<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <ProteomeXchangeDataset id="PXD033703" formatVersion="1.4.0" xsi:noNamespaceSchemaLocation="proteomeXchange-1.4.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <CvList> <Cv fullName="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" id="MS"/> <Cv fullName="PSI-MOD" uri="https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo" id="MOD"/> <Cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/> </CvList> <ChangeLog> <ChangeLogEntry date="2023-11-14">Updated project metadata.</ChangeLogEntry> </ChangeLog> <DatasetSummary announceDate="2023-11-14" hostingRepository="PRIDE" title="The proteomic and transcriptomic landscapes altered by Rgg2/3 activity in Streptococcus pyogenes"> <Description>Streptococcus pyogenes, otherwise known as Group A Streptococcus (GAS), is an important and highly adaptable human pathogen with the ability to cause both superficial and severe diseases. Understanding how S. pyogenes senses and responds to its environment will likely aid in determining how it causes a breadth of diseases. One regulatory network involved in GAS’s ability to sense and respond to the changing environment is the Rgg2/3 quorum sensing (QS) system, which responds to metal and carbohydrate availability and regulates changes to the bacterial surface. To better understand the impact of Rgg2/3 QS on S. pyogenes physiology, we performed RNA-seq and TMT (tandem mass tag)-LC-MS/MS analysis on cells in which this system was induced with SHP pheromone or disrupted. Primary findings confirmed that pheromone stimulation in wildtype cultures is limited to the induction of operons whose promoters contain previously determined Rgg2/3 binding sequences. However, a deletion mutant of rgg3, a strain that endogenously produces elevated amounts of pheromone, led to extended alterations of the transcriptome and proteome, ostensibly by stress-induced pathways. Under such exaggerated pheromone conditions, a connection was identified between Rgg2/3 and the stringent response. Mutation of relA, the bifunctional guanosine tetra- and penta-phosphate nucleoside synthetase/hydrolase, and alarmone synthase genes sasA and sasB, impacted culture doubling times and disabled induction of Rgg2/3 in response to mannose, while manipulation of Rgg2/3 signaling modestly altered nucleotide levels. Our findings indicate that excessive pheromone production or exposure places stress on GAS resulting in an indirect altered proteome and transcriptome beyond primary pheromone signaling. </Description> <ReviewLevel> <cvParam cvRef="MS" accession="MS:1002854" name="Peer-reviewed dataset"/> </ReviewLevel> <RepositorySupport> <cvParam cvRef="MS" accession="MS:1002856" name="Supported dataset by repository"/> </RepositorySupport> </DatasetSummary> <DatasetIdentifierList> <DatasetIdentifier> <cvParam cvRef="MS" accession="MS:1001919" name="ProteomeXchange accession number" value="PXD033703"/> <cvParam cvRef="MS" accession="MS:1001921" name="ProteomeXchange accession number version number" value="2"/> </DatasetIdentifier> <DatasetIdentifier> <cvParam cvRef="MS" accession="MS:1001922" name="Digital Object Identifier (DOI)" value="10.6019/PXD033703"/> </DatasetIdentifier> </DatasetIdentifierList> <DatasetOriginList> <DatasetOrigin> <cvParam cvRef="MS" accession="MS:1002868" name="Original data"/> </DatasetOrigin> </DatasetOriginList> <SpeciesList> <Species> <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Streptococcus pyogenes NZ131"/> <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="471876"/> </Species> </SpeciesList> <InstrumentList> <Instrument id="Instrument_1"> <cvParam cvRef="MS" accession="MS:1001742" name="LTQ Orbitrap Velos"/> </Instrument> </InstrumentList> <ModificationList> <cvParam cvRef="MS" accession="MS:1002864" name="No PTMs are included in the dataset"/> </ModificationList> <ContactList> <Contact id="project_submitter"> <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Britta Rued"/> <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="brued@uic.edu"/> <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="University of Illinois at Chicago"/> <cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/> </Contact> <Contact id="project_lab_head"> <cvParam cvRef="MS" accession="MS:1002332" name="lab head"/> <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Michael Federle"/> <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="mfederle@uic.edu"/> <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="University of Illinois at Chicago"/> </Contact> </ContactList> <PublicationList> <Publication id="DOI-10_6019_PXD033703"> <cvParam cvRef="MS" accession="MS:1001922" name="Digital Object Identifier (DOI)" value="10.6019/PXD033703"/> </Publication> </PublicationList> <KeywordList> <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="Rgg3,Streptococcus pyogenes, Rgg2, quorum sensing"/> </KeywordList> <FullDatasetLinkList> <FullDatasetLink> <cvParam cvRef="MS" accession="MS:1002852" name="Dataset FTP location" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/10/PXD033703"/> </FullDatasetLink> <FullDatasetLink> <cvParam 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