PT  - JOURNAL ARTICLE
AU  - Luitzen de Jong
AU  - Edward A. de Koning
AU  - Winfried Roseboom
AU  - Hansuk Buncherd
AU  - Martin Wanner
AU  - Irena Dapic
AU  - Petra J. Jansen
AU  - Jan H. van Maarseveen
AU  - Garry L. Corthals
AU  - Peter J. Lewis
AU  - Leendert W. Hamoen
AU  - Chris G. de Koster
TI  - In culture cross-linking of bacterial cells reveals proteome scale dynamic protein-protein interactions at peptide level
AID  - 10.1101/094961
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 094961
4099  - http://biorxiv.org/content/early/2016/12/17/094961.short
4100  - http://biorxiv.org/content/early/2016/12/17/094961.full
AB  - Identification 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 rapidly cross-link cells in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). Using the Gram positive model bacterium Bacillus subtilis 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 β′ subunit of RNA polymerase close to the downstream DNA channel, providing insight into how δ regulates promoter selectivity and promotes RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth.