title: Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.
abstract: 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.
authors.affiliation: MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. ashevche@mpi-cbg.de
authors.forename: Anna
authors.initials: A
authors.lastname: Shevchenko
authors.forename: Assen
authors.initials: A
authors.lastname: Roguev
authors.forename: Daniel
authors.initials: D
authors.lastname: Schaft
authors.forename: Luke
authors.initials: L
authors.lastname: Buchanan
authors.forename: Bianca
authors.initials: B
authors.lastname: Habermann
authors.forename: Cagri
authors.initials: C
authors.lastname: Sakalar
authors.forename: Henrik
authors.initials: H
authors.lastname: Thomas
authors.forename: Nevan J
authors.initials: NJ
authors.lastname: Krogan
authors.forename: Andrej
authors.initials: A
authors.lastname: Shevchenko
authors.forename: A Francis
authors.initials: AF
authors.lastname: Stewart
mesh_terms: D025941:Protein Interaction Mapping; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis*; D012568:Schizosaccharomyces / Q000737:chemistry*; D029702:Schizosaccharomyces pombe Proteins / Q000032:analysis*
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D029702:Schizosaccharomyces pombe Proteins