J. A. Paulo

The paper identifies how nutrients regulate the Mitotic Exit Network (MEN) in budding yeast by modulating cell growth and phosphorylation of MEN components.

The paper identifies high-impact DUBs and their substrates using Xenopus egg extract and proteomics, revealing substrate characteristics influencing DUB specificity.

The paper demonstrates bidirectional substrate shuttling between the 26S proteasome and Cdc48 ATPase in yeast, showing how this process facilitates protein degradation.

This study identifies a targetable dependency on noncanonical PI3Kγ signaling in acute leukemias, showing that PI3Kγ inhibition with eganelisib improves survival when combined with cytarabine.

This study shows that SARS-CoV-2 variants differ in syncytia formation, which affects host chromatin accessibility, cellular senescence, and inflammation via TP53.

The paper quantifies ER proteome remodeling during neurogenesis using ER-phagy receptors and identifies receptor-specific ER protein clearance mechanisms.

The paper investigates neural progenitor cells in breast cancer using proteomics and co-culture models, finding DCX+/NFL+ cells in tumors and their role in aggressive cancer phenotypes.

This study uses transdifferentiated neurons to show lysosomal deficits are an early event in aging and Alzheimer's disease, leading to proteotoxic deposits and cell death.

The paper identifies YIPF3 and YIPF4 as membrane receptors for Golgiphagy during nutrient stress and shows their role in autophagic degradation of Golgi proteins.

This study shows FBXO7 is not required for PINK1/Parkin-dependent mitophagy in HeLa and iNeuron cells, as its absence does not impair key mitophagy processes.

This study identifies REEP1 proteins as essential for autophagosome formation by stabilizing the high curvature of the phagophore rim.

This study examines how proteome conformational stability changes in aging C. elegans due to missense mutations and polyglutamine expansions, revealing age-dependent metastable protein networks.

This paper develops a method to isolate early endosomes and uses it to study amyloid precursor protein processing by β and γ-secretases in these compartments.

This study determines the cryo-EM structure of active-state RXFP1 bound to relaxin-2 and Gs protein, revealing an autoinhibition mechanism.

This study shows TXNRD3 is essential for male fertility by regulating redox balance during spermatogenesis, as demonstrated through knockout mice and proteomic analysis.

This study elucidates how the Cdc48 ATPase complex unfolds and translocates polyubiquitinated protein substrates through cooperative binding with Ufd1/Npl4.

This study shows that progranulin deficiency reduces bis(monoacylglycero)phosphate levels, leading to gangliosidosis and neurodegeneration.

This study identifies TAX1BP1 as essential for lysophagy by using proteomics and flux reporters to show its role in damaged lysosome turnover.

This study shows autophosphorylation of small GTPases like H-RAS and K-RAS alters their nucleotide exchange and effector interactions, changing their functional behavior.

This study identifies age-associated clonal B cells (ACBCs) as drivers of B-cell lymphoma in mice, linking aging-related epigenetic and cellular changes to cancer development and proposing mTOR/c-Myc inhibition as a therapeutic strategy.

This study investigates how temozolomide induces DNA double-strand breaks through crosstalk between repair pathways in Xenopus egg extracts.

This paper shows that OGT's noncatalytic functions are essential for cell proliferation, while its glycosyltransferase activity is sufficient for viability.

This study identifies DPP9 as a repressor of NLRP1 inflammasome activation by sequestering the NLRP1 C-terminus, preventing inflammation during protein turnover.

This study shows poison frogs rapidly accumulate toxins, altering protein abundance in immune response and small molecule transport across tissues.

This study shows that mitochondrial fatty acid synthesis (mtFAS) regulates electron transport chain (ETC) complexes and skeletal myoblast differentiation, linking fatty acid synthesis to oxidative metabolism.

The paper identifies proteomic changes in Ubqln2 mutant mice and finds that TRIM32, PEG10, and CXX1B are linked to UBQLN2 function and degradation.

This study identifies PfPP1 as essential for Plasmodium falciparum egress from host erythrocytes and shows it integrates internal and external signals for this process.

The paper introduces a real-time database search platform, Orbiter, that improves the efficiency and accuracy of multiplexed quantitative proteomics by reducing data acquisition time and increasing protein quantification.