ArticleJournal of proteome research2017
In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein-Protein Interactions at the Peptide Level.
Article in Journal of proteome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin.Analytical chemistry · 2024Article
- Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo.Analytical chemistry · 2023Article
- Cross-linking mass spectrometry for mapping protein complex topologies in situ.Essays in biochemistry · 2023Article
- Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows.Nature communications · 2022Article
- Article
- Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae.Methods in molecular biology (Clifton, N.J.) · 2022Article
- RNA polymerases from low G+C gram-positive bacteria.Transcription · 2021Review
- Recent progress in mass spectrometry-based strategies for elucidating protein-protein interactions.Cellular and molecular life sciences : CMLS · 2021Review
- Advances in integrative structural biology: Towards understanding protein complexes in their cellular context.Computational and structural biotechnology journal · 2021Review
- The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling.Nature communications · 2020Article
- Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications.Chemical reviews · 2020Review
- Chance and pleiotropy dominate genetic diversity in complex bacterial environments.Nature microbiology · 2019Article
- Chemical cross-linking with mass spectrometry: a tool for systems structural biology.Current opinion in chemical biology · 2019Review
- A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein-protein interactions.Nature protocols · 2018Article
- Efficient and robust proteome-wide approaches for cross-linking mass spectrometry.Nature protocols · 2018Article
- Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology.Analytical chemistry · 2018Review
Corrections and comments
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Authors and funding
12 authors.
Funding
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Abstract
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 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 <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 δ and β' 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. Data are available via ProteomeXchange with identifier PXD006287.
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