PXD009592

PXD009592 is an original dataset announced via ProteomeXchange.

Title	A proteomics approach to profiling the temporal translational response to stress and growth
Description	One major knowledge gap in systems biology is the quantification of dynamic protein synthesis rates in response to cell perturbation. To address this gap, we have developed MITNCAT, multiplex isotope tagging / non-canonical amino acid tagging, a novel method enabling the robust quantification of proteome-wide protein synthesis rates with high temporal resolution (15-30 minutes) across multiple time points or treatment conditions, in a single analysis. MITNCAT combines multiplexed isobaric mass tagging with bioorthogonal non-canonical amino acid tagging (BONCAT) to label newly synthesized proteins with azidohomoalanine (Aha) and pulsed SILAC (pSILAC), thus providing enrichment and multiplexed quantification of newly synthesized proteins. We demonstrate the application of MITNCAT to quantify altered protein synthesis rates following induction of the unfolded protein response (UPR) and epidermal growth factor (EGF) stimulation. Eliciting the UPR by blocking N-glycosylation results in a global down-regulation of protein synthesis, with stronger down-regulation of proteins involved in the glycolysis pathway and protein synthesis machinery (ribosomal proteins, initiation factors, and elongation factors), but up-regulation of several key protein-folding chaperones. MITNCAT enables the quantification of waves of temporally distinct protein synthesis in response to EGF stimulation, with altered protein synthesis on dozens of proteins detectable in the first 15 minutes. Comparison of protein synthesis with RNA sequencing and ribosome footprinting allowed the distinction between protein synthesis driven by an increase in transcription versus that driven by an increase in translational efficiency. Temporal delays between ribosome occupancy and protein synthesis were observed and found to correlate with altered codon usage in significantly delayed proteins.
HostingRepository	PRIDE
AnnounceDate	2018-12-04
AnnouncementXML	Submission_2018-12-04_08:36:38.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Daniel Rothenberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-04-24 08:40:22	ID requested
⏵ 1	2018-12-04 08:36:40	announced

Rothenberg DA, Taliaferro JM, Huber SM, Begley TJ, Dedon PC, White FM, A Proteomics Approach to Profiling the Temporal Translational Response to Stress and Growth. iScience, 9():367-381(2018) [pubmed]

curator keyword: Biological

submitter keyword: Translation, Translatome, Synthesis

Forest White
contact affiliation	Massachusetts Institute of Technology, Koch Inistitute for Integrative Cancer Research, Department of Biological Engineering
contact email	fwhite@mit.edu
lab head
Daniel Rothenberg
contact affiliation	MIT
contact email	drothenberg0121@gmail.com
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/2018/12/PXD009592

PRIDE project URI

• PRIDE
  1. PXD009592
     1. Label: PRIDE project
     2. Name: A proteomics approach to profiling the temporal translational response to stress and growth