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BioProject

KAP241433

BioProject Title

Formyl-methionine-mediated eukaryotic ribosome quality control pathway for cold adaptation (DDBJ: PRJDB37362)

Eukaryotic cytosolic protein synthesis typically begins with methionine (Met), but formyl-methionine (fMet) can also be incorporated. However, the mechanism regulating fMet incorporation and preventing potential toxicity remains unclear. This study reveals that the fMet-mediated ribosome quality control (fMet-RQC) pathway in Saccharomyces cerevisiae plays a crucial role in maintaining translation fidelity. Nip1, a subunit of eukaryotic translation initiation factor 3, recognizes N-terminal fMet in nascent polypeptides and recruits Arf1, leading to ribosome stalling and dissociation. This prevents the accumulation of toxic fMet-polypeptides, which can disrupt N-terminal Met modifications and aggregate with ribosomes. Notably, loss of the fMet-RQC pathway impairs stress granule formation and increases sensitivity to cold stress. These findings suggest that regulating fMet incorporation and clearance is essential for maintaining cellular homeostasis and adapting to environmental stress.

Common Fields

Common Fields - BioProject, Data Type, Submission date, Access, Release date, Runs
BioProject	KAP241433
Data Type	fastq
Submission date	2025-02-04
Access	Public
Release date	2025-02-04
Runs	24

Accession

Accession - Division, BIOSAMPLEs
Division	Run	Bytes	Download
Total	24	52,484,956,654 52,484,956,654	Metadata

BioProject * All samples * All experiments

Run Metadata

Primary

(24 cases)

