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A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria

Protein cross-linking and the analysis of cross-linked peptides by mass spectrometry is currently receiving much attention. Not only is this approach applied to isolated complexes to provide information about spatial arrangements of proteins, but it is also increasingly applied to entire cells and t...

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Autores principales: Linden, Andreas, Deckers, Markus, Parfentev, Iwan, Pflanz, Ralf, Homberg, Bettina, Neumann, Piotr, Ficner, Ralf, Rehling, Peter, Urlaub, Henning
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The American Society for Biochemistry and Molecular Biology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338081/
https://www.ncbi.nlm.nih.gov/pubmed/32332106
http://dx.doi.org/10.1074/mcp.RA120.002028
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author Linden, Andreas
Deckers, Markus
Parfentev, Iwan
Pflanz, Ralf
Homberg, Bettina
Neumann, Piotr
Ficner, Ralf
Rehling, Peter
Urlaub, Henning
author_facet Linden, Andreas
Deckers, Markus
Parfentev, Iwan
Pflanz, Ralf
Homberg, Bettina
Neumann, Piotr
Ficner, Ralf
Rehling, Peter
Urlaub, Henning
author_sort Linden, Andreas
collection PubMed
description Protein cross-linking and the analysis of cross-linked peptides by mass spectrometry is currently receiving much attention. Not only is this approach applied to isolated complexes to provide information about spatial arrangements of proteins, but it is also increasingly applied to entire cells and their organelles. As in quantitative proteomics, the application of isotopic labeling further makes it possible to monitor quantitative changes in the protein-protein interactions between different states of a system. Here, we cross-linked mitochondria from Saccharomyces cerevisiae grown on either glycerol- or glucose-containing medium to monitor protein-protein interactions under non-fermentative and fermentative conditions. We investigated qualitatively the protein-protein interactions of the 400 most abundant proteins applying stringent data-filtering criteria, i.e. a minimum of two cross-linked peptide spectrum matches and a cut-off in the spectrum scoring of the used search engine. The cross-linker BS3 proved to be equally suited for connecting proteins in all compartments of mitochondria when compared with its water-insoluble but membrane-permeable derivative DSS. We also applied quantitative cross-linking to mitochondria of both the growth conditions using stable-isotope labeled BS3. Significant differences of cross-linked proteins under glycerol and glucose conditions were detected, however, mainly because of the different copy numbers of these proteins in mitochondria under both the conditions. Results obtained from the glycerol condition indicate that the internal NADH:ubiquinone oxidoreductase Ndi1 is part of an electron transport chain supercomplex. We have also detected several hitherto uncharacterized proteins and identified their interaction partners. Among those, Min8 was found to be associated with cytochrome c oxidase. BN-PAGE analyses of min8Δ mitochondria suggest that Min8 promotes the incorporation of Cox12 into cytochrome c oxidase.
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spelling pubmed-73380812021-07-01 A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria Linden, Andreas Deckers, Markus Parfentev, Iwan Pflanz, Ralf Homberg, Bettina Neumann, Piotr Ficner, Ralf Rehling, Peter Urlaub, Henning Mol Cell Proteomics Research Protein cross-linking and the analysis of cross-linked peptides by mass spectrometry is currently receiving much attention. Not only is this approach applied to isolated complexes to provide information about spatial arrangements of proteins, but it is also increasingly applied to entire cells and their organelles. As in quantitative proteomics, the application of isotopic labeling further makes it possible to monitor quantitative changes in the protein-protein interactions between different states of a system. Here, we cross-linked mitochondria from Saccharomyces cerevisiae grown on either glycerol- or glucose-containing medium to monitor protein-protein interactions under non-fermentative and fermentative conditions. We investigated qualitatively the protein-protein interactions of the 400 most abundant proteins applying stringent data-filtering criteria, i.e. a minimum of two cross-linked peptide spectrum matches and a cut-off in the spectrum scoring of the used search engine. The cross-linker BS3 proved to be equally suited for connecting proteins in all compartments of mitochondria when compared with its water-insoluble but membrane-permeable derivative DSS. We also applied quantitative cross-linking to mitochondria of both the growth conditions using stable-isotope labeled BS3. Significant differences of cross-linked proteins under glycerol and glucose conditions were detected, however, mainly because of the different copy numbers of these proteins in mitochondria under both the conditions. Results obtained from the glycerol condition indicate that the internal NADH:ubiquinone oxidoreductase Ndi1 is part of an electron transport chain supercomplex. We have also detected several hitherto uncharacterized proteins and identified their interaction partners. Among those, Min8 was found to be associated with cytochrome c oxidase. BN-PAGE analyses of min8Δ mitochondria suggest that Min8 promotes the incorporation of Cox12 into cytochrome c oxidase. The American Society for Biochemistry and Molecular Biology 2020-07 2020-04-24 /pmc/articles/PMC7338081/ /pubmed/32332106 http://dx.doi.org/10.1074/mcp.RA120.002028 Text en © 2020 Linden et al. Author's Choice—Final version open access under the terms of the Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0) .
spellingShingle Research
Linden, Andreas
Deckers, Markus
Parfentev, Iwan
Pflanz, Ralf
Homberg, Bettina
Neumann, Piotr
Ficner, Ralf
Rehling, Peter
Urlaub, Henning
A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
title A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
title_full A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
title_fullStr A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
title_full_unstemmed A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
title_short A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria
title_sort cross-linking mass spectrometry approach defines protein interactions in yeast mitochondria
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338081/
https://www.ncbi.nlm.nih.gov/pubmed/32332106
http://dx.doi.org/10.1074/mcp.RA120.002028
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