Ubiquitin and proteasome pathways

This study identifies JOSD1 as a deubiquitinase that mitigates hepatic proteotoxicity by stabilizing SOCS1 and enhancing cell survival under proteasome inhibitor stress.

This study shows that nucleic acids can be ubiquitylated by DTX3L, an E3 ligase, and this modification is reversible by DUBs like USP2 and SARS-CoV-2 PLpro.

The paper investigates the mechanism of action of the USP1 inhibitor KSQ-4279 using biochemical assays and cryo-EM, showing it binds to the same site as ML323 but alters protein structure differently.

This study shows that polyubiquitinated substrates modulate UBQLN2 phase separation in a linkage-dependent manner, affecting proteasome activity and deubiquitination.

This study identifies the structural requirements of MIB1 for ubiquitin transfer in Notch signaling, showing that RING3 is essential for catalytic activity and dimerization.

This study identifies PA28γ's role in promoting oral squamous cell carcinoma progression by enhancing mitochondrial function through interaction with C1QBP.

This study shows bacteria have a complete ubiquitination pathway similar to eukaryotes, with structural and functional parallels to eukaryotic systems.

The paper identifies USP43 as a deubiquitinating enzyme that enhances HIF-1 nuclear accumulation and target gene binding through interaction with 14-3-3 proteins under hypoxia.

This study shows that USP9X stabilizes RIT1 protein and that its depletion reduces RIT1 abundance and sensitizes cells to EGFR inhibitors.

This study shows that DTX3L ubiquitinates single-stranded DNA and RNA, expanding the known substrates of ubiquitination beyond proteins.

The paper identifies high-impact DUBs and their substrates using Xenopus egg extract and proteomics, revealing substrate characteristics influencing DUB specificity.

This paper identifies NopD as a rhizobial effector with deconjugation activities against SUMO, ubiquitin, and Nedd8, revealing its structural basis for substrate specificity.

This study investigates how glycine-rich sequences affect proteasome unfolding by positioning them relative to a folded domain, revealing that proximity to the domain reduces unfolding efficiency.

This study introduces proteome birthdating to measure protein age and finds that ubiquitinated proteins are predominantly newly synthesized, with distinct age distributions across cellular pathways.

The paper identifies branch- and length-specific ubiquitin chain interactors in humans and yeast, revealing how different Ub architectures are decoded by proteins.

The paper identifies TOPORS as a SUMO-targeted ubiquitin ligase (STUbL) essential for SUMO-dependent DNA-protein crosslink repair and stress responses, showing its cooperative function with RNF4.

The paper presents the cryo-EM structure of a pentameric KCTD5/CUL3/Gβγ E3 ubiquitin ligase complex, revealing its dynamic architecture and mechanism for ubiquitylating Gβγ.

The paper uses cryo-EM to visualize the assembly of the human 20S proteasome, revealing how chaperones and propeptides guide subunit incorporation and proteasome activation.

This study investigates Cu2+ ion binding and conformational flexibility in SUMO2, showing its impact on aggregation and non-covalent interactions with SIMs.

The paper investigates the proteasome-dependent degradation of histone H1 subtypes, showing that their C-terminal domain mediates degradation by the 20S proteasome.

This study shows that PI31 inhibits constitutive 20S proteasomes more effectively than immuno-20S proteasomes due to differential interactions and proteolysis.

This study identifies the D2 domain of DTX3L as critical for forming oligomeric complexes that enable the DTX3L-PARP9 complex to read mono-ADP-ribosylated androgen receptor.

DEGRONOPEDIA provides a web server for analyzing degron motifs across seven model organisms, integrating sequence, structure, and modification data to support degron research.

The paper identifies ubiquitinated proteins in ischemic stroke using proteomics and shows that ubiquitination modulates kinase activity at the postsynaptic density.

This study defines the substrate recognition mechanism of Doa10 using structural and functional analyses in yeast, revealing a lateral tunnel and fence-like domains that facilitate substrate access.

This study identifies the interaction between MAGEA4 and RAD18 using NMR and AlphaFold2, revealing structural insights into how MAGEA4 regulates RAD18's ubiquitination activity and its implications for cancer.

The paper demonstrates bidirectional substrate shuttling between the 26S proteasome and Cdc48 ATPase in yeast, showing how this process facilitates protein degradation.

This study identifies shared and distinct mechanisms of UBA1 inactivation in VEXAS syndrome and related diseases, revealing how different mutations affect ubiquitin transfer to E2 enzymes.

This study shows that everolimus, a rapamycin analog, uniquely affects the ubiquitin-proteasome system by increasing ubiquitin levels and altering polyubiquitination patterns, distinct from its analogs.