PXD030076

PXD030076 is an original dataset announced via ProteomeXchange.

Title	Distinct ribosome states trigger diverse mRNA quality control pathways
Description	Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on nonoptimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully-designed reporter mRNAs to perform genetic screens and functional assays in S. cerevisiae. We characterize the roles of Hel2 and Syh1 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 acts as the primary link to mRNA decay in NGD. Importantly we, observe that these NGD factors are not involved in the degradation of mRNAs enriched in nonoptimal codons. Further, we establish that key factors previously implicated in COMD, Not5 and Dhh1 , contribute modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new mechanistic insight into the role of Syh1 in NGD and define the molecular triggers that determine how distinct pathways target mRNAs for degradation in yeast.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:54:47.309.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anthony Veltri
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-30 15:12:31	ID requested
1	2022-08-08 14:06:09	announced
⏵ 2	2023-11-14 08:54:48	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: COMD, NGD,SYH1, RNA decay, SMY2, codon-optimality-mediated decay, no-go decay

Rachel Green
contact affiliation	Johns Hopkins School of Medicine, Department of Molecular Biology and Genetics, Baltimore, MD, USA
contact email	ragreen@jhmi.edu
lab head
Anthony Veltri
contact affiliation	Johns Hopkins University
contact email	aveltri1@jh.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/08/PXD030076

PRIDE project URI

• PRIDE
  1. PXD030076
     1. Label: PRIDE project
     2. Name: Distinct ribosome states trigger diverse mRNA quality control pathways