Cargando…

Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries

Protein-correlation-profiling (PCP), in combination with quantitative proteomics, has emerged as a high-throughput method for the rapid identification of dynamic protein complexes in native conditions. While PCP has been successfully applied to soluble proteomes, characterization of the membrane int...

Descripción completa

Detalles Bibliográficos
Autores principales: Carlson, Michael Luke, Stacey, R Greg, Young, John William, Wason, Irvinder Singh, Zhao, Zhiyu, Rattray, David G, Scott, Nichollas, Kerr, Craig H, Babu, Mohan, Foster, Leonard J, Duong Van Hoa, Franck
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697469/
https://www.ncbi.nlm.nih.gov/pubmed/31364989
http://dx.doi.org/10.7554/eLife.46615
_version_ 1783444390927138816
author Carlson, Michael Luke
Stacey, R Greg
Young, John William
Wason, Irvinder Singh
Zhao, Zhiyu
Rattray, David G
Scott, Nichollas
Kerr, Craig H
Babu, Mohan
Foster, Leonard J
Duong Van Hoa, Franck
author_facet Carlson, Michael Luke
Stacey, R Greg
Young, John William
Wason, Irvinder Singh
Zhao, Zhiyu
Rattray, David G
Scott, Nichollas
Kerr, Craig H
Babu, Mohan
Foster, Leonard J
Duong Van Hoa, Franck
author_sort Carlson, Michael Luke
collection PubMed
description Protein-correlation-profiling (PCP), in combination with quantitative proteomics, has emerged as a high-throughput method for the rapid identification of dynamic protein complexes in native conditions. While PCP has been successfully applied to soluble proteomes, characterization of the membrane interactome has lagged, partly due to the necessary use of detergents to maintain protein solubility. Here, we apply the peptidisc, a ‘one-size fits all’ membrane mimetic, for the capture of the Escherichia coli cell envelope proteome and its high-resolution fractionation in the absence of detergent. Analysis of the SILAC-labeled peptidisc library via PCP allows generation of over 4900 possible binary interactions out of >700,000 random associations. Using well-characterized membrane protein systems such as the SecY translocon, the Bam complex and the MetNI transporter, we demonstrate that our dataset is a useful resource for identifying transient and surprisingly novel protein interactions. For example, we discover a trans-periplasmic supercomplex comprising subunits of the Bam and Sec machineries, including membrane-bound chaperones YfgM and PpiD. We identify RcsF and OmpA as bone fide interactors of BamA, and we show that MetQ association with the ABC transporter MetNI depends on its N-terminal lipid anchor. We also discover NlpA as a novel interactor of MetNI complex. Most of these interactions are largely undetected by standard detergent-based purification. Together, the peptidisc workflow applied to the proteomic field is emerging as a promising novel approach to characterize membrane protein interactions under native expression conditions and without genetic manipulation.
format Online
Article
Text
id pubmed-6697469
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher eLife Sciences Publications, Ltd
record_format MEDLINE/PubMed
spelling pubmed-66974692019-08-19 Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries Carlson, Michael Luke Stacey, R Greg Young, John William Wason, Irvinder Singh Zhao, Zhiyu Rattray, David G Scott, Nichollas Kerr, Craig H Babu, Mohan Foster, Leonard J Duong Van Hoa, Franck eLife Biochemistry and Chemical Biology Protein-correlation-profiling (PCP), in combination with quantitative proteomics, has emerged as a high-throughput method for the rapid identification of dynamic protein complexes in native conditions. While PCP has been successfully applied to soluble proteomes, characterization of the membrane interactome has lagged, partly due to the necessary use of detergents to maintain protein solubility. Here, we apply the peptidisc, a ‘one-size fits all’ membrane mimetic, for the capture of the Escherichia coli cell envelope proteome and its high-resolution fractionation in the absence of detergent. Analysis of the SILAC-labeled peptidisc library via PCP allows generation of over 4900 possible binary interactions out of >700,000 random associations. Using well-characterized membrane protein systems such as the SecY translocon, the Bam complex and the MetNI transporter, we demonstrate that our dataset is a useful resource for identifying transient and surprisingly novel protein interactions. For example, we discover a trans-periplasmic supercomplex comprising subunits of the Bam and Sec machineries, including membrane-bound chaperones YfgM and PpiD. We identify RcsF and OmpA as bone fide interactors of BamA, and we show that MetQ association with the ABC transporter MetNI depends on its N-terminal lipid anchor. We also discover NlpA as a novel interactor of MetNI complex. Most of these interactions are largely undetected by standard detergent-based purification. Together, the peptidisc workflow applied to the proteomic field is emerging as a promising novel approach to characterize membrane protein interactions under native expression conditions and without genetic manipulation. eLife Sciences Publications, Ltd 2019-07-31 /pmc/articles/PMC6697469/ /pubmed/31364989 http://dx.doi.org/10.7554/eLife.46615 Text en © 2019, Carlson et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Biochemistry and Chemical Biology
Carlson, Michael Luke
Stacey, R Greg
Young, John William
Wason, Irvinder Singh
Zhao, Zhiyu
Rattray, David G
Scott, Nichollas
Kerr, Craig H
Babu, Mohan
Foster, Leonard J
Duong Van Hoa, Franck
Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries
title Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries
title_full Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries
title_fullStr Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries
title_full_unstemmed Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries
title_short Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries
title_sort profiling the escherichia coli membrane protein interactome captured in peptidisc libraries
topic Biochemistry and Chemical Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697469/
https://www.ncbi.nlm.nih.gov/pubmed/31364989
http://dx.doi.org/10.7554/eLife.46615
work_keys_str_mv AT carlsonmichaelluke profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT staceyrgreg profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT youngjohnwilliam profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT wasonirvindersingh profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT zhaozhiyu profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT rattraydavidg profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT scottnichollas profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT kerrcraigh profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT babumohan profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT fosterleonardj profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries
AT duongvanhoafranck profilingtheescherichiacolimembraneproteininteractomecapturedinpeptidisclibraries