Ubiquitin and proteasome pathways

Identification and Characterization of Interacting Proteins of TARANI/ Ubiquitin Specific Protease-14 in Arabidopsis thaliana

The study identifies interacting proteins of TARANI/UBIQUITIN SPECIFIC PROTEASE-14 in Arabidopsis thaliana using immunoprecipitation mass spectrometry and other methods, revealing 92 interactors involved in various biological processes.

Localized K63 ubiquitin signaling is regulated by VCP/p97 during oxidative stress

The paper shows that K63 ubiquitin chains accumulate in non-cytosolic compartments during oxidative stress and that VCP/p97 and NPLOC4 regulate their localization and removal.

Convergence of orphan quality control pathways at a ubiquitin chain-elongating ligase

The paper identifies the UBR4-KCMF1 ubiquitin ligase complex as a convergence point for quality control pathways that degrade orphan subunits, highlighting its role in protein homeostasis and cancer vulnerability.

The Cul3 ubiquitin ligase engages Insomniac as an adaptor to impact sleep and synaptic homeostasis

This paper identifies Insomniac as a Cul3 adaptor protein that regulates sleep and synaptic homeostasis in Drosophila, linking Cul3 dysfunction to autism and schizophrenia.

Chemical tools to define and manipulate interferon-inducible Ubl protease USP18

The paper develops activity-based probes to selectively detect USP18 activity and screen for inhibitors, enabling analysis of USP18's role in disease states.

Structures of the 26S proteasome in complex with the Hsp70 cochaperone Bag1 reveal a novel mechanism of ubiquitin-independent proteasomal degradation

This study presents cryo-EM structures of the Bag1-bound 26S proteasome, revealing a mechanism for ubiquitin-independent proteasomal degradation through conformational changes in the 19S regulatory particle.

Inhibition of SQSTM1/p62 oligomerization and Keap1 sequestration by the Cullin-3 adaptor SHKBP1

This study identifies SHKBP1 as a regulator of p62 oligomerization and antioxidant response by preventing Keap1 sequestration into p62 bodies, independent of ubiquitination.

Redistribution of proteasomes through diffusion and cytoskeleton-dependent mechanisms upon stress induced by protein aggregates

The paper quantifies proteasome re-organization during proteotoxic stress using single-molecule microscopy and shows cytoskeleton-dependent movement restrictions.

Structural Dynamics of the Ubiquitin Specific Protease USP30 in Complex with a Cyanopyrrolidine-Containing Covalent Inhibitor

This study investigates the structural dynamics of USP30 inhibition by a covalent inhibitor, revealing its binding mechanism and selectivity advantages over non-covalent inhibitors.

19S proteasome loss causes monopolar spindles through ubiquitin-independent KIF11 degradation

The paper shows that loss of 19S proteasome subunits causes monopolar spindles by ubiquitin-independent degradation of KIF11, highlighting a non-canonical role for the proteasome in mitosis.

Modeling liquid-liquid phase separation and its impact on proteasomal substrate degradation

This study develops a reaction-diffusion model to quantify proteasome-associated liquid-liquid phase separation and its bidirectional impact on degradation efficiency.

Genesis and regulation of C-terminal cyclic imides from protein damage

The paper investigates C-terminal cyclic imides as protein damage products, their formation mechanisms, and their impact on protein stability and quality control via CRBN.

Crosslinking-mediated Interactome Analysis Identified PHD2-HIF1α Interaction Hotspots and the Role of PHD2 in Regulating Protein Neddylation

This study identifies PHD2 interaction hotspots and reveals its role in regulating protein neddylation through interaction with the COP9 Signalosome complex.

Recombinant Expression of Photo-crosslinkable 26S Proteasome Base Subcomplex

The paper describes a method to incorporate a photo-crosslinkable amino acid into the 26S proteasome base subcomplex using recombinant expression in E. coli.

Small molecule targeting of FBXO21 mediated p85αubiquitylation in acute myeloid leukemia

The paper identifies FBXO21 as a therapeutic target in AML by developing a small molecule that inhibits p85 ubiquitination, reducing PI3K pathway activity and inducing cell death.

Temporal control of acute protein aggregate turnover by UBE3C and NRF1-dependent proteasomal pathways

This study identifies UBE3C and NRF1-dependent proteasomal pathways that regulate acute protein aggregate turnover in response to misfolded protein accumulation.

PITHD1: An Endogenous Inhibitor of the 26S Proteasome During Cellular Dormancy

The paper identifies PITHD1 as an endogenous inhibitor of the 26S proteasome in dormant cells, revealing a triple-lock mechanism that prevents protein degradation during cellular dormancy.

Quiescent cells maintain active degradation-mediated protein quality control requiring proteasome, autophagy and nucleus-vacuole junctions

The paper investigates protein quality control (PQC) in quiescent yeast cells, showing that degradation pathways like proteasomes, autophagy, and nucleus-vacuole junctions are active and required for misfolded protein clearance.

Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53

This study identifies USP53 and USP54 as active deubiquitinases specific for K63-linked polyubiquitin, revealing their role in regulating tricellular junctions and correcting previous annotations of them as pseudo-enzymes.

Structural diversity and oligomerization of bacterial ubiquitin-like proteins

This study identifies structural diversity and Ca2+-mediated oligomerization in bacterial ubiquitin-like proteins, suggesting a role in stress response.

Knockdown proteomics reveals USP7 as a regulator of cell-cell adhesion in colorectal cancer via AJUBA

This study identifies USP7 as a regulator of cell-cell adhesion in colorectal cancer through its interaction with Ajuba, showing reduced adhesion upon USP7 or Ajuba knockdown.

Salt-dependent non-catalytic allostery of human USP14-regulated 26S proteasome

This study uses cryo-EM and genetic engineering to show how USP14 non-catalytically regulates proteasome activity through salt-dependent allosteric changes.

Elucidating the Mechanism Underlying UBA7-UBE2L6 Disulfide Complex Formation

The paper determines the cryo-EM structure of the UBA7-UBE2L6 disulfide complex and identifies factors influencing its formation, revealing its role in ISG15 conjugation and immune response regulation.

The USP12/46 deubiquitinases protect integrins from ESCRT-mediated lysosomal degradation

The paper identifies USP12/46 deubiquitinases that prevent ESCRT-mediated lysosomal degradation of β1 integrin by removing ubiquitin from its cytoplasmic tail in early endosomes.

Distinct Perception Mechanisms of BACH1 Quaternary Structure Degrons by Two F-box Proteins under Oxidative Stress

This study reveals how two F-box proteins, FBXO22 and FBXL17, recognize distinct structural features of the BACH1 BTB dimer under oxidative stress, leading to its ubiquitination and degradation.

Identification of a non-canonical function of prefoldin subunit 5 in proteasome assembly

This study identifies a non-canonical role for prefoldin subunit 5 in proteasome assembly, showing its necessity for Rpt ring subcomplex formation and proteasome activity.

Elevated Ubiquitin Phosphorylation by PINK1 Contributes to Proteasomal Impairment and Promotes Neurodegeneration

This study shows that elevated phosphorylated ubiquitin (pUb) caused by PINK1 impairs proteasomal activity and promotes neurodegeneration in multiple conditions.

Altered Proteasome Composition in Aging Brains, Genetic Proteasome Augmentation Mitigates Age-Related Cognitive Declines, and Acute Proteasome Agonist Treatment Rescues Age-Related Cognitive Deficits in Mice

This study shows that aging reduces proteasome function in mice brains, and enhancing proteasome activity through genetic or pharmacological means improves cognitive and neuromuscular function in aged mice.

ProEnd: A Comprehensive Database for Identifying HbYX Motif-Containing Proteins Across the Tree of Life

ProEnd identifies and catalogs HbYX motif-containing proteins across diverse organisms, revealing their evolutionary conservation and potential role in proteasome interactions.

Redox control of the deubiquitinating enzyme Ubp2 regulates translation during stress

This study shows that Ubp2, a DUB, is redox-regulated during oxidative stress in yeast, controlling K63-ub chains on ribosomes and restoring translation post-stress.