In-Culture Cross-Linking of Bacterial Cells Reveals Large-Scale Dynamic Protein-Protein Interactions at the Peptide Level

Journal of Proteome Research
Luitzen de JongChris G de Koster

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 functiona...Continue Reading

References

Apr 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·J PeroT D Fox
Oct 1, 1985·Analytical Biochemistry·P K SmithD C Klenk
Sep 1, 1974·Journal of Bacteriology·F C NeidhardtD F Smith
May 21, 1999·The Journal of Biological Chemistry·F J López de SaroJ D Helmann
Dec 11, 2003·Microbiology and Molecular Biology Reviews : MMBR·Hiroshi Nikaido
Jun 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·John E P SykaDonald F Hunt
Apr 26, 2007·Science Progress·Walid M El-Sharoud, Peter L Graumann
Jun 22, 2007·Nature·Dmitry G VassylyevIrina Artsimovitch
Jun 30, 2007·Chembiochem : a European Journal of Chemical Biology·Piotr T KasperLuitzen de Jong
Mar 11, 2008·Nature Methods·Oliver RinnerRuedi Aebersold
Aug 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Susan E CohenGraham C Walker
Jun 24, 2011·Molecular & Cellular Proteomics : MCP·Chunxiang ZhengJames E Bruce
Dec 16, 2011·Molecular & Cellular Proteomics : MCP·Johannes GraumannMatthias Mann
Mar 6, 2012·The EMBO Journal·Takeshi YokoyamaRajendra K Agrawal
Jul 10, 2012·Nature Methods·Bing YangMeng-Qiu Dong
Jul 10, 2012·Nature Methods·Thomas WalzthoeniRuedi Aebersold
Jan 29, 2013·Molecular & Cellular Proteomics : MCP·Juan D ChavezJames E Bruce
Feb 8, 2013·The Journal of Biological Chemistry·Katsuhiko S Murakami
May 1, 2013·Proceedings of the National Academy of Sciences of the United States of America·Crystal E FaganChristine M Dunham
Jul 23, 2013·Chembiochem : a European Journal of Chemical Biology·Veronika PapouškováLukáš Žídek
Nov 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Brian BaeSeth A Darst
Dec 18, 2013·Molecular & Cellular Proteomics : MCP·Michael J TrnkaRobert J Chalkley
Feb 13, 2014·Nucleic Acids Research·Jana WiedermannováLibor Krásny
Sep 26, 2014·Molecular & Cellular Proteomics : MCP·Robyn M KaakeLan Huang
Feb 19, 2015·Nucleic Acids Research·Cong MaPeter J Lewis
Apr 17, 2015·FEMS Microbiology Reviews·Andy Weiss, Lindsey N Shaw
Apr 24, 2015·Nature Communications·Daniel SohmenDaniel N Wilson
Sep 28, 2015·Journal of Molecular Biology·G C P van ZundertA M J J Bonvin

❮ Previous
Next ❯

Citations

Aug 2, 2018·Expert Review of Proteomics·Sara Artigas-JerónimoMargarita Villar
Sep 14, 2020·Molecular Microbiology·Juha KurkelaTaina Tyystjärvi
Nov 18, 2018·Nature Protocols·Oleg KlykovRichard A Scheltema
Apr 3, 2019·Nature Microbiology·Lianet Noda-GarcíaDan S Tawfik
Jan 12, 2021·Computational and Structural Biotechnology Journal·Samantha J ZieglerYannick J Bomble
Apr 4, 2021·Biochimica Et Biophysica Acta. Proteins and Proteomics·Luitzen de JongGertjan Kramer
May 29, 2021·Cellular and Molecular Life Sciences : CMLS·Teck Yew LowChris Soon Heng Tan
Aug 21, 2018·Analytical Chemistry·Martial ReyJulia Chamot-Rooke
Aug 18, 2021·Transcription·Michael MillerPeter J Lewis
Nov 13, 2018·Analytical Chemistry·Huiming YuanYukui Zhang

❮ Previous
Next ❯

Methods Mentioned

BETA
affinity purification
cross-linking studies
gel filtration
Electrophoresis
protein assay
size exclusion chromatography

Software Mentioned

Reang
PyMol
BAMG
Bruker Daltonics DataAnalysis
Mascot Distiller
Mascot
HADDOCK2
Analyst
DeepView
QStar

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.