TY - JOUR
T1 - Chromatin Central
T2 - Towards the comparative proteome by accurate mapping of the yeast proteomic environment
AU - Shevchenko, Anna
AU - Roguev, Assen
AU - Schaft, Daniel
AU - Buchanan, Luke
AU - Habermann, Bianca
AU - Sakalar, Cagri
AU - Thomas, Henrik
AU - Krogan, Nevan J.
AU - Shevchenko, Andrej
AU - Stewart, A. Francis
N1 - Funding Information:
We are grateful for members of the Shevchenko and Stewart groups for continuous support and stimulating discussions. Work in the Shevchenko lab was, in part, supported by the grant 1R01GM070986-01A1 from NIH NIGMS. Work in the Stewart lab was supported by funding from the BMBF (Bundesministerium für Bildung und Forschung), Proteomics Program, and the 6th Framework Program of the European Union, Integrated EuTRACC (LSHG-CT-2007-037445).
PY - 2008/11/28
Y1 - 2008/11/28
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=57949091054&partnerID=8YFLogxK
U2 - 10.1186/gb-2008-9-11-r167
DO - 10.1186/gb-2008-9-11-r167
M3 - Article
C2 - 19040720
AN - SCOPUS:57949091054
SN - 1474-7596
VL - 9
JO - Genome Biology
JF - Genome Biology
IS - 11
M1 - R167
ER -