Run Metadata - RUN ID, EXPERIMENT ID, BIOSAMPLE ID, LIBRARY IDENTIFIER, TYPE OF PRIMARY DATA FILE, NAME OF PRIMARY DATA FILE
Run ID	identifier	Experiment ID	BioSample ID	library name	filetype	file name	bytes (total)	Registration date	Release date	Access type	Protocol
KAR24087335	DRA : DRR878997	KAE24087335	KAS24109218	RFP MTF replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	RFP_MTF_rep1_1.fastq.gz \| RFP_MTF_rep1_2.fastq.gz	2,565,665,803 2,565,665,803	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087336	DRA : DRR878998	KAE24087336	KAS24109219	RFP MTF replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	RFP_MTF_rep2_1.fastq.gz \| RFP_MTF_rep2_2.fastq.gz	2,768,022,028 2,768,022,028	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087337	DRA : DRR878999	KAE24087337	KAS24109220	RFP MTFi replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	RFP_MTFi_rep1_1.fastq.gz \| RFP_MTFi_rep1_2.fastq.gz	2,660,268,791 2,660,268,791	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087338	DRA : DRR879000	KAE24087338	KAS24109221	RFP MTFi replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	RFP_MTFi_rep2_1.fastq.gz \| RFP_MTFi_rep2_2.fastq.gz	4,027,297,105 4,027,297,105	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087339	DRA : DRR879001	KAE24087339	KAS24109222	RNA MTF replicate 1 [RNA-seq]_TRANSCRIPTOMIC	fastq	RNA_MTF_rep1_1.fastq.gz \| RNA_MTF_rep1_2.fastq.gz	3,653,232,286 3,653,232,286	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087340	DRA : DRR879002	KAE24087340	KAS24109223	RNA MTF replicate 2 [RNA-seq]_TRANSCRIPTOMIC	fastq	RNA_MTF_rep2_1.fastq.gz \| RNA_MTF_rep2_2.fastq.gz	3,896,236,551 3,896,236,551	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087341	DRA : DRR879003	KAE24087341	KAS24109224	RNA MTFi replicate 1 [RNA-seq]_TRANSCRIPTOMIC	fastq	RNA_MTFi_rep1_1.fastq.gz \| RNA_MTFi_rep1_2.fastq.gz	4,297,235,223 4,297,235,223	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087342	DRA : DRR879004	KAE24087342	KAS24109225	RNA MTFi replicate 2 [RNA-seq]_TRANSCRIPTOMIC	fastq	RNA_MTFi_rep2_1.fastq.gz \| RNA_MTFi_rep2_2.fastq.gz	4,578,329,059 4,578,329,059	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087343	DRA : DRR879005	KAE24087343	KAS24109226	arf1D EcFMT replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	arf1D.EcFMT.rep1_1.fastq.gz \| arf1D.EcFMT.rep1_2.fastq.gz	1,771,497,127 1,771,497,127	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087344	DRA : DRR879006	KAE24087344	KAS24109227	arf1D EcFMT replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	arf1D.EcFMT.rep2_1.fastq.gz \| arf1D.EcFMT.rep2_2.fastq.gz	1,535,446,934 1,535,446,934	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087345	DRA : DRR879007	KAE24087345	KAS24109228	arf1D R42L replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	arf1D.R42L.rep1_1.fastq.gz \| arf1D.R42L.rep1_2.fastq.gz	1,484,382,709 1,484,382,709	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087346	DRA : DRR879008	KAE24087346	KAS24109229	arf1D R42L replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	arf1D.R42L.rep2_1.fastq.gz \| arf1D.R42L.rep2_2.fastq.gz	1,454,991,175 1,454,991,175	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087347	DRA : DRR879009	KAE24087347	KAS24109230	hcr1D EcFMT replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	hcr1D.EcFMT.rep1_1.fastq.gz \| hcr1D.EcFMT.rep1_2.fastq.gz	1,605,791,717 1,605,791,717	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087348	DRA : DRR879010	KAE24087348	KAS24109231	hcr1D EcFMT replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	hcr1D.EcFMT.rep2_1.fastq.gz \| hcr1D.EcFMT.rep2_2.fastq.gz	1,643,094,661 1,643,094,661	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087349	DRA : DRR879011	KAE24087349	KAS24109232	hcr1D R42L replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	hcr1D.R42L.rep1_1.fastq.gz \| hcr1D.R42L.rep1_2.fastq.gz	1,345,866,104 1,345,866,104	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087350	DRA : DRR879012	KAE24087350	KAS24109233	hcr1D R42L replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	hcr1D.R42L.rep2_1.fastq.gz \| hcr1D.R42L.rep2_2.fastq.gz	1,173,774,858 1,173,774,858	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087351	DRA : DRR879013	KAE24087351	KAS24109234	NIP1_depl EcFMT replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	NIP1_depl.EcFMT.rep1_1.fastq.gz \| NIP1_depl.EcFMT.rep1_2.fastq.gz	1,523,341,296 1,523,341,296	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087352	DRA : DRR879014	KAE24087352	KAS24109235	NIP1_depl EcFMT replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	NIP1_depl.EcFMT.rep2_1.fastq.gz \| NIP1_depl.EcFMT.rep2_2.fastq.gz	1,649,798,832 1,649,798,832	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087353	DRA : DRR879015	KAE24087353	KAS24109236	NIP1_depl.R42L replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	NIP1_depl.R42L.rep1_1.fastq.gz \| NIP1_depl.R42L.rep1_2.fastq.gz	1,389,933,346 1,389,933,346	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087354	DRA : DRR879016	KAE24087354	KAS24109237	NIP1_depl.R42L replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	NIP1_depl.R42L.rep2_1.fastq.gz \| NIP1_depl.R42L.rep2_2.fastq.gz	1,468,266,004 1,468,266,004	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087355	DRA : DRR879017	KAE24087355	KAS24109238	RLI1_depl.EcFMT replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	RLI1_depl.EcFMT.rep1_1.fastq.gz \| RLI1_depl.EcFMT.rep1_2.fastq.gz	1,581,705,968 1,581,705,968	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087356	DRA : DRR879018	KAE24087356	KAS24109239	RLI1_depl.EcFMT replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	RLI1_depl.EcFMT.rep2_1.fastq.gz \| RLI1_depl.EcFMT.rep2_2.fastq.gz	1,476,545,850 1,476,545,850	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087357	DRA : DRR879019	KAE24087357	KAS24109240	RLI1_depl.R42L replicate 1 [RIBO-seq]_TRANSCRIPTOMIC	fastq	RLI1_depl.R42L.rep1_1.fastq.gz \| RLI1_depl.R42L.rep1_2.fastq.gz	1,330,085,168 1,330,085,168	2025-02-04	2025-02-04	PUBLIC	Protocol
KAR24087358	DRA : DRR879020	KAE24087358	KAS24109241	RLI1_depl.R42L replicate 2 [RIBO-seq]_TRANSCRIPTOMIC	fastq	RLI1_depl.R42L.rep2_1.fastq.gz \| RLI1_depl.R42L.rep2_2.fastq.gz	1,604,148,059 1,604,148,059	2025-02-04	2025-02-04	PUBLIC	Protocol

Analysis

(0 cases)

Run Metadata - RUN ID, EXPERIMENT ID, BIOSAMPLE ID, LIBRARY IDENTIFIER, TYPE OF PRIMARY DATA FILE, NAME OF PRIMARY DATA FILE
Analysis ID	analysis type	analysis file	bytes(GB)	Release date	Processed method
No Run data.

Reference

(0 cases)

Run Metadata - RUN ID, EXPERIMENT ID, BIOSAMPLE ID, LIBRARY IDENTIFIER, TYPE OF PRIMARY DATA FILE, NAME OF PRIMARY DATA FILE
reference type	RefSeq accession ID	file name
No Run data.

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