J. A. Paulo

Cell growth and nutrient availability control the mitotic exit signaling network in budding yeast

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

Recharacterization of RSL3 reveals that the selenoproteome is a druggable target in colorectal cancer

This study recharacterizes RSL3 as a broad selenoprotein inhibitor, showing its potential as a therapeutic target for colorectal cancer by inducing ferroptosis.

Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST

This study uses nMOST to profile proteo-lipidomics in lysosomal storage disease mutants, revealing autophagy defects and mitochondrial dysfunction.

BRD4-mediated epigenetic regulation of endoplasmic reticulum-mitochondria contact sites is governed by the mitochondrial complex III

The paper identifies fedratinib as a drug that increases endoplasmic reticulum-mitochondria contact sites by inhibiting BRD4, revealing a novel epigenetic pathway linking ERMCS to cellular metabolism.

Substrate identification and specificity profiling of deubiquitylases against endogenously-generatedubiquitin-protein conjugates

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

Bidirectional substrate shuttling between the 26S proteasome and the Cdc48 ATPase promotes protein degradation

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

Targetable leukemia dependency on noncanonical PI3Kγ signaling

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.

Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53

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

Combinatorial selective ER-phagy remodels the ER during neurogenesis

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

Global and single-cell proteomics view of the co-evolution between neural progenitors and breast cancer cells in a co-culture model

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.

Proteostasis and lysosomal repair deficits in transdifferentiated neurons of Alzheimer's disease

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.

Quantitative mapping of autophagic cargo during nutrient stress reveals YIPF3-YIPF4 as membrane receptors for Golgiphagy

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

PARK15/FBXO7 is dispensable for PINK1/Parkin-dependent mitophagy in iNeuron and HeLa cell systems

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.

Membrane curvature-generating proteins crucial for autophagosome formation

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

Global proteome metastability response in isogenic animals to missense mutations and polyglutamine expansions in aging

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.

Early Endosome Capture Proteomics and its Application to Amyloid Precursor Protein Intramembrane Processing by β and γ-Secretases

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.

The relaxin receptor RXFP1 signals through a mechanism of autoinhibition

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

TXNRD3 supports male fertility via the redox control of spermatogenesis

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

Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase

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

Progranulin deficiency results in reduced bis(monoacylglycero)phosphate (BMP) levels and gangliosidosis

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

Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy

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

Regulation of GTPase function by autophosphorylation

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

Integrative analyses uncover mechanisms by which aging drives B cell lymphoma

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.

Crosstalk between repair pathways elicits Double-Strand Breaks in alkylated DNA: implications for the action of temozolomide

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

Mammalian Cell Proliferation Requires Noncatalytic Functions of O-GlcNAc Transferase

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

DPP9 directly sequesters the NLRP1 C-terminus to repress inflammasome activation

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

Rapid toxin sequestration modifies poison frog physiology

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

Mitochondrial fatty acid synthesis coordinates mitochondrial oxidative metabolism

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.

Global proteomics of Ubqln2-based murine models of ALS

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

Co-option of Plasmodium falciparum PP1 for egress from host erythrocytes

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