title: An inventory of yeast proteins associated with nucleolar and ribosomal components.
abstract: BACKGROUND
  Although baker's yeast is a primary model organism for research on eukaryotic ribosome assembly and nucleoli, the list of its proteins that are functionally associated with nucleoli or ribosomes is still incomplete. We trained a naïve Bayesian classifier to predict novel proteins that are associated with yeast nucleoli or ribosomes based on parts lists of nucleoli in model organisms and large-scale protein interaction data sets. Phylogenetic profiling and gene expression analysis were carried out to shed light on evolutionary and regulatory aspects of nucleoli and ribosome assembly.
  
  
  RESULTS
  We predict that, in addition to 439 known proteins, a further 62 yeast proteins are associated with components of the nucleolus or the ribosome. The complete set comprises a large core of archaeal-type proteins, several bacterial-type proteins, but mostly eukaryote-specific inventions. Expression of nucleolar and ribosomal genes tends to be strongly co-regulated compared to other yeast genes.
  
  
  CONCLUSIONS
  The number of proteins associated with nucleolar or ribosomal components in yeast is at least 14% higher than known before. The nucleolus probably evolved from an archaeal-type ribosome maturation machinery by recruitment of several bacterial-type and mostly eukaryote-specific factors. Not only expression of ribosomal protein genes, but also expression of genes encoding the 90S processosome, are strongly co-regulated and both regulatory programs are distinct from each other.
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany. eike.staub@nucleolus.net
authors.forename: Eike
authors.initials: E
authors.lastname: Staub
authors.forename: Sebastian
authors.initials: S
authors.lastname: Mackowiak
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
mesh_terms: D029681:Arabidopsis Proteins / Q000235:genetics; D001499:Bayes Theorem; D002466:Cell Nucleolus / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D009687:Nuclear Proteins / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics; D012270:Ribosomes / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D009687:Nuclear Proteins; D012269:Ribosomal Proteins; D029701:Saccharomyces cerevisiae Proteins