Ubiquitin and proteasome pathways

Neuronal membrane proteasomes homeostatically regulate neural circuit activity in vivo and are required for learning-induced behavioral plasticity

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

Sumoylation is largely dispensable for normal growth but facilitates heat tolerance in yeast

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.

Variation in Ubiquitin System Genes Creates Substrate-Specific Effects on Proteasomal Protein Degradation

The paper identifies genetic variants affecting UPS activity in yeast by mapping loci influencing N-degron recognition and ubiquitination.

Electrophile scanning by chemical proteomics reveals a potent pan-active DUB probe for investigation of deubiquitinase activity in live cells

The paper identifies a small molecule DUB probe, IMP-2373, that quantitatively engages multiple DUBs in live cells and demonstrates its use in studying DUB activity changes during MYC deregulation.

Consequences of alanine-126 mutations in helix-3 on structure and functions of Rad6 E2 ubiquitin-conjugating enzymes

This study investigates how mutations at alanine-126 in helix-3 of Rad6 affect its ubiquitination activity and structural stability in yeast and human homologs.

Characterizing the differential distribution and targets of Sumo paralogs in the mouse brain

The paper characterizes the differential distribution and targets of Sumo paralogs in the mouse brain using knock-in mouse models and proteomic analysis.

Prediction of SUMOylation targets in Drosophila melanogaster

The paper predicts SUMOylation targets in Drosophila melanogaster using sequence homology from human and mouse SUMOylation data, identifying motifs, protein families, and functional preferences.

Proteasomal subunit depletions differentially affect germline integrity in C. elegans

This study investigates the germline-specific functions of 19S RP proteasome subunits in C. elegans, revealing roles in meiotic processes and proteasome assembly.

Multiple UBX proteins reduce the ubiquitin threshold of the mammalian p97-UFD1-NPL4 unfoldase

The paper shows that UBX proteins lower the ubiquitin threshold for p97-UFD1-NPL4 to unfold substrates, similar to yeast.

Trim-Away degrades lysine-less substrates without requiring ligase autoubiquitination

This study shows TRIM21 can degrade lysine-less substrates without autoubiquitination, revealing a non-canonical ubiquitination mechanism for Trim-Away.

Heterotypic Assembly Mechanism Regulates CHIP E3 Ligase Activity

The paper investigates how the CHN-1/UFD-2 complex enhances ubiquitin chain formation through dimerization and chaperone-mediated regulation of substrate ubiquitylation.

The Role of UBE2-Conjugating Enzymes in the Mechanism of MuRF1 Ubiquitylation

This study identifies UBE2 family members that interact with MuRF1 to mediate ubiquitylation, revealing a two-step mechanism for mono- and poly-ubiquitin chain formation.

Ubiquitin ligases and a processive proteasome facilitate protein clearance during the oocyte-to-embryo transition in Caenorhabditis elegans

The paper shows that ETC-1 promotes proteasome processivity to degrade oocyte regulatory proteins during the oocyte-to-embryo transition in C. elegans.

SUMO monoclonal antibodies vary in sensitivity, specificity, and ability to detect SUMO conjugate types.

The paper evaluates twenty-four anti-SUMO monoclonal antibodies for their sensitivity, specificity, and ability to detect different SUMO conjugation states across multiple assays.

RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control

This study identifies RTL8 as a novel UBQLN2 interactor that promotes its nuclear translocation and subnuclear localization in protein quality control.

Sequence and structural variations determining the recruitment of WNK kinases to the KLHL3 E3 ligase

This paper determines the crystal structure of KLHL3 in complex with a WNK3 peptide, revealing structural features and phosphorylation-dependent regulation of WNK3 binding.

UbE3-APA: A Bioinformatic Strategy to Elucidate Ubiquitin E3 Ligase Activities in Quantitative Proteomics Study

The paper introduces a computational tool to analyze ubiquitin E3 ligase activity using quantitative proteomics data and validates it with experimental results.

Study of an FBXO7 patient mutation reveals Fbxo7 and PI31 co-regulate proteasomes and mitochondria

This study identifies an FBXO7 mutation that disrupts its interaction with PI31, affecting proteasome and mitochondrial function in patient cells.

ReporterSeq reveals genome-wide determinants of proteasome expression

ReporterSeq identifies Trr1 and ribosomal proteins as novel regulators of the UPS master regulator Rpn4 in yeast under stress conditions.

ATR facilitates the degradation of Api5 through the ubiquitin-proteasome pathway via FBXW2 to regulate apoptosis upon DNA damage

This study shows that ATR promotes Api5 degradation via the ubiquitin-proteasome pathway through FBXW2, thereby regulating apoptosis in response to DNA damage.

Modular HUWE1 architecture serves as hub for degradation of cell-fate decision factors

The paper presents the cryo-EM structure of HUWE1, revealing its modular architecture and its role in degrading cell-fate decision factors.

Big fish, little fish: N-terminal acetyltransferase Naa40p proteoforms caught in the act

The paper identifies a conserved Naa40p proteoform, Naa40S, which exhibits distinct substrate specificity and subcellular localization compared to Naa40L, expanding the known substrate repertoire of Naa40p.

Altered phosphorylation of the proteasome subunit Rpt6 has minimal impact on synaptic plasticity and learning

This study investigates the impact of Rpt6 phosphorylation on synaptic plasticity and learning using mouse models, finding no significant effects on synaptic function or behavior.

Behavioral phenotyping of mice lacking the deubiquitinase USP2

This study investigates the behavioral effects of USP2 deletion in mice, finding altered locomotor activity, motor coordination, anxiety-like behavior, and memory, but no impact on spatial memory.

SLAP2 adaptor binding disrupts c-CBL autoinhibition to activate ubiquitin ligase function.

This study identifies how SLAP2 binding to CBL disrupts its autoinhibition, revealing a mechanism for activating CBL's ubiquitin ligase function.

Mono-ubiquitination of Rabphilin 3A by UBE3A serves a non-degradative function

This study identifies RPH3A as a novel UBE3A ubiquitination target and shows that UBE3A mono-ubiquitination of RPH3A does not mediate degradation.

Nα-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae

The paper investigates the distinct physiological roles of NatA and NatB in S. cerevisiae through transcriptome, translatome, and proteome profiling of mutants, revealing specific effects on gene expression and protein folding.

Transient deSUMOylation of IRF2BP proteins controls early transcription in EGFR signaling

The paper identifies transient deSUMOylation of IRF2BP proteins as critical for regulating immediate early gene expression in EGFR signaling.

Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

The paper develops a DIA-based workflow for ubiquitinome analysis, revealing circadian regulation through novel ubiquitination sites and clusters.

Crosstalk and Ultrasensitivity in Protein Degradation Pathways

This study shows that protein turnover reduces the switch-like behavior of PTM cycles and highlights the impact of E3 ligase crosstalk on protein expression changes.