1
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Michon M, Müller-Schiffmann A, Lingappa AF, Yu SF, Du L, Deiter F, Broce S, Mallesh S, Crabtree J, Lingappa UF, Macieik A, Müller L, Ostermann PN, Andrée M, Adams O, Schaal H, Hogan RJ, Tripp RA, Appaiah U, Anand SK, Campi TW, Ford MJ, Reed JC, Lin J, Akintunde O, Copeland K, Nichols C, Petrouski E, Moreira AR, Jiang IT, DeYarman N, Brown I, Lau S, Segal I, Goldsmith D, Hong S, Asundi V, Briggs EM, Phyo NS, Froehlich M, Onisko B, Matlack K, Dey D, Lingappa JR, Prasad DM, Kitaygorodskyy A, Solas D, Boushey H, Greenland J, Pillai S, Lo MK, Montgomery JM, Spiropoulou CF, Korth C, Selvarajah S, Paulvannan K, Lingappa VR. A pan-respiratory antiviral chemotype targeting a transient host multi-protein complex. Open Biol 2024; 14:230363. [PMID: 38889796 DOI: 10.1098/rsob.230363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/02/2024] [Indexed: 06/20/2024] Open
Abstract
We present a novel small molecule antiviral chemotype that was identified by an unconventional cell-free protein synthesis and assembly-based phenotypic screen for modulation of viral capsid assembly. Activity of PAV-431, a representative compound from the series, has been validated against infectious viruses in multiple cell culture models for all six families of viruses causing most respiratory diseases in humans. In animals, this chemotype has been demonstrated efficacious for porcine epidemic diarrhoea virus (a coronavirus) and respiratory syncytial virus (a paramyxovirus). PAV-431 is shown to bind to the protein 14-3-3, a known allosteric modulator. However, it only appears to target the small subset of 14-3-3 which is present in a dynamic multi-protein complex whose components include proteins implicated in viral life cycles and in innate immunity. The composition of this target multi-protein complex appears to be modified upon viral infection and largely restored by PAV-431 treatment. An advanced analog, PAV-104, is shown to be selective for the virally modified target, thereby avoiding host toxicity. Our findings suggest a new paradigm for understanding, and drugging, the host-virus interface, which leads to a new clinical therapeutic strategy for treatment of respiratory viral disease.
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Affiliation(s)
- Maya Michon
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | - Li Du
- Vitalant Research Institute, San Francisco, CA, 94118-4417 USA
| | - Fred Deiter
- Veterans Administration Medical Center, San Francisco, CA, USA
| | - Sean Broce
- Prosetta Biosciences, San Francisco, CA, USA
| | | | - Jackelyn Crabtree
- University of Georgia, Animal Health Research Center, Athens, GA, 28130 USA
| | | | | | - Lisa Müller
- Institute of Virology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | | | - Marcel Andrée
- Institute of Virology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | - Ortwin Adams
- Institute of Virology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | - Robert J Hogan
- Vitalant Research Institute, San Francisco, CA, 94118-4417 USA
| | - Ralph A Tripp
- Vitalant Research Institute, San Francisco, CA, 94118-4417 USA
| | | | | | | | | | | | - Jim Lin
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Ian Brown
- Prosetta Biosciences, San Francisco, CA, USA
| | - Sharon Lau
- Prosetta Biosciences, San Francisco, CA, USA
| | - Ilana Segal
- Prosetta Biosciences, San Francisco, CA, USA
| | | | - Shi Hong
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Jaisri R Lingappa
- Department of Global Health, University of Washington, Seattle, WA, 98195, USA
| | | | | | | | - Homer Boushey
- University of California, San Francisco, CA, 94143, USA
| | - John Greenland
- Veterans Administration Medical Center, San Francisco, CA, USA
- University of California, San Francisco, CA, 94143, USA
| | - Satish Pillai
- Vitalant Research Institute, San Francisco, CA, 94118-4417 USA
- University of California, San Francisco, CA, 94143, USA
| | - Michael K Lo
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel M Montgomery
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Carsten Korth
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | | | | | - Vishwanath R Lingappa
- Prosetta Biosciences, San Francisco, CA, USA
- University of California, San Francisco, CA, 94143, USA
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2
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Michon M, Müller-Schiffmann A, Lingappa AF, Yu SF, Du L, Deiter F, Broce S, Mallesh S, Crabtree J, Lingappa UF, Macieik A, Müller L, Ostermann PN, Andrée M, Adams O, Schaal H, Hogan RJ, Tripp RA, Appaiah U, Anand SK, Campi TW, Ford MJ, Reed JC, Lin J, Akintunde O, Copeland K, Nichols C, Petrouski E, Moreira AR, Jiang IT, DeYarman N, Brown I, Lau S, Segal I, Goldsmith D, Hong S, Asundi V, Briggs EM, Phyo NS, Froehlich M, Onisko B, Matlack K, Dey D, Lingappa JR, Prasad MD, Kitaygorodskyy A, Solas D, Boushey H, Greenland J, Pillai S, Lo MK, Montgomery JM, Spiropoulou CF, Korth C, Selvarajah S, Paulvannan K, Lingappa VR. A Pan-Respiratory Antiviral Chemotype Targeting a Host Multi-Protein Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2021.01.17.426875. [PMID: 34931190 PMCID: PMC8687465 DOI: 10.1101/2021.01.17.426875] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a novel small molecule antiviral chemotype that was identified by an unconventional cell-free protein synthesis and assembly-based phenotypic screen for modulation of viral capsid assembly. Activity of PAV-431, a representative compound from the series, has been validated against infectious virus in multiple cell culture models for all six families of viruses causing most respiratory disease in humans. In animals this chemotype has been demonstrated efficacious for Porcine Epidemic Diarrhea Virus (a coronavirus) and Respiratory Syncytial Virus (a paramyxovirus). PAV-431 is shown to bind to the protein 14-3-3, a known allosteric modulator. However, it only appears to target the small subset of 14-3-3 which is present in a dynamic multi-protein complex whose components include proteins implicated in viral lifecycles and in innate immunity. The composition of this target multi-protein complex appears to be modified upon viral infection and largely restored by PAV-431 treatment. Our findings suggest a new paradigm for understanding, and drugging, the host-virus interface, which leads to a new clinical therapeutic strategy for treatment of respiratory viral disease.
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Affiliation(s)
- Maya Michon
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | - Li Du
- Vitalant Research Institute, San Francisco, CA, USA
| | - Fred Deiter
- Veterans Administration Medical Center, San Francisco, CA, USA
| | - Sean Broce
- Prosetta Biosciences, San Francisco, CA, USA
| | | | - Jackelyn Crabtree
- University of Georgia, Animal Health Research Center, Athens, GA, USA
| | | | | | - Lisa Müller
- Institute of Virology, Heinrich Heine University, Düsseldorf, Germany
| | | | - Marcel Andrée
- Institute of Virology, Heinrich Heine University, Düsseldorf, Germany
| | - Ortwin Adams
- Institute of Virology, Heinrich Heine University, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich Heine University, Düsseldorf, Germany
| | - Robert J. Hogan
- University of Georgia, Animal Health Research Center, Athens, GA, USA
| | - Ralph A. Tripp
- University of Georgia, Animal Health Research Center, Athens, GA, USA
| | | | | | | | | | - Jonathan C. Reed
- Dept. of Global Health, University of Washington, Seattle, WA, USA
| | - Jim Lin
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Ian Brown
- Prosetta Biosciences, San Francisco, CA, USA
| | - Sharon Lau
- Prosetta Biosciences, San Francisco, CA, USA
| | - Ilana Segal
- Prosetta Biosciences, San Francisco, CA, USA
| | | | - Shi Hong
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - John Greenland
- Veterans Administration Medical Center, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Satish Pillai
- Vitalant Research Institute, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Michael K. Lo
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Carsten Korth
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
| | | | | | - Vishwanath R. Lingappa
- Prosetta Biosciences, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
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3
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Weber JN, Minner-Meinen R, Behnecke M, Biedendieck R, Hänsch VG, Hercher TW, Hertweck C, van den Hout L, Knüppel L, Sivov S, Schulze J, Mendel RR, Hänsch R, Kaufholdt D. Moonlighting Arabidopsis molybdate transporter 2 family and GSH-complex formation facilitate molybdenum homeostasis. Commun Biol 2023; 6:801. [PMID: 37532778 PMCID: PMC10397214 DOI: 10.1038/s42003-023-05161-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/21/2023] [Indexed: 08/04/2023] Open
Abstract
Molybdenum (Mo) as essential micronutrient for plants, acts as active component of molybdenum cofactor (Moco). Core metabolic processes like nitrate assimilation or abscisic-acid biosynthesis rely on Moco-dependent enzymes. Although a family of molybdate transport proteins (MOT1) is known to date in Arabidopsis, molybdate homeostasis remained unclear. Here we report a second family of molybdate transporters (MOT2) playing key roles in molybdate distribution and usage. KO phenotype-analyses, cellular and organ-specific localization, and connection to Moco-biosynthesis enzymes via protein-protein interaction suggest involvement in cellular import of molybdate in leaves and reproductive organs. Furthermore, we detected a glutathione-molybdate complex, which reveals how vacuolar storage is maintained. A putative Golgi S-adenosyl-methionine transport function was reported recently for the MOT2-family. Here, we propose a moonlighting function, since clear evidence of molybdate transport was found in a yeast-system. Our characterization of the MOT2-family and the detection of a glutathione-molybdate complex unveil the plant-wide way of molybdate.
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Affiliation(s)
- Jan-Niklas Weber
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
| | - Rieke Minner-Meinen
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
| | - Maria Behnecke
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
| | - Rebekka Biedendieck
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Rebenring 56, D-38106, Braunschweig, Germany
| | - Veit G Hänsch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Research and Infection Biology (HKI), Beutenbergstrasse 11a, Faculty of Biological Sciences, Friedrich Schiller University Jena, D-07743, Jena, Germany
| | - