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Falco JA, Wynia-Smith SL, McCoy J, Smith BC, Weerapana E. Identification of Protein Targets of S-Nitroso-Coenzyme A-Mediated S-Nitrosation Using Chemoproteomics. ACS Chem Biol 2024; 19:193-207. [PMID: 38159293 DOI: 10.1021/acschembio.3c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
S-Nitrosation is a cysteine post-translational modification fundamental to cellular signaling. This modification regulates protein function in numerous biological processes in the nervous, cardiovascular, and immune systems. Small molecule or protein nitrosothiols act as mediators of NO signaling by transferring the NO group (formally NO+) to a free thiol on a target protein through a transnitrosation reaction. The protein targets of specific transnitrosating agents and the extent and functional effects of S-nitrosation on these target proteins have been poorly characterized. S-nitroso-coenzyme A (CoA-SNO) was recently identified as a mediator of endogenous S-nitrosation. Here, we identified direct protein targets of CoA-SNO-mediated transnitrosation using a competitive chemical-proteomic approach that quantified the extent of modification on 789 cysteine residues in response to CoA-SNO. A subset of cysteines displayed high susceptibility to modification by CoA-SNO, including previously uncharacterized sites of S-nitrosation. We further validated and functionally characterized the functional effects of S-nitrosation on the protein targets phosphofructokinase (platelet type), ATP citrate synthase, and ornithine aminotransferase.
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Affiliation(s)
- Julia A Falco
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Sarah L Wynia-Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - James McCoy
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Brian C Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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2
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Chan AN, Chen X, Falco JA, Bak DW, Weerapana E, Li B. Chemoproteomics Reveals Disruption of Metal Homeostasis and Metalloproteins by the Antibiotic Holomycin. ACS Chem Biol 2023; 18:1909-1914. [PMID: 37561838 PMCID: PMC10569480 DOI: 10.1021/acschembio.3c00360] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The natural product holomycin contains a unique cyclic ene-disulfide and exhibits broad-spectrum antimicrobial activities. Reduced holomycin chelates metal ions with a high affinity and disrupts metal homeostasis in the cell. To identify cellular metalloproteins inhibited by holomycin, reactive-cysteine profiling was performed using isotopic tandem orthogonal proteolysis-activity-based protein profiling (isoTOP-ABPP). This chemoproteomic analysis demonstrated that holomycin treatment increases the reactivity of metal-coordinating cysteine residues in several zinc-dependent and iron-sulfur cluster-dependent enzymes, including carbonic anhydrase II and fumarase A. We validated that holomycin inhibits fumarase A activity in bacterial cells and diminishes the presence of iron-sulfur clusters in fumarase A. Whole-proteome abundance analysis revealed that holomycin treatment induces zinc and iron starvation and cellular stress. This study suggests that holomycin inhibits bacterial growth by impairing the functions of multiple metalloenzymes and sets the stage for investigating the impact of metal-binding molecules on metalloproteomes by using chemoproteomics.
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Affiliation(s)
- Andrew N Chan
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiaoyan Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Julia A Falco
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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3
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Kisty EA, Falco JA, Weerapana E. Redox proteomics combined with proximity labeling enables monitoring of localized cysteine oxidation in cells. Cell Chem Biol 2023; 30:321-336.e6. [PMID: 36889310 PMCID: PMC10069010 DOI: 10.1016/j.chembiol.2023.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/06/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023]
Abstract
Reactive oxygen species (ROS) can modulate protein function through cysteine oxidation. Identifying protein targets of ROS can provide insight into uncharacterized ROS-regulated pathways. Several redox-proteomic workflows, such as oxidative isotope-coded affinity tags (OxICAT), exist to identify sites of cysteine oxidation. However, determining ROS targets localized within subcellular compartments and ROS hotspots remains challenging with existing workflows. Here, we present a chemoproteomic platform, PL-OxICAT, which combines proximity labeling (PL) with OxICAT to monitor localized cysteine oxidation events. We show that TurboID-based PL-OxICAT can monitor cysteine oxidation events within subcellular compartments such as the mitochondrial matrix and intermembrane space. Furthermore, we use ascorbate peroxidase (APEX)-based PL-OxICAT to monitor oxidation events within ROS hotspots by using endogenous ROS as the source of peroxide for APEX activation. Together, these platforms further hone our ability to monitor cysteine oxidation events within specific subcellular locations and ROS hotspots and provide a deeper understanding of the protein targets of endogenous and exogenous ROS.
