Ubiquitin and proteasome pathways

The paper investigates CTLA4 turnover, showing ubiquitylation at K203 and K213 drives lysosomal degradation, with USP8 and HD-PTP modulating this process through distinct mechanisms.

The paper analyzes ubiquitylated peptides to identify spectral features that can improve detection of the dark ubiquitylome in non-tryptic proteomics.

This study identifies that HCV infection promotes PA28γ acetylation and heptamerization, enhancing proteasomal degradation of RNF2 and leading to HOX gene expression.

The paper investigates how linear ubiquitin chains affect the proteome in Drosophila by analyzing proteomic changes in flies expressing chains of different lengths.

This study identifies how geranylgeranylation of FBXO10 enables its targeting to the outer mitochondrial membrane, where it regulates PGAM5 ubiquitination and mitochondrial function.

This study shows proteasome inhibitors are more effective against NSCLC cells with mutant p53 by inducing oxidative stress and mitochondrial apoptosis, suggesting a new therapeutic strategy.

This study reveals the structural steps of human 20S proteasome assembly using cryo-EM, showing how chaperones facilitate intermediate stages and trigger final maturation.

This study shows that serine ubiquitination of p62 by Legionella pneumophila SidE effectors inhibits Nrf2 signaling, altering redox homeostasis and host metabolism during infection.

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.

The paper introduces a proximity-based labeling method to identify ubiquitin ligase substrates and validates it using RAD18, TRAF6, and CHIP.

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.

This study measures 26S proteasome activity in different Arabidopsis tissues using two extraction methods and a fluorogenic assay, revealing tissue-specific activity patterns.

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 identifies STUB1 as a tumor suppressor in ccRCC by promoting YTHDF1 degradation, with low STUB1 expression linked to poor patient outcomes.

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.

This study identifies MARCH family ubiquitin ligases as regulators of cadherin degradation, showing differential targeting of VE-cadherin versus N-cadherin through specific domains and lysine residues.

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.

This paper quantifies ubiquitylation site occupancy and turnover rates, revealing their relationship to phosphorylation and identifying a surveillance mechanism protecting E1/E2 enzymes.