GSE243675

GSE GEO

View on GEO Export SRA CSV

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

R1 data was processed using the single ended eCLIP pipeline and available at: http://github.com/yeolab/eclip.
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with umi_tools extract
Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
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)
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)
Uniquely mapped reads were removed of PCR duplicates with umi_tools
Peak clusters were identified with CLIPper, available at: https://github.com/YeoLab/clipper
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 (2)

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

Nucleic acids research · 2024

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

Nucleic acids research · 2024

Data Files (8)

Accession	File Name	Stored Type	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
—	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