Ubiquitin and proteasome pathways

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.

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

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.

The paper develops subunit-specific proteasome substrates for Schistosoma species, showing improved performance and cross-species applicability.

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

The paper shows that ZNRF3/RNF43 ubiquitinates and degrades EGFR, and their loss increases EGFR signaling, promoting cancer growth.

The paper identifies the intrinsically disordered N-terminus of SUMO1 as an intramolecular inhibitor of SUMO-SIM interactions, revealing a mechanism of disorder-based autoinhibition.

This study compares the expression of three HECT E3 ligases in E. coli, finding that lower temperatures improve solubility and yield, while full-length proteins are less successfully expressed than isolated domains.

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 identifies UBE2D/eff as critical for maintaining proteostasis and a youthful proteome during aging by regulating protein degradation and preventing aggregate accumulation.

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.

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.

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.

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.

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

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

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

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.

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

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

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

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

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

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.