Biology subjects

Julio, A. R.

Publications and source records attributed to Julio, A. R..

4 recordsLinked to original sources

bioRxiv2024

Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome

The physical properties of cellular membranes, including fluidity and function, are influenced by protein and lipid interactions. In situ labeling chemistries, most notably proximity-labeling interactomics are well suited to characterize these dynamic and often fleeting interactions. Established methods require distinct chemistries for proteins and lipids, which limits the scope of such studies. Here we establish a singlet-oxygen-based photocatalytic proximity labeling platform (POCA) that reports intracellular interactomes for both proteins and lipids with tight spatiotemporal resolution using cell-penetrant photosensitizer reagents. Using both physiologically relevant lipoprotein-complexed probe delivery and genetic manipulation of cellular cholesterol handling machinery, cholesterol-directed POCA captured established and unprecedented cholesterol binding proteins, including protein complexes sensitive to intracellular cholesterol levels and proteins uniquely captured by lipoprotein uptake. Protein-directed POCA accurately mapped known intracellular membrane complexes, defined sterol-dependent changes to the non-vesicular cholesterol transport protein interactome, and captured state-dependent changes in the interactome of the cholesterol transport protein Aster-B. More broadly, we find that POCA is a versatile interactomics platform that is straightforward to implement, using the readily available HaloTag system, and fulfills unmet needs in intracellular singlet oxygen-based proximity labeling proteomics. Thus, we expect widespread utility for POCA across a range of interactome applications, spanning imaging to proteomics.

biochemistry↗

bioRxiv2023

Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds

Protein homeostasis is tightly regulated, with damaged or misfolded proteins quickly eliminated by the proteasome and autophagosome pathways. By co-opting these processes, targeted protein degradation technologies enable pharmacological manipulation of protein abundance. Recently, cysteine-reactive molecules have been added to the degrader toolbox, which offer the benefit of unlocking the therapeutic potential of undruggable protein targets. The proteome-wide impact of these molecules remains to be fully understood and given the general reactivity of many classes of cysteine-reactive electrophiles, on- and off-target effects are likely. Using chemical proteomics, we identified a cysteine-reactive small molecule degrader of the SARS-CoV-2 non- structural protein 14 (nsp14), which effects degradation through direct modification of cysteines in both nsp14 and in host chaperones together with activation of global cell stress response pathways. We find that cysteine-reactive electrophiles increase global protein ubiquitylation, trigger proteasome activation, and result in widespread aggregation and depletion of host proteins, including components of the nuclear pore complex. Formation of stress granules was also found to be a remarkably ubiquitous cellular response to nearly all cysteine-reactive compounds and degraders. Collectively, our study sheds light on complexities of covalent target protein degradation and highlights untapped opportunities in manipulating and characterizing proteostasis processes via deciphering the cysteine-centric regulation of stress response pathways.

biochemistry↗

bioRxiv2023

Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome

Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxiCat, Biotin Switch, and SP3-Rox, they typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. To obviate requirements for laborious biochemical fractionation, here, we develop and apply an unprecedented two step cysteine capture method to establish the Local Cysteine Capture (Cys-LoC), and Local Cysteine Oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole cell proteomic analysis. Application of the Cys-LOx method to LPS stimulated murine immortalized bone marrow-derived macrophages (iBMDM), revealed previously unidentified mitochondria-specific inflammation-induced cysteine oxidative modifications including those associated with oxidative phosphorylation. These findings shed light on post-translational mechanisms regulating mitochondrial function during the cellular innate immune response.

biochemistry↗

bioRxiv2019

1-Methyl-tryptophan enantiomers differently affect the cross- talking between mononuclear and tumor cells and interferon-γ production.

The inhibition of the enzyme indoleamine-2,3-dioxygenase (IDO), that catalyzes the oxidation of the amino acid tryptophan to kynurenine (KYN), is considered a good target for immunoadjuvants in antineoplastic therapy. 1-Methyl-tryptophan (1-MT) is the most studied molecule for this purpose. Although L-1-MT is better than D-1-MT in inhibiting IDO, for an unknown reason the D-enantiomer has higher clinical efficacy. Here we took advantage of co-cultures of tumor cells (SK-Mel 19 melanoma line; 1x105 cells/well) with peripheral blood mononuclear cells (PBMC; 5x106 cells/well) to verify the effect of 1-MT enantiomers on cytokine production and tumoricidal activity. At a concentration that did not affect KYN production, 1-MT (50 {micro}M) affected the production of TNF-, IL-10, and IFN-{gamma} measured in co-cultures supernatants. Stereospecificity was only observed for IFN-{gamma} production. D-1-MT inhibited more than 30% of IFN-{gamma} production, while L-1-MT had no effect. Stereospecific effect was also seen in PBMC tumoricidal activity, estimated by tumor cell viability (Trypan assay). The racemic mixture DL- and D-1-MT almost doubled the tumoricidal activity of PBMCs, while L-1-MT had no effect. These are previous unknown off-target effects of D-1-MT. Our data suggest the modulation of IFN-{gamma} and the activation of tumor recognition and killing processes by immune cells as important features for the in vivo effects of the D-1-MT. These findings should be considered in future studies of immunoadjuvants for cancer treatment.

pharmacology and toxicology↗