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In silico APC/C substrate discovery reveals cell-cycle-dependent degradation of UHRF1 and other chromatin regulators

ABSTRACT: E3 ubiquitin ligases are the final regulatory enzymes in the ubiquitin cascade, responsible for choosing substrates for ubiquitylation. Despite their central role in governing ubiquitin pathways, technical challenges have precluded development of simple and robust methods to systematically map their substrates. The Anaphase Promoting Complex/Cyclosome (APC/C) is an E3 ligase and master regulator of cell cycle progression and genome maintenance. Here, we develop a sensitive and specific computational strategy to predict APC/C substrates, leveraging orthogonal features among known targets. Interestingly, chromatin regulatory proteins are enriched among putative substrates and we validate several here. We reveal detailed ubiquitylation mechanisms of a key reader and writer of histone modifications, UHRF1, and show that its degradation regulates cell cycle and D methylation maintenance. Our results uncover mechanisms underlying the coordination between cell cycle and the chromatin landscape, and suggest an extensive, post-translational crosstalk with far-reaching consequences in normal cell physiology and disease.

ORGANISM(S): Homo sapiens

PROVIDER: GSE137913 | GEO | 2020/09/23

REPOSITORIES: GEO

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Project description:Maintenance of protein homeostasis is essential for cellular survival. Central to this regulation are mechanisms of protein quality control in which misfolded proteins are recognized and degraded by the ubiquitin-proteasome system. One well-studied protein quality control pathway requires ER resident, multi-subunit E3 ubiquitin ligases that function in ER-associated degradation (ERAD). Using fission yeast, our lab identified the Golgi Dsc E3 ligase as required for proteolytic activation of fungal sterol regulatory element-binding protein (SREBP) transcription factors. The Dsc E3 ligase contains 5 integral membrane subunits and structurally resembles ERAD E3 ligases. S. cerevisiae codes for homologs of Dsc E3 ligase subunits, including the Dsc1 E3 ligase homolog Tul1 that functions in Golgi protein quality control. Interestingly, S. cerevisiae lacks SREBP homologs, indicating that novel Tul1 E3 ligase substrates exist. Here, we show that the S. cerevisiae Tul1 E3 ligase consists of Tul1, Dsc2, Dsc3, and Ubx3 and define Tul1 complex architecture. Tul1 E3 ligase function required each subunit as judged by vacuolar sorting of the artificial substrate Pep12D. Genetic studies demonstrated that Tul1 E3 ligase is required in cells lacking the multivesicular body pathway and under conditions of ubiquitin depletion. To identify candidate substrates, we used quantitative diGly proteomics to survey ubiquitylation in wild-type and tul1∆ cells. We identified 3,116 non-redundant ubiquitylation sites, including 10 sites in candidate substrates. Quantitative proteomics found 4.5% of quantified proteins (53/1172) to be differentially expressed in tul1∆ cells. Correcting the diGly dataset for these differences increased the number of Tul1-dependent ubiquitylation sites. Together, these data demonstrate that the Tul1 E3 ligase plays a minor role in protein homeostasis under non-stress conditions, consistent with functions in protein quality control. Furthermore, this quantitative diGly proteomics methodology serves as a robust platform to screen for stress conditions that require Tul1 activity.

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In silico APC/C substrate discovery reveals cell-cycle-dependent degradation of UHRF1 and other chromatin regulators

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