0 MB link
— SRR26130302_GSM7793999 RIP-Seq 588.0 MB link
— SRR26130305_GSM7793996 RIP-Seq 604.0 MB link
— SRR26130306_GSM7793995 RIP-Seq 272.0 MB link
— SA_gp61-sfGFP_IN_1_S7_L002_R1_001.fastq.gz RNA-Seq 682.9 MB link
— SA_gp61-sfGFP_IN_2_S5_L002_R1_001.fastq.gz RNA-Seq 640.0 MB link
— SA_sfGFP_IN_1_S4_L002_R1_001.fastq.gz RNA-Seq 476.7 MB link
— SA_sfGFP_IN_2_S6_L002_R1_001.fastq.gz RNA-Seq 551.8 MB link
— SRR26130299_GSM7794002 RNA-Seq 639.0 MB link
— SRR26130300_GSM7794001 RNA-Seq 682.0 MB link
— SRR26130303_GSM7793998 RNA-Seq 551.0 MB link
— SRR26130304_GSM7793997 RNA-Seq 476.0 MB link