PXD042990

PXD042990 is an original dataset announced via ProteomeXchange.

Title	Regulation of transcript abundance and translationny decapping activators Pat1 and Dhh1
Description	We have examined the roles of yeast mRNA decapping-activators Pat1 and Dhh1 in repressing the translation and abundance of specific mRNAs in nutrient-replete cells using ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs, RNA Polymerase II ChIP-Seq, and TMT-mass spectrometry of mutants lacking one or both factors. Although the Environmental Stress Response (ESR) is activated in dhh1 and pat1 mutants, hundreds of non-ESR transcripts are elevated in a manner indicating cumulative repression by Pat1 and Dhh1 in WT. These mRNAs show reduced decapping and diminished transcription in the mutants, indicating that impaired mRNA turnover drives transcript derepression in cells lacking Dhh1 or Pat1. mRNA degradation stimulated by Dhh1/Pat1 is not dictated by poor translation nor enrichment for suboptimal codons. Pat1 and Dhh1 also collaborate to reduce translation and protein production from many mRNAs. Transcripts showing concerted translational repression by Pat1/Dhh1 include mRNAs involved in cell adhesion or utilization of the poor nitrogen source allantoin. Pat1/Dhh1 also repress numerous transcripts involved in respiration, catabolism of non-preferred carbon or nitrogen sources, or autophagy; and we obtained evidence for elevated respiration and autophagy in the mutants. Thus, Pat1 and Dhh1 function as post-transcriptional repressors of multiple pathways normally activated only during nutrient limitation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:11:40.017.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD042990
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Anil Kumar Vijjamarri
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-14 11:35:51	ID requested
1	2023-10-24 13:32:26	announced
⏵ 2	2023-11-14 09:11:42	announced	2023-11-14: Updated project metadata.

Vijjamarri AK, Gupta N, Onu C, Niu X, Zhang F, Kumar R, Lin Z, Greenberg ML, Hinnebusch AG, mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability. Nucleic Acids Res, 51(17):9314-9336(2023) [pubmed]

10.6019/PXD042990;

submitter keyword: mRNA decay,S. cerevesiea, translation

Alan G Hinnebusch
contact affiliation	Head, Section on Nutrient Control of Gene Expression Building 6, Room 230 6 Center Drive Bethesda, MD 20892 Phone: 301-496-4480
contact email	alanh@mail.nih.gov
lab head
Anil Kumar Vijjamarri
contact affiliation	National Institutes of Health
contact email	anilkumar.vijjamarri@nih.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD042990
     1. Label: PRIDE project
     2. Name: Regulation of transcript abundance and translationny decapping activators Pat1 and Dhh1