Journal Article

A global S. cerevisiae small ubiquitin‐related modifier (SUMO) system interactome

Lewicki, Megan C, Raught, Brian, Srikumar, Tharan

2013

Overview

The small ubiquitin‐related modifier (SUMO) system has been implicated in a number of biological functions, yet the individual components of the SUMO machinery involved in each of these activities were largely unknown. Here we report the first global SUMO system interactome. Using affinity purification coupled with mass spectrometry, we identify >450 protein–protein interactions surrounding the SUMO E2, Siz type E3s and SUMO‐specific proteases in budding yeast. Exploiting this information‐rich resource, we validate several Siz1‐ and Siz2‐specific substrates, identify a nucleoporin required for proper Ulp1 localization, and uncover important new roles for Ubc9 and Ulp2 in the maintenance of ribosomal DNA. A global physical interaction map of the SUMO system was generated to study its functional organization. This resource was used to validate several E3‐specific substrates and uncover novel roles for Ubc9 and Ulp2 in ribosomal DNA maintenance. Synopsis A global physical interaction map of the SUMO system was generated to study its functional organization. This resource was used to validate several E3‐specific substrates and uncover novel roles for Ubc9 and Ulp2 in ribosomal DNA maintenance. Affinity purification coupled to mass spectrometry was used to construct the first global SUMO interactome in yeast. The analysis identified more than 450 proteins interacting physically with the SUMO E2 Ubc9, the E3 ligases Siz1 and Siz2, and the SUMO‐specific proteases Ulp1 and Ulp2. Several Siz1‐ and Siz2‐specific substrates were validated, such as Cdc12, Sum1, Tup1, Top2, Rpb3 and Spt16. Follow‐up investigations revealed new important roles for Ubc9 and Ulp2 in ribosomal DNA maintenance.

• Publisher: Nature Publishing Group UK,John Wiley & Sons, Ltd,EMBO Press,European Molecular Biology Organization,Springer Nature
• Subject: affinity purification‐mass spectrometry / Biosynthesis / Cell Cycle - genetics / Cysteine Endopeptidases - genetics / Cysteine Endopeptidases - metabolism / Deoxyribonucleic acid / DNA / DNA, Ribosomal - genetics / EMBO31 / EMBO37 / Endopeptidases - genetics / Endopeptidases - metabolism / Experiments / Gene Expression Regulation, Fungal / Localization / Mass spectrometry / Mass spectroscopy / Microscopy / Nuclear Pore Complex Proteins - genetics / Nuclear Pore Complex Proteins - metabolism / Peptides / Protein interaction / Protein Interaction Mapping / Protein purification / Proteins / Proteomics / ribosomal DNA / S. cerevisiae / Saccharomyces cerevisiae - genetics / Saccharomyces cerevisiae - metabolism / Saccharomyces cerevisiae Proteins - genetics / Saccharomyces cerevisiae Proteins - metabolism / Signal Transduction / Small Ubiquitin-Related Modifier Proteins - genetics / Small Ubiquitin-Related Modifier Proteins - metabolism / Substrates / SUMO / Transcriptome / Ubiquitin / Ubiquitin - genetics / Ubiquitin - metabolism / Ubiquitin-Conjugating Enzymes - genetics / Ubiquitin-Conjugating Enzymes - metabolism / Ubiquitin-Protein Ligases - genetics / Ubiquitin-Protein Ligases - metabolism / Yeast