Ubiquitin and proteasome pathways

Post-ischemic ubiquitination at the postsynaptic density reversibly influences the activity of ischemia-relevant kinases

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

Interplay between β-propeller subunits WDR26 and muskelin regulates the CTLH E3 ligase supramolecular complex

The paper shows that the CTLH E3 ligase complex regulates substrate selectivity and autoregulation by exchanging its β-propeller subunits WDR26 and muskelin.

Hypoxia-driven deSUMOylation of EXOSC10 promotes adaptive changes in the transcriptome profile

The paper shows hypoxia reduces EXOSC10 SUMOylation, leading to its nuclear translocation and changes in mRNA transcriptome related to hypoxia.

Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons

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.

Profiling ubiquitin signaling with UBIMAX reveals DNA damage- and SCFβTRCP-dependent ubiquitylation of the actin-organizing protein Dbn1

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

Remodeling of the protein ubiquitylation landscape in the aging vertebrate brain

This study identifies age-related changes in ubiquitylation, acetylation, and phosphorylation sites in mouse brains and finds conserved effects in killifish, linking proteasome inhibition to aging ubiquitylome remodeling.

Nrf1 is not a direct target gene of SREBP1, albeit both are integrated into the rapamycin-responsive regulatory network in human hepatoma cells

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.

Multiple Cullin-Associated E3 Ligases Regulate Cyclin D1 Protein Stability

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.

N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity

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 E3 ubiquitin ligase RNF216 contains a linear ubiquitin chain-determining-like domain that functions to regulate dendritic arborization and dendritic spine type in hippocampal neurons

This study identifies a domain in RNF216 that regulates dendritic arborization and spine morphology through ubiquitin chain assembly, independent of its catalytic activity.

A conserved N-terminal motif of CUL3 mediates assembly and licenses E3 ligase activation of CRL3KLHL22

The paper identifies a conserved N-terminal motif in CUL3 that mediates dimerization and activates CRL3KLHL22 E3 ligase function.

Structure-function analysis of histone H2B and PCNA ubiquitination dynamics using deubiquitinase-deficient strains.

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

Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development

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

USP48/USP31 Is a Nuclear Deubiquitinase that Potently Regulates Synapse Remodeling

This study identifies USP48 as a nuclear deubiquitinase that regulates synapse remodeling by promoting spine pruning and reducing synaptic protein clustering.

Mechanism and evolutionary origins of Alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10

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 E3/E4 ubiquitin ligase UFD-2 mediates negative feedback on Raf protein stability

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

SUMO Activated Target Traps (SATTs) enable the identification of a comprehensive E3-specific SUMO proteome.

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

VCF1 is an unconventional p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates

This paper identifies VCF1 as a novel p97 cofactor that enhances p97-UFD1-NPL4 interactions with ubiquitylated substrates, promoting proteasomal degradation.

Chemogenetic profiling of ubiquitin-like modifier pathways identifies NFATC2IP as a mediator of SUMO-dependent genome integrity

The paper identifies NFATC2IP as a mediator of SUMO-dependent genome integrity through CRISPR/Cas9 screens and functional validation.

Species-specific protein-protein interactions govern the humanization of the 20S proteasome in yeast

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

HUWE1 Amplifies Ubiquitin Modifications to Broadly Stimulate Clearance of Proteins and Aggregates

This paper identifies HUWE1 as a ubiquitin ligase that enhances ubiquitin modifications on proteins and aggregates, promoting their degradation via proteasome and autophagy pathways.

An Abundance of Free Proteasomal Regulatory (19S) Particles Regulate Neuronal Synapses Independent of the Proteasome

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

High resolution structure of mammalian PI31-20S proteasome complex reveals mechanism of proteasome inhibition

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

Molecular mechanisms for activation of the 26S proteasome

The paper investigates how ZFAND5 activates the 26S proteasome by inducing conformational changes that enhance substrate degradation.

HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways

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

Ubiquitin proteomics uncovers RNA polymerase I as a critical target of the Nse1 RING domain

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

Lysine-independent ubiquitination and degradation of REV-ERBα involves a bi-functional degradation control sequence at its N-terminus

This study identifies a bi-functional N-terminal degradation control sequence in REV-ERBα that regulates its ubiquitination and degradation through interactions with E3 ligases.

Substrate-Specific Effects of Natural Genetic Variation on Proteasome Activity

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

Immunoproteasome deficiency results in accelerated brain aging and epilepsy

This study shows that immunoproteasome deficiency accelerates brain aging and causes epilepsy in mice, with reduced immunoproteasome expression also observed in human epilepsy patients.

Lysine-deficient proteome can be regulated through non-canonical ubiquitination and ubiquitin-independent proteasomal degradation

The paper identifies lysine deserts in UPS components across species and shows they can be regulated by non-lysine ubiquitination and ubiquitin-independent proteasomal degradation.