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Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment

BACKGROUND: Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need...

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Autores principales: Shevchenko, Anna, Roguev, Assen, Schaft, Daniel, Buchanan, Luke, Habermann, Bianca, Sakalar, Cagri, Thomas, Henrik, Krogan, Nevan J, Shevchenko, Andrej, Stewart, A Francis
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614481/
https://www.ncbi.nlm.nih.gov/pubmed/19040720
http://dx.doi.org/10.1186/gb-2008-9-11-r167
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author Shevchenko, Anna
Roguev, Assen
Schaft, Daniel
Buchanan, Luke
Habermann, Bianca
Sakalar, Cagri
Thomas, Henrik
Krogan, Nevan J
Shevchenko, Andrej
Stewart, A Francis
author_facet Shevchenko, Anna
Roguev, Assen
Schaft, Daniel
Buchanan, Luke
Habermann, Bianca
Sakalar, Cagri
Thomas, Henrik
Krogan, Nevan J
Shevchenko, Andrej
Stewart, A Francis
author_sort Shevchenko, Anna
collection PubMed
description BACKGROUND: Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before comparative proteomics can be fruitful. RESULTS: The Saccharomyces cerevisiae proteome presents the highest quality proteomic data available. To evaluate the accuracy of these data, we intensively mapped a proteomic environment, termed 'Chromatin Central', which encompasses eight protein complexes, including the major histone acetyltransferases and deacetylases, interconnected by twelve proteomic hyperlinks. Using sequential tagging and a new method to eliminate background, we confirmed existing data but also uncovered new subunits and three new complexes, including ASTRA, which we suggest is a widely conserved aspect of telomeric maintenance, and two new variations of Rpd3 histone deacetylase complexes. We also examined the same environment in fission yeast and found a very similar architecture based on a scaffold of orthologues comprising about two-thirds of all proteins involved, whereas the remaining one-third is less constrained. Notably, most of the divergent hyperlinks were found to be due to gene duplications, hence providing a mechanism for the fixation of gene duplications in evolution. CONCLUSIONS: We define several prerequisites for comparative proteomics and apply them to examine a proteomic environment in unprecedented detail. We suggest that high resolution mapping of proteomic environments will deliver the highest quality data for comparative proteomics.
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spelling pubmed-26144812009-01-08 Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment Shevchenko, Anna Roguev, Assen Schaft, Daniel Buchanan, Luke Habermann, Bianca Sakalar, Cagri Thomas, Henrik Krogan, Nevan J Shevchenko, Andrej Stewart, A Francis Genome Biol Research BACKGROUND: Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before comparative proteomics can be fruitful. RESULTS: The Saccharomyces cerevisiae proteome presents the highest quality proteomic data available. To evaluate the accuracy of these data, we intensively mapped a proteomic environment, termed 'Chromatin Central', which encompasses eight protein complexes, including the major histone acetyltransferases and deacetylases, interconnected by twelve proteomic hyperlinks. Using sequential tagging and a new method to eliminate background, we confirmed existing data but also uncovered new subunits and three new complexes, including ASTRA, which we suggest is a widely conserved aspect of telomeric maintenance, and two new variations of Rpd3 histone deacetylase complexes. We also examined the same environment in fission yeast and found a very similar architecture based on a scaffold of orthologues comprising about two-thirds of all proteins involved, whereas the remaining one-third is less constrained. Notably, most of the divergent hyperlinks were found to be due to gene duplications, hence providing a mechanism for the fixation of gene duplications in evolution. CONCLUSIONS: We define several prerequisites for comparative proteomics and apply them to examine a proteomic environment in unprecedented detail. We suggest that high resolution mapping of proteomic environments will deliver the highest quality data for comparative proteomics. BioMed Central 2008 2008-11-28 /pmc/articles/PMC2614481/ /pubmed/19040720 http://dx.doi.org/10.1186/gb-2008-9-11-r167 Text en Copyright © 2008 Shevchenko et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Shevchenko, Anna
Roguev, Assen
Schaft, Daniel
Buchanan, Luke
Habermann, Bianca
Sakalar, Cagri
Thomas, Henrik
Krogan, Nevan J
Shevchenko, Andrej
Stewart, A Francis
Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
title Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
title_full Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
title_fullStr Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
title_full_unstemmed Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
title_short Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
title_sort chromatin central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614481/
https://www.ncbi.nlm.nih.gov/pubmed/19040720
http://dx.doi.org/10.1186/gb-2008-9-11-r167
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