PXD009614

PXD009614 is an original dataset announced via ProteomeXchange.

Title	Quantitative analysis of the exoproteome from a Staphylococcus aureus LAC sarA mutant
Description	The staphylococcal accessory regulator A (sarA) impacts the extracellular accumulation of Staphylococcus aureus virulence factors at the level of intracellular production and extracellular protease-mediated degradation. To assess the relative impact of these two functions, we previously used a proteomics approach that measures protein abundance as a function of all proteoforms to demonstrate that mutation of sarA results in increased levels of extracellular proteases and assess the impact of this on the accumulation of S. aureus exoproteins1. While this approach confirmed that protease-mediated degradation has a significant impact on the S. aureus exoproteome, it was potentially limited in that it did not take into account the possibility that large, stable proteolytic products from a given protein could result in false negatives when quantified by total proteoforms. Here, we present an expanded proteomics approach that utilizes a dual quantitative method for measuring abundance at both the total proteoform and full-length exoprotein levels. Specifically, proteins present in conditioned medium from overnight, stationary phase cultures of the USA300 strain LAC, an isogenic sarA mutant, and a sarA mutant unable to produce any of the known extracellular proteases (sarA/protease) were resolved using one-dimensional gel electrophoresis. Using methods that focus on total proteoforms vs. methods that focus specifically on full-length proteins, quantitative proteomic comparisons of sarA vs sarA/protease mutants identified proteins that were degraded in a protease dependent manner owing to mutation of sarA, while comparisons of a sarA/protease mutant vs the LAC parent strain identified proteins in which abundance was altered in a sarA mutant in a protease-independent manner. Furthermore, the proteins uniquely identified by the full-length data analysis approach eliminated false negatives observed in the total proteoform analysis. This approach provided for a more comprehensive and robust analysis of the impact of mutating sarA and protease-mediated degradation on the S. aureus exoproteome.
HostingRepository	PRIDE
AnnounceDate	2018-11-21
AnnouncementXML	Submission_2018-11-21_06:01:52.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD009614
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Stephanie Byrum
SpeciesList	scientific name: Staphylococcus aureus; NCBI TaxID: 1280;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-04-26 03:15:56	ID requested
⏵ 1	2018-11-21 06:01:53	announced

Byrum SD, Loughran AJ, Beenken KE, Orr LM, Storey AJ, Mackintosh SG, Edmondson RD, Tackett AJ, Smeltzer MS, Label-Free Proteomic Approach to Characterize Protease-Dependent and -Independent Effects of sarA Inactivation on the Staphylococcus aureus Exoproteome. J Proteome Res, 17(10):3384-3395(2018) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: protease, proteolysis, Staphylococcus aureus, sarA, GelCMS

Alan J. Tackett
contact affiliation	Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR 72205, USA Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72205, USA
contact email	ajtackett@uams.edu
lab head
Stephanie Byrum
contact affiliation	UAMS
contact email	sbyrum@uams.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/2018/11/PXD009614

PRIDE project URI

• PRIDE
  1. PXD009614
     1. Label: PRIDE project
     2. Name: Quantitative analysis of the exoproteome from a Staphylococcus aureus LAC sarA mutant