A proteome-wide approach identifies sumoylated substrate proteins in yeast

J Biol Chem. 2004 Oct 1;279(40):41346-51. doi: 10.1074/jbc.M407950200. Epub 2004 Jul 30.


The ubiquitin-related protein SUMO-1 is covalently attached to proteins by SUMO-1 ligases. We have performed a proteome-wide analysis of sumoylated substrate proteins in yeast. Employing the powerful affinity purification of Protein A-Smt3 (Smt3 is the yeast homologue of SUMO-1) from yeast lysates in combination with tandem liquid chromatography mass spectrometry, we have isolated potential Smt3-carrying substrate proteins involved in DNA replication and repair, chromatin remodeling, transcription activation, Pol-I, Pol-II, and Pol-III transcription, 5' pre-mRNA capping, 3' pre-mRNA processing, proteasome function, and tubulin folding. Employing tandem affinity purifications or a rapid biochemical assay referred to as "SUMO fingerprint," we showed that several subunits of RNA polymerases I, II, and III, members of the transcription repression and chromatin remodeling machineries previously not known to be sumoylated, are modified by SUMO-1. Thus, the identification of a broad range of SUMO-1 substrate proteins is expected to lead to further insight into the regulatory aspects of sumoylation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Affinity
  • Chromatography, High Pressure Liquid
  • Fungal Proteins / analysis
  • Fungal Proteins / isolation & purification*
  • Fungal Proteins / physiology*
  • Genetic Phenomena
  • Mass Spectrometry
  • Proteomics / methods*
  • Repressor Proteins
  • SUMO-1 Protein / analysis*
  • SUMO-1 Protein / physiology
  • Saccharomyces cerevisiae Proteins*
  • Small Ubiquitin-Related Modifier Proteins
  • Staphylococcal Protein A


  • Fungal Proteins
  • Repressor Proteins
  • SMT3 protein, S cerevisiae
  • SUMO-1 Protein
  • Saccharomyces cerevisiae Proteins
  • Small Ubiquitin-Related Modifier Proteins
  • Staphylococcal Protein A