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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 interprotein cross-linked peptides with &amp;lt;1% false discovery rate by mass spectrometry and genome-wide database searching. Nearly 60% of the interprotein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the \u03b4 and \u03b2\u2032 subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how \u03b4 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. Data are available via ProteomeXchange with identifier PXD006287.<\/jats:p>","DOI":"10.1021\/acs.jproteome.7b00068","type":"journal-article","created":{"date-parts":[[2017,5,18]],"date-time":"2017-05-18T06:55:43Z","timestamp":1495090543000},"page":"2457-2471","source":"Crossref","is-referenced-by-count":47,"title":["In-Culture Cross-Linking\nof Bacterial Cells Reveals\nLarge-Scale Dynamic Protein\u2013Protein Interactions at the Peptide\nLevel"],"prefix":"10.1021","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9894-6512","authenticated-orcid":true,"given":"Luitzen","family":"de Jong","sequence":"first","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward A.","family":"de Koning","sequence":"additional","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Winfried","family":"Roseboom","sequence":"additional","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hansuk","family":"Buncherd","sequence":"additional","affiliation":[{"name":"Prince of Songkla University , , ,","place":["Hatyai, Songkhla, Thailand, 90110"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin J.","family":"Wanner","sequence":"additional","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irena","family":"Dapic","sequence":"additional","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petra J.","family":"Jansen","sequence":"additional","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1483-436X","authenticated-orcid":true,"given":"Jan H.","family":"van Maarseveen","sequence":"additional","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9423-5596","authenticated-orcid":true,"given":"Garry L.","family":"Corthals","sequence":"additional","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter J.","family":"Lewis","sequence":"additional","affiliation":[{"name":"University of Newcastle , , , ,","place":["Callaghan, New South Wales, Australia, 2308"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9251-1403","authenticated-orcid":true,"given":"Leendert W.","family":"Hamoen","sequence":"additional","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris G.","family":"de Koster","sequence":"additional","affiliation":[{"name":"University of Amsterdam , , ,","place":["Amsterdam, The Netherlands, 1098 XH"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2017,5,18]]},"reference":[{"key":"2026090223340948000_cit1","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.tibs.2015.10.008","article-title":"Crosslinking\nand Mass Spectrometry: An Integrated Technology to Understand the\nStructure and Function of Molecular Machines","volume":"41","author":"Leitner","year":"2016","journal-title":"Trends Biochem. 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