High-definition macromolecular composition of yeast RNA-processing complexes

Mol Cell. 2004 Jan 30;13(2):225-39. doi: 10.1016/s1097-2765(04)00003-6.


A remarkably large collection of evolutionarily conserved proteins has been implicated in processing of noncoding RNAs and biogenesis of ribonucleoproteins. To better define the physical and functional relationships among these proteins and their cognate RNAs, we performed 165 highly stringent affinity purifications of known or predicted RNA-related proteins from Saccharomyces cerevisiae. We systematically identified and estimated the relative abundance of stably associated polypeptides and RNA species using a combination of gel densitometry, protein mass spectrometry, and oligonucleotide microarray hybridization. Ninety-two discrete proteins or protein complexes were identified comprising 489 different polypeptides, many associated with one or more specific RNA molecules. Some of the pre-rRNA-processing complexes that were obtained are discrete sub-complexes of those previously described. Among these, we identified the IPI complex required for proper processing of the ITS2 region of the ribosomal RNA primary transcript. This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Blotting, Northern
  • Fungal Proteins / chemistry
  • Mass Spectrometry
  • Models, Biological
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic
  • RNA / chemistry*
  • RNA / metabolism
  • RNA Processing, Post-Transcriptional*
  • RNA, Ribosomal / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / physiology
  • Sequence Homology, Amino Acid
  • Time Factors


  • Fungal Proteins
  • RNA, Ribosomal
  • RNA