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Affiliation(s)
- Eleni A Kisty
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Julia A Falco
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
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Benns HJ, Storch M, Falco JA, Fisher FR, Tamaki F, Alves E, Wincott CJ, Milne R, Wiedemar N, Craven G, Baragaña B, Wyllie S, Baum J, Baldwin GS, Weerapana E, Tate EW, Child MA. CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery. Nat Microbiol 2022; 7:1891-1905. [PMID: 36266336 PMCID: PMC9613468 DOI: 10.1038/s41564-022-01249-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022]
Abstract
Nucleophilic amino acids are important in covalent drug development yet underutilized as anti-microbial targets. Chemoproteomic technologies have been developed to mine chemically accessible residues via their intrinsic reactivity towards electrophilic probes but cannot discern which chemically reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based oligo recombineering (CORe) platform to support the rapid identification, functional prioritization and rational targeting of chemically reactive sites in haploid systems. Our approach couples protein sequence and function with biological fitness of live cells. Here we profile the electrophile sensitivity of proteinogenic cysteines in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. Electrophile-sensitive cysteines decorating the ribosome were found to be critical for parasite growth, with target-based screening identifying a parasite-selective anti-malarial lead molecule and validating the apicomplexan translation machinery as a target for ongoing covalent ligand development.
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Affiliation(s)
- H J Benns
- Department of Life Sciences, Imperial College London, London, UK
- Department of Chemistry, Imperial College London, London, UK
| | - M Storch
- London Biofoundry, Imperial College Translation & Innovation Hub, London, UK
| | - J A Falco
- Department of Chemistry, Boston College, Boston, MA, USA
| | - F R Fisher
- Department of Life Sciences, Imperial College London, London, UK
| | - F Tamaki
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - E Alves
- Department of Life Sciences, Imperial College London, London, UK
| | - C J Wincott
- Department of Life Sciences, Imperial College London, London, UK
| | - R Milne
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - N Wiedemar
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - G Craven
- Department of Chemistry, Imperial College London, London, UK
| | - B Baragaña
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - S Wyllie
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - J Baum
- Department of Life Sciences, Imperial College London, London, UK
- School of Biomedical Sciences, UNSW, Sydney, NSW, Australia
| | - G S Baldwin
- Department of Life Sciences, Imperial College London, London, UK
| | - E Weerapana
- Department of Chemistry, Boston College, Boston, MA, USA
| | - E W Tate
- Department of Chemistry, Imperial College London, London, UK.
| | - M A Child
- Department of Life Sciences, Imperial College London, London, UK.
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Tagoe DNA, Drozda AA, Falco JA, Bechtel TJ, Weerapana E, Gubbels MJ. Ferlins and TgDOC2 in Toxoplasma Microneme, Rhoptry and Dense Granule Secretion. Life (Basel) 2021; 11:217. [PMID: 33803212 PMCID: PMC7999867 DOI: 10.3390/life11030217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
The host cell invasion process of apicomplexan parasites like Toxoplasma gondii is facilitated by sequential exocytosis of the microneme, rhoptry and dense granule organelles. Exocytosis is facilitated by a double C2 domain (DOC2) protein family. This class of C2 domains is derived from an ancestral calcium (Ca2+) binding archetype, although this feature is optional in extant C2 domains. DOC2 domains provide combinatorial power to the C2 domain, which is further enhanced in ferlins that harbor 5-7 C2 domains. Ca2+ conditionally engages the C2 domain with lipids, membranes, and/or proteins to facilitating vesicular trafficking and membrane fusion. The widely conserved T. gondii ferlins 1 (FER1) and 2 (FER2) are responsible for microneme and rhoptry exocytosis, respectively, whereas an unconventional TgDOC2 is essential for microneme exocytosis. The general role of ferlins in endolysosmal pathways is consistent with the repurposed apicomplexan endosomal pathways in lineage specific secretory organelles. Ferlins can facilitate membrane fusion without SNAREs, again pertinent to the Apicomplexa. How temporal raises in Ca2+ combined with spatiotemporally available membrane lipids and post-translational modifications mesh to facilitate sequential exocytosis events is discussed. In addition, new data on cross-talk between secretion events together with the identification of a new microneme protein, MIC21, is presented.
