PXD029577

PXD029577 is an original dataset announced via ProteomeXchange.

Title	Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance
Description	Upf1, Upf2, and Upf3 are the central regulators of nonsense-mediated mRNA decay (NMD), the eukaryotic mRNA quality control pathway generally triggered when a premature termination codon is recognized by the ribosome. The NMD-related functions of the Upf proteins likely commence while these factors are ribosome-associated, but little is known of the timing of their ribosome binding, their specificity for ribosomes translating NMD substrates, or the nature and role of any ribosome:Upf complexes. Here, we have elucidated details of the ribosome-associated steps of NMD. By combining yeast genetics with selective ribosome profiling and co-sedimentation analyses of polysomes with wild-type and mutant Upf proteins, our approaches have identified distinct states of ribosome:Upf association. All three Upf factors manifest progressive polysome association as mRNA translation proceeds, but these events appear to be preceded by formation of a Upf1:80S complex as mRNAs initiate translation. This complex is likely executing an early mRNA surveillance function.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_06:50:28.412.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD029577
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Robin Ganesan
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	2-pyrrolidone-5-carboxylic acid (Glu); 2-pyrrolidone-5-carboxylic acid (Gln); ubiquitination signature dipeptidyl lysine; phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-04 10:18:00	ID requested
1	2022-10-21 06:16:53	announced
⏵ 2	2023-11-14 06:50:29	announced	2023-11-14: Updated project metadata.

Ganesan R, Mangkalaphiban K, Baker RE, He F, Jacobson A, Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance. RNA, 28(12):1621-1642(2022) [pubmed]

10.6019/PXD029577;

submitter keyword: Upf proteins, NMD substrates,ribosome, selective ribosome profiling

Allan Jacobson
contact affiliation	Department of Microbiology and Physiological Systems UMass Chan Medical School 368 Plantation Street Worcester, MA 01655
contact email	allan.jacobson@umassmed.edu
lab head
Robin Ganesan
contact affiliation	UMass Chan Medical School
contact email	robin.ganesan@umassmed.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD029577
     1. Label: PRIDE project
     2. Name: Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance