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Molecular & Cellular Proteomics 8:2243-2255, 2009.
© 2009 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Proteomics Analysis of Nucleolar SUMO-1 Target Proteins upon Proteasome Inhibition^*,

Vittoria Matafora^,, Alfonsina D'Amato^,, Silvia Mori^¶,||, Francesco Blasi^¶,||,** and Angela Bachi^,

From the Biomolecular Mass Spectrometry Unit and
¶Molecular Genetics Unit, Division of Genomics and Cell Biology, San Raffaele Scientific Institute and
||Università Vita Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy and
** FIRC Institute of Molecular Oncology (IFOM), via Adamello 16, 20139 Milan, Italy

Many cellular processes are regulated by the coordination of several post-translational modifications that allow a very fine modulation of substrates. Recently it has been reported that there is a relationship between sumoylation and ubiquitination. Here we propose that the nucleolus is the key organelle in which SUMO-1 conjugates accumulate in response to proteasome inhibition. We demonstrated that, upon proteasome inhibition, the SUMO-1 nuclear dot localization is redirected to nucleolar structures. To better understand this process we investigated, by quantitative proteomics, the effect of proteasome activity on endogenous nucleolar SUMO-1 targets. 193 potential SUMO-1 substrates were identified, and interestingly in several purified SUMO-1 conjugates ubiquitin chains were found to be present, confirming the coordination of these two modifications. 23 SUMO-1 targets were confirmed by an in vitro sumoylation reaction performed on nuclear substrates. They belong to protein families such as small nuclear ribonucleoproteins, heterogeneous nuclear ribonucleoproteins, ribosomal proteins, histones, RNA-binding proteins, and transcription factor regulators. Among these, histone H1, histone H3, and p160 Myb-binding protein 1A were further characterized as novel SUMO-1 substrates. The analysis of the nature of the SUMO-1 targets identified in this study strongly indicates that sumoylation, acting in coordination with the ubiquitin-proteasome system, regulates the maintenance of nucleolar integrity.

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