Ubiquitin and proteasome pathways

The paper characterizes the differential distribution and targets of Sumo paralogs in the mouse brain using knock-in mouse models and proteomic analysis.

The paper predicts SUMOylation targets in Drosophila melanogaster using sequence homology from human and mouse SUMOylation data, identifying motifs, protein families, and functional preferences.

This study shows TRIM21 can degrade lysine-less substrates without autoubiquitination, revealing a non-canonical ubiquitination mechanism for Trim-Away.

This study identifies UBE2 family members that interact with MuRF1 to mediate ubiquitylation, revealing a two-step mechanism for mono- and poly-ubiquitin chain formation.

The paper evaluates twenty-four anti-SUMO monoclonal antibodies for their sensitivity, specificity, and ability to detect different SUMO conjugation states across multiple assays.

This study identifies an FBXO7 mutation that disrupts its interaction with PI31, affecting proteasome and mitochondrial function in patient cells.

ReporterSeq identifies Trr1 and ribosomal proteins as novel regulators of the UPS master regulator Rpn4 in yeast under stress conditions.

This study shows that ATR promotes Api5 degradation via the ubiquitin-proteasome pathway through FBXW2, thereby regulating apoptosis in response to DNA damage.

The paper identifies Caf1 as a novel ubiquitin shuttle factor that facilitates the degradation of ubiquitin-modified proteins by the 26S proteasome in yeast.

This study identifies functionally conserved roles of Drosophila SINA and human SIAH1/2 in RAS/EGFR pathway regulation, showing their efficacy in blocking neuronal cell fate determination in Drosophila.

The paper identifies two novel Legionella OTU-like deubiquitinases, LotB and LotC, and describes their structural and functional differences in ubiquitin chain cleavage during infection.

This study identifies Ccr4 as a novel shuttle factor that facilitates ubiquitin-dependent proteolysis by the 26S proteasome in yeast.

This paper develops and characterizes nanobodies as first-in-class inhibitors of NEDP1, showing high-affinity binding and specific inhibition of its deconjugating activity.

The paper identifies 2747 SUMO modification sites in budding yeast meiosis, revealing SUMO's role in chromosome organization and recombination.

The paper identifies a redox-sensitive site in Cdc48 that regulates its localization and activity during oxidative stress and aging in yeast.

This study identifies Gcn5 and Ubp8-dependent ubiquitylation of glycolytic enzymes in yeast, linking epigenetic regulation to metabolic function.

The paper shows that NEDP1 regulates the NEDD8 cycle upon DNA damage, modulating HSP70 ATPase activity to promote apoptosis and identifies this as relevant in hepatocellular carcinoma.

This study identifies a family of FYVE-type-RING finger proteins as E3 ligases that cooperate with Ubc13-Mms2 in K63-polyubiquitylation at internal membranes across species.

The paper identifies degrons and E3 ligase alterations across cancer types, finding that at least 1 in 7 driver mutations affect these components.

The paper shows that mitotic replisome disassembly in vertebrates depends on TRAIP-mediated ubiquitylation of Mcm7 and p97/VCP activity, and is conserved across higher eukaryotes.

The paper identifies USP21 and OTUD3 as deubiquitylating enzymes that counteract ZNF598-mediated ribosomal ubiquitylation, facilitating ribosome-associated quality control.

The paper identifies PSMA3 as a receptor for 20S proteasome-mediated degradation of intrinsically disordered proteins (IDPs) and shows its C-terminal fragment inhibits IDP degradation.

iSUMO integrates sequence and protein features to predict functional SUMOylation events, identifying more targets in human and yeast than existing tools at the same false positive rate.

The paper re-analyzes protein half-life data in yeast to provide consistent estimates, finding that protein stability correlates with abundance and function.