Ubiquitin and proteasome pathways

The paper investigates how a small-molecule inhibitor binds to and inactivates Cbl-b, revealing a structural mechanism that locks the protein in an inactive conformation.

The paper identifies over 5000 C-degrons in budding yeast and shows that the SCF ubiquitin ligase targets ~40% of them via the F-box receptor Das1.

The paper introduces UBIMAX, a method to profile ubiquitylation, and identifies Dbn1 as a novel DNA damage-induced ubiquitylation target regulated by SCFβTRCP.

This study determines the crystal structures of TssM, a USP-type deubiquitinase from B. pseudomallei and B. mallei, revealing its unique structural features and mechanism of ubiquitin recognition.

This study identifies and characterizes bacterial HECT-like E3 ligases, revealing structural insights into their polyUb ligation mechanism and specificity.

This paper reports the crystal structures of SAP05 complexes and reveals their bimodular architecture enabling ubiquitin-independent targeted protein degradation in eukaryotic cells.

This study identifies N-myristoylation of Rpt2 as a mechanism for proteasome-membrane interaction, showing its role in membrane protein homeostasis and its impact on cellular processes and tumor growth.

The paper investigates the regulatory relationship between Nrf1 and SREBP1, finding that Nrf1 is not a direct target of SREBP1, despite both being part of the rapamycin-responsive network in human hepatoma cells.

BioE3 identifies substrates of UbL E3 ligases by site-specific biotinylation and proteomic analysis, revealing both known and novel targets for various E3 ligases.

This study uses ion mobility mass spectrometry to assess DUB selectivity in mixtures of ubiquitin chains, revealing preferences for branched Ub trimers with specific linkages.

This study identifies multiple cullin-associated E3 ligases that regulate cyclin D1 protein stability through ubiquitination and proteasome degradation, affecting cell cycle progression and proliferation.

This study identifies UBXD1 as a p97 ATPase inhibitor and shows how its domains induce structural remodeling and ring opening of the p97 hexamer.

This study identifies novel E3 ligases that regulate tankyrase stability through ubiquitylation, revealing mechanisms that oppose degradation and may inform cancer therapy.

The paper shows that N-terminal acetylation by NatC protects proteins from degradation, enhancing longevity and motility, and that UBR4-KCMF1 targets unacetylated N-terminal Met followed by hydrophobic residues.

The paper shows proteasome activity recovers quickly after inhibitor treatment without needing DDI2 or gene transcription, but requires protein translation.

The paper demonstrates that deleting deubiquitinases in yeast enables studying ubiquitination dynamics of target proteins like histone H2B and PCNA in vivo.

The paper investigates ribosome ubiquitination dynamics during zebrafish development, identifying Znf598-mediated ubiquitination of Rps10/eS10 as a key regulatory mechanism.

This study identifies FAM104 proteins as novel p97 interactors that facilitate nuclear import and chromatin binding of p97, highlighting their role in cellular processes and disease.

The paper investigates how Pirh2 and CRL2-KLHDC10 E3 ligases recognize Ala-tails, showing conserved binding sites and convergent evolution of their recognition mechanisms.

The paper identifies UFD-2 as a negative regulator of LIN-45 Raf protein stability through interaction with CDC-48 unfoldase.

This study uses cryo-EM to reveal the structural mechanism of K48-linked ubiquitin chain formation by the HECT E3 ligase UBR5, showing how it orchestrates ubiquitin transfer through conformational changes.

The paper introduces SATTs to identify E3-specific SUMO substrates, finding 1681 SUMO substrates across eight E3s with distinct preferences.

The paper identifies protein-protein interactions and proteolytic activity as key factors determining the functional replaceability of human proteasome subunits in yeast.

The paper identifies a proteasomal 19S subcomplex that regulates neuronal synapses independently of the 20S catalytic subunit through deubiquitylation of Lys63-ubiquitin.

The paper reports a high-resolution cryo-EM structure of the mammalian 20S proteasome complex with PI31, revealing how PI31 inhibits proteasome activity.

This study identifies HAPSTR1 as a HUWE1 substrate that facilitates its nuclear localization, thereby regulating stress signaling pathways and cell proliferation.

The paper identifies RNA polymerase I as a target of Nse1's RING domain through ubiquitin proteomics, revealing a role in rDNA segregation.

The paper identifies 15 genomic loci influencing proteasome activity in yeast using single-cell measurements and CRISPR-based engineering, revealing substrate-specific genetic effects.

This study shows neuronal membrane proteasomes regulate neural activity and are essential for learning-induced behavioral plasticity in Xenopus laevis tadpoles.

This study shows that sumoylation is largely dispensable for normal yeast growth but essential for heat tolerance, as reduced Ubc9 activity leads to temperature sensitivity and transcriptional dysregulation.