1
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Shaw TA, Powdrill MH, Sherratt AR, Garland K, Li BJ, Beauchemin AM, Pezacki JP. Reactivity of N-acyl hydrazone probes with the mammalian proteome. RSC Med Chem 2021; 12:797-803. [PMID: 34124678 DOI: 10.1039/d1md00027f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/16/2021] [Indexed: 11/21/2022] Open
Abstract
Small molecule probes with distinct reactivities are useful tools for the identification and characterization of protein modifications and function. Herein, we show that hydrazone probes with an N-carbamate structural motif react differently from N-carbamates within the human proteome. Mass spectrometry analysis of probe-treated mammalian cell lysates identified several proteins that were covalently modified by the hydrazone probes, including the cytidine deaminase APOBEC3A. We used this enzyme as a model to explore the reactivity of the probes with amino acid residues using LC-MS/MS. Both reactive serine and cysteine residues outside of the enzyme active site were covalently modified. A 1-napthol leaving group provided the most extensive reactivity. These results confirm a unique chemotype for hydrazone probes which can be further optimized to target distinct targets of the human proteome.
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Affiliation(s)
- Tyler A Shaw
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - Megan H Powdrill
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - Allison R Sherratt
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - Keira Garland
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - Bin-Jie Li
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - André M Beauchemin
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
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2
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Shaw TA, Ablenas CJ, Desrochers GF, Powdrill MH, Bilodeau DA, Vincent-Rocan JF, Niu M, Monette A, Mouland AJ, Beauchemin AM, Pezacki JP. A Bifunctional Nucleoside Probe for the Inhibition of the Human Immunodeficiency Virus-Type 1 Reverse Transcriptase. Bioconjug Chem 2020; 31:1537-1544. [DOI: 10.1021/acs.bioconjchem.0c00191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Christopher J. Ablenas
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Jean-François Vincent-Rocan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Meijuan Niu
- Lady Davis Institute at the Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, Québec H3T 1E2, Canada
| | - Anne Monette
- Lady Davis Institute at the Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, Québec H3T 1E2, Canada
| | - Andrew J. Mouland
- Lady Davis Institute at the Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, Québec H3T 1E2, Canada
- Department of Medicine, McGill University, 3999 Côte-Ste-Catherine Road, Montréal, Québec H3T 1E2, Canada
| | - André M. Beauchemin
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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3
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Ablenas CJ, Gidi Y, Powdrill MH, Ahmed N, Shaw TA, Mesko M, Götte M, Cosa G, Pezacki JP. Hepatitis C Virus Helicase Binding Activity Monitored through Site-Specific Labeling Using an Expanded Genetic Code. ACS Infect Dis 2019; 5:2118-2126. [PMID: 31640339 DOI: 10.1021/acsinfecdis.9b00220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of unwinding catalyzed by the hepatitis C virus nonstructural protein 3 helicase (NS3h) has been a subject of considerable interest, with NS3h serving as a prototypical enzyme in the study of helicase function. Recent studies support an ATP-fueled, inchworm-like stepping of NS3h on the nucleic acid that would result in the displacement of the complementary strand of the duplex during unwinding. Here, we describe the screening of a site of incorporation of an unnatural amino acid in NS3h for fluorescent labeling of the enzyme to be used in single-molecule Förster resonance energy transfer (FRET) experiments. From the nine potential sites identified in NS3h for incorporation of the unnatural amino acid, only one allowed for expression and fluorescent labeling of the recombinant protein. Incorporation of the unnatural amino acid was confirmed via bulk assays to not interfere with unwinding activity of the helicase. Binding to four different dsDNA sequences bearing a ssDNA overhang segment of varying length (either minimal 6 or 7 base length overhang to ensure binding or a long 24 base overhang) and sequence was recorded with the new NS3h construct at the single-molecule level. Single-molecule fluorescence displayed time intervals with anticorrelated donor and acceptor emission fluctuations associated with protein binding to the substrates. An apparent FRET value was estimated from the binding events showing a single FRET value of ∼0.8 for the 6-7 base overhangs. A smaller mean value and a broad distribution was in turn recorded for the long ssDNA overhang, consistent with NS3h exploring a larger physical space while bound to the DNA construct. Notably, intervals where NS3h binding was recorded were exhibited at time periods where the acceptor dye reversibly bleached. Protein induced fluorescence intensity enhancement in the donor channel became apparent at these intervals. Overall, the site-specific fluorescent labeling of NS3h reported here provides a powerful tool for future studies to monitor the dynamics of enzyme translocation during unwinding by single-molecule FRET.
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Affiliation(s)
- Christopher J. Ablenas
- Department of Biochemistry, McGill University, Montreal, Quebec H3G1Y6, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
| | - Yasser Gidi
- Department of Chemistry, McGill University, Montreal, Quebec H3A0B8, Canada
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
| | - Noreen Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
| | - Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
| | - Mihai Mesko
- Department of Chemistry, McGill University, Montreal, Quebec H3A0B8, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G2R7, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, Montreal, Quebec H3A0B8, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N6N5, Canada
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Ahmed N, Foss DV, Powdrill MH, Pezacki JP. Site-Specific Cross-Linking of a p19 Viral Suppressor of RNA Silencing Protein and Its RNA Targets Using an Expanded Genetic Code. Biochemistry 2019; 58:3520-3526. [PMID: 31329415 DOI: 10.1021/acs.biochem.9b00428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The p19 viral suppressor of RNA silencing protein has useful applications in biotechnology due to its high affinity for binding to small RNAs such as small interfering RNAs (siRNAs). Also, its applications for the study and modulation of microRNAs are actively expanding. Here we demonstrate the successful site-specific incorporation of a photoactivatable unnatural amino acid, p-azido-l-phenylalanine (AzF), for cross-linking to RNA substrates into the p19 sequence. Incorporation of AzF was performed at three positions in the protein near the RNA binding site: K67, R115, and T111. Incorporation of AzF at position T111 of p19 did not affect the binding affinity of p19 for siRNAs and also showed nanomolar affinity for human microRNA miR-122. The affinity was less favorable with AzF incorporation at two other positions, suggesting the sensitivity of placement of the unnatural amino acid. Exposure of the T111AzF in complex with either siRNA or miRNA to ultraviolet light resulted in cross-linking of the protein with the RNA, but no cross-linking could be detected with the wild-type protein. Our results demonstrate that p19-T111AzF can be used for detection of small RNAs, including human miR-122, with high sensitivity and to irreversibly sequester these RNAs through covalent photo-cross-linking.
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Affiliation(s)
- Noreen Ahmed
- Department of Biochemistry, Microbiology and Immunology , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
| | - Dana V Foss
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
| | - Megan H Powdrill
- Department of Biochemistry, Microbiology and Immunology , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
| | - John Paul Pezacki
- Department of Biochemistry, Microbiology and Immunology , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada.,Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
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5
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Shaw TA, Singaravelu R, Powdrill MH, Nhan J, Ahmed N, Özcelik D, Pezacki JP. MicroRNA-124 Regulates Fatty Acid and Triglyceride Homeostasis. iScience 2018; 10:149-157. [PMID: 30528902 PMCID: PMC6282456 DOI: 10.1016/j.isci.2018.11.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/01/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are part of a complex regulatory network that modulates cellular lipid metabolism. Here, we identify miR-124 as a regulator of triglyceride (TG) metabolism. This study advances our knowledge of the role of miR-124 in human hepatoma cells. Transcriptional profiling of Huh7.5 cells overexpressing miR-124 reveals enrichment for host factors involved in fatty acid oxidation among repressed miRNA targets. In addition, miR-124 down-regulates arylacetamide deacetylase (AADAC) and adipose triglyceride lipase, lipases proposed to mediate breakdown of hepatic TG stores for lipoprotein assembly and mitochondrial β-oxidation. Consistent with the inhibition of TG and fatty acid catabolism, miR-124 expression promotes cellular TG accumulation. Interestingly, miR-124 inhibits the production of hepatitis C virus, a virus that hijacks lipid pathways during its life cycle. Antiviral activity of miR-124 is consistent with repression of AADAC, a pro-viral host factor. Overall, our data highlight miR-124 as a novel regulator of TG metabolism in human hepatoma cells. miR-124 regulates triglyceride and fatty acid metabolism miR-124 represses genes associated with fatty acid and triglyceride breakdown miR-124 promotes triglyceride accumulation in hepatoma cells
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Affiliation(s)
- Tyler A Shaw
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Ragunath Singaravelu
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Megan H Powdrill
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Jordan Nhan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Nadine Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Dennis Özcelik
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada.
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6
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Singaravelu R, Quan C, Powdrill MH, Shaw TA, Srinivasan P, Lyn RK, Alonzi RC, Jones DM, Filip R, Russell RS, Pezacki JP. MicroRNA-7 mediates cross-talk between metabolic signaling pathways in the liver. Sci Rep 2018; 8:361. [PMID: 29321595 PMCID: PMC5762714 DOI: 10.1038/s41598-017-18529-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 12/08/2017] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as critical regulators of cellular metabolism. To characterise miRNAs crucial to the maintenance of hepatic lipid homeostasis, we examined the overlap between the miRNA signature associated with inhibition of peroxisome proliferator activated receptor-α (PPAR-α) signaling, a pathway regulating fatty acid metabolism, and the miRNA profile associated with 25-hydroxycholesterol treatment, an oxysterol regulator of sterol regulatory element binding protein (SREBP) and liver X receptor (LXR) signaling. Using this strategy, we identified microRNA-7 (miR-7) as a PPAR-α regulated miRNA, which activates SREBP signaling and promotes hepatocellular lipid accumulation. This is mediated, in part, by suppression of the negative regulator of SREBP signaling: ERLIN2. miR-7 also regulates genes associated with PPAR signaling and sterol metabolism, including liver X receptor β (LXR-β), a transcriptional regulator of sterol synthesis, efflux, and excretion. Collectively, our findings highlight miR-7 as a novel mediator of cross-talk between PPAR, SREBP, and LXR signaling pathways in the liver.
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Affiliation(s)
- Ragunath Singaravelu
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Curtis Quan
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Megan H Powdrill
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Tyler A Shaw
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Prashanth Srinivasan
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rodney K Lyn
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rhea C Alonzi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel M Jones
- Immunology and Infectious Diseases, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1B 3V6, Canada
| | - Roxana Filip
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rodney S Russell
- Immunology and Infectious Diseases, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1B 3V6, Canada
| | - John P Pezacki
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada.
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada.
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7
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Lafreniere MA, Powdrill MH, Singaravelu R, Pezacki JP. 6-Hydroxydopamine Inhibits the Hepatitis C Virus through Alkylation of Host and Viral Proteins and the Induction of Oxidative Stress. ACS Infect Dis 2016; 2:863-871. [PMID: 27682680 DOI: 10.1021/acsinfecdis.6b00098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Many viruses, including the hepatitis C virus (HCV), are dependent on the host RNA silencing pathway for replication. In this study, we screened small molecule probes, previously reported to disrupt loading of the RNA-induced silencing complex (RISC), including 6-hydroxydopamine (6-OHDA), suramin (SUR), and aurintricarboxylic acid (ATA), to examine their effects on viral replication. We found that 6-OHDA inhibited HCV replication; however, 6-OHDA was a less potent inhibitor of RISC than either SUR or ATA. By generating a novel chemical probe (6-OHDA-yne), we determined that 6-OHDA covalently modifies host and virus proteins. Moreover, 6-OHDA was shown to be an alkylating agent that is capable of generating adducts with a number of enzymes involved in the oxidative stress response. Furthermore, modification of viral enzymes with 6-OHDA and 6-OHDA-yne was found to inhibit their enzymatic activity. Our findings suggest that 6-OHDA is a probe for oxidative stress as well as protein alkylation, and these properties together contribute to the antiviral effects of this compound.
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Affiliation(s)
- Matthew A. Lafreniere
- Department of Chemistry
and Biomolecular Sciences, University of Ottawa, 10 Marie Curie
Private, Ottawa, ON, Canada K1N 6N5
| | - Megan H. Powdrill
- Department of Chemistry
and Biomolecular Sciences, University of Ottawa, 10 Marie Curie
Private, Ottawa, ON, Canada K1N 6N5
| | - Ragunath Singaravelu
- Department
of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H 8M5
| | - John Paul Pezacki
- Department of Chemistry
and Biomolecular Sciences, University of Ottawa, 10 Marie Curie
Private, Ottawa, ON, Canada K1N 6N5
- Department
of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H 8M5
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8
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Abstract
Interactions between host and pathogen proteins constitute an important aspect of both infectivity and the host immune response. Different viruses have evolved complex mechanisms to hijack host-cell machinery and metabolic pathways to redirect resources and energy flow toward viral propagation. These interactions are often critical to the virus, and thus understanding these interactions at a molecular level gives rise to opportunities to develop novel antiviral strategies for therapeutic intervention. This review summarizes current advances in chemoproteomic methods for studying these molecular altercations between different viruses and their hosts.
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Affiliation(s)
- Miroslava Strmiskova
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew A. Lafreniere
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
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9
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Powdrill MH, Desrochers GF, Singaravelu R, Pezacki JP. The role of microRNAs in metabolic interactions between viruses and their hosts. Curr Opin Virol 2016; 19:71-6. [PMID: 27475325 DOI: 10.1016/j.coviro.2016.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 02/07/2023]
Abstract
Productive viral infection requires changes to the cellular metabolic landscape in order to obtain the building blocks and create the microenvironments necessary for the viral life cycle. In mammals, these alterations of metabolic pathways have been shown to be mediated in part by host and virus-encoded microRNAs. To counteract virally-induced changes in the cellular metabolic profile, the interferon-regulated antiviral response restricts viral access to key metabolites by altering cellular metabolism, mediated through induction of specific microRNAs regulating key lipid biosynthetic processes. In this review, we examine recent studies demonstrating the important role of microRNAs in the regulation of metabolic flux during viral infection.
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Affiliation(s)
- Megan H Powdrill
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario, Canada K1N 6N5
| | - Geneviève F Desrochers
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario, Canada K1N 6N5
| | - Ragunath Singaravelu
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, 10 Marie Curie, Ottawa, Ontario, Canada K1N 6N5; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5.
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10
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Nasheri N, McKay CS, Fulton K, Twine S, Powdrill MH, Sherratt AR, Pezacki JP. Back Cover: Hydrophobic Triaryl-Substituted β-Lactams as Activity-Based Probes for Profiling Eukaryotic Enzymes and Host-Pathogen Interactions (ChemBioChem 15/2014). Chembiochem 2014. [DOI: 10.1002/cbic.201490054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Nasheri N, McKay CS, Fulton K, Twine S, Powdrill MH, Sherratt AR, Pezacki JP. Hydrophobic triaryl-substituted β-lactams as activity-based probes for profiling eukaryotic enzymes and host-pathogen interactions. Chembiochem 2014; 15:2195-200. [PMID: 25179744 DOI: 10.1002/cbic.201402097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Neda Nasheri
- Life Sciences Division, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6 (Canada); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5 (Canada)
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12
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Karam P, Powdrill MH, Liu HW, Vasquez C, Mah W, Bernatchez J, Götte M, Cosa G. Dynamics of hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B in complex with RNA. J Biol Chem 2014; 289:14399-411. [PMID: 24692556 DOI: 10.1074/jbc.m113.529743] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hepatitis C virus (HCV) non-structural protein 5B (NS5B) is an RNA-dependent RNA polymerase that is essentially required for viral replication. Although previous studies revealed important properties of static NS5B-RNA complexes, the nature and relevance of dynamic interactions have yet to be elucidated. Here, we devised a single molecule Förster Resonance Energy Transfer (SM-FRET) assay to monitor temporal changes upon binding of NS5B to surface immobilized RNA templates. The data show enzyme association-dissociation events that occur within the time resolution of our setup as well as FRET-fluctuations in association with stable binary complexes that extend over prolonged periods of time. Fluctuations are shown to be dependent on the length of the RNA substrate, and enzyme concentration. Mutations in close proximity to the template entrance (K98E, K100E), and in the center of the RNA binding channel (R394E), reduce both the population of RNA-bound enzyme and the fluctuations associated to the binary complex. Similar observations are reported with an allosteric nonnucleoside NS5B inhibitor. Our assay enables for the first time the visualization of association-dissociation events of HCV-NS5B with RNA, and also the direct monitoring of the interaction between HCV NS5B, its RNA template, and finger loop inhibitors. We observe both a remarkably low dissociation rate for wild type HCV NS5B, and a highly dynamic enzyme-RNA binary complex. These results provide a plausible mechanism for formation of a productive binary NS5B-RNA complex, here NS5B slides along the RNA template facilitating positioning of its 3' terminus at the enzyme active site.
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Affiliation(s)
| | - Megan H Powdrill
- the Department of Microbiology and Immunology, McGill University, Montréal, Quebec H3A 2B4, Canada
| | | | - Colins Vasquez
- the Department of Microbiology and Immunology, McGill University, Montréal, Quebec H3A 2B4, Canada
| | - Wayne Mah
- From the Department of Chemistry and
| | - Jean Bernatchez
- the Department of Microbiology and Immunology, McGill University, Montréal, Quebec H3A 2B4, Canada
| | - Matthias Götte
- From the Department of Chemistry and the Department of Biochemistry, McGill University, Montréal, Quebec H3G 1Y6, Canada and the Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Quebec H3A 1A3, Canada
| | - Gonzalo Cosa
- From the Department of Chemistry and the Centre for Self-Assembled Chemical Structures (CSACS/CRMAA), McGill University, Montréal, Quebec H3A 2K6, Canada,
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13
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Powdrill MH, Bernatchez JA, Götte M. Inhibitors of the Hepatitis C Virus RNA-Dependent RNA Polymerase NS5B. Viruses 2010; 2:2169-2195. [PMID: 21994615 PMCID: PMC3185568 DOI: 10.3390/v2102169] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [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: 07/29/2010] [Revised: 09/06/2010] [Accepted: 09/06/2010] [Indexed: 12/26/2022] Open
Abstract
More than 20 years after the identification of the hepatitis C virus (HCV) as a novel human pathogen, the only approved treatment remains a combination of pegylated interferon-α and ribavirin. This rather non-specific therapy is associated with severe side effects and by far not everyone benefits from treatment. Recently, progress has been made in the development of specifically targeted antiviral therapy for HCV (STAT-C). A major target for such direct acting antivirals (DAAs) is the HCV RNA-dependent RNA polymerase or non-structural protein 5B (NS5B), which is essential for viral replication. This review will examine the current state of development of inhibitors targeting the polymerase and issues such as the emergence of antiviral resistance during treatment, as well as strategies to address this problem.
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Affiliation(s)
- Megan H. Powdrill
- McGill University, Department of Microbiology and Immunology, 3775 University Room D6, Montreal Quebec, H3A2B4, Canada; E-Mail:
| | - Jean A. Bernatchez
- McGill University, Department of Biochemistry, 3775 University Room D6, Montreal Quebec, H3A2B4, Canada; E-Mail:
| | - Matthias Götte
- McGill University, Department of Microbiology and Immunology, 3775 University Room D6, Montreal Quebec, H3A2B4, Canada; E-Mail:
- McGill University, Department of Biochemistry, 3775 University Room D6, Montreal Quebec, H3A2B4, Canada; E-Mail:
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Deval J, Powdrill MH, D'Abramo CM, Cellai L, Götte M. Pyrophosphorolytic excision of nonobligate chain terminators by hepatitis C virus NS5B polymerase. Antimicrob Agents Chemother 2007; 51:2920-8. [PMID: 17502402 PMCID: PMC1932539 DOI: 10.1128/aac.00186-07] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonobligate chain terminators, such as 2'-C-methylated nucleotides, block RNA synthesis by the RNA-dependent RNA polymerase (RdRp) of hepatitis C virus (HCV). Previous studies with related viral polymerases have shown that classical chain terminators lacking the 3'-hydroxyl group can be excised in the presence of pyrophosphate (PP(i)), which is detrimental to the inhibitory activity of these compounds. Here we demonstrate that the HCV RdRp enzyme is capable of removing both obligate and clinically relevant nonobligate chain terminators. Pyrimidines are more efficiently excised than are purines. The presence of the next complementary templated nucleotide literally blocks the excision of obligate chain terminators through the formation of a dead-end complex (DEC). However, 2'-C-methylated CMP is still cleaved efficiently under these conditions. These findings show that a 2'-methylated primer terminus impedes nucleotide binding. The S282T mutation, associated with resistance to 2'-C-methylated nucleotides, does not affect the excision patterns. Thus, the decreased susceptibility to 2'-C-methylated nucleotides appears to be based solely on improved discrimination between the inhibitor and its natural counterpart. In conclusion, our data suggest that the phosphorolytic excision of nonobligate, pyrimidine-based chain terminators can diminish their potency. The templated nucleotide does not appear to provide protection from excision through DEC formation.
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Affiliation(s)
- Jérôme Deval
- Department of Microbiology & Immunology, McGill University, Duff Medical Building, Montreal, Quebec, Canada
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