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PXD006287

PXD006287 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIn culture cross-linking of bacterial cells reveals large scale dynamic protein-protein interactions at the peptide level.
DescriptionIdentification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram positive model bacterium Bacillus subtilis as an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species, Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG. We were able to identify 82 unique inter-protein cross-linked peptides with less than a 1% false discovery rate by mass spectrometry and genome-wide data base searching. Nearly 60% of the inter-protein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the δ and βʹ subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how δ might regulate promoter selectivity and promote RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth.
HostingRepositoryPRIDE
AnnounceDate2017-05-23
AnnouncementXMLSubmission_2017-05-23_00:40:12.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterWinfried Roseboom
SpeciesList scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308;
ModificationListiodoacetamide derivatized residue
InstrumentBruker Daltonics amaZon series
Dataset History
RevisionDatetimeStatusChangeLog Entry
02017-04-11 08:24:20ID requested
12017-05-23 00:40:13announced
Publication List
de Jong L, de Koning EA, Roseboom W, Buncherd H, Wanner MJ, Dapic I, Jansen PJ, van Maarseveen JH, Corthals GL, Lewis PJ, Hamoen LW, de Koster CG, In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein-Protein Interactions at the Peptide Level. J Proteome Res, 16(7):2457-2471(2017) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: Bacillus subtilis, Escherichia coli, BAMG (bis(succinimidyl)-3-azidomethyl-glutarate), in vivo cross-linking, membrane permeability, RNA polymerase, translation, transcription.
Contact List
Chris de Koster
contact affiliationMass spectrometry of Biomacromolecules, SILS, Universiteit van Amsterdam, The Netherlands
contact emailC.G.deKoster@uva.nl
lab head
Winfried Roseboom
contact affiliationUniversiteit van Amsterdam
contact emailw.roseboom@uva.nl
dataset submitter
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