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Affiliation(s)
- Daniel N. A. Tagoe
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA; (D.N.A.T.); (A.A.D.)
| | - Allison A. Drozda
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA; (D.N.A.T.); (A.A.D.)
| | - Julia A. Falco
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA; (J.A.F.); (T.J.B.); (E.W.)
| | - Tyler J. Bechtel
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA; (J.A.F.); (T.J.B.); (E.W.)
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA; (J.A.F.); (T.J.B.); (E.W.)
| | - Marc-Jan Gubbels
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA; (D.N.A.T.); (A.A.D.)
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Peeler JC, Falco JA, Kelemen RE, Abo M, Chartier BV, Edinger LC, Chen J, Chatterjee A, Weerapana E. Generation of Recombinant Mammalian Selenoproteins through Genetic Code Expansion with Photocaged Selenocysteine. ACS Chem Biol 2020; 15:1535-1540. [PMID: 32330002 DOI: 10.1021/acschembio.0c00147] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Selenoproteins contain the amino acid selenocysteine (Sec) and are found in all domains of life. The functions of many selenoproteins are poorly understood, partly due to difficulties in producing recombinant selenoproteins for cell-biological evaluation. Endogenous mammalian selenoproteins are produced through a noncanonical translation mechanism requiring suppression of the UGA stop codon and a Sec insertion sequence (SECIS) element in the 3' untranslated region of the mRNA. Here, recombinant selenoproteins are generated in mammalian cells through genetic code expansion, circumventing the requirement for the SECIS element and selenium availability. An engineered orthogonal E. coli leucyl-tRNA synthetase/tRNA pair is used to incorporate a photocaged Sec (DMNB-Sec) at the UAG amber stop codon. DMNB-Sec is successfully incorporated into GFP and uncaged by irradiation of living cells. Furthermore, DMNB-Sec is used to generate the native selenoprotein methionine-R-sulfoxide reductase B1 (MsrB1). Importantly, MsrB1 is shown to be catalytically active after uncaging, constituting the first use of genetic code expansion to generate a functional selenoprotein in mammalian systems. The ability to site-specifically introduce Sec directly in mammalian cells, and temporally modulate selenoprotein activity, will aid in the characterization of mammalian selenoprotein function.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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Bak DW, Bechtel TJ, Falco JA, Weerapana E. Cysteine reactivity across the subcellular universe. Curr Opin Chem Biol 2018; 48:96-105. [PMID: 30508703 DOI: 10.1016/j.cbpa.2018.11.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/25/2018] [Accepted: 11/02/2018] [Indexed: 01/01/2023]
Abstract
Cysteine residues are concentrated at key functional sites within proteins, performing diverse roles in metal binding, catalysis, and redox chemistry. Chemoproteomic platforms to interrogate the reactive cysteinome have developed significantly over the past 10 years, resulting in a greater understanding of cysteine functionality, modification, and druggability. Recently, chemoproteomic methods to examine reactive cysteine residues from specific subcellular organelles have provided significantly improved proteome coverage and highlights the unique functionalities of cysteine residues mediated by cellular localization. Here, the diverse physicochemical properties of the mammalian subcellular organelles are explored in the context of their effects on cysteine reactivity. The unique functions of cysteine residues found in the mitochondria and endoplasmic reticulum are highlighted, together with an overview into chemoproteomic platforms employed to investigate cysteine reactivity in subcellular organelles.
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Affiliation(s)
- Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, United States.
| | - Tyler J Bechtel
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, United States
| | - Julia A Falco
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, United States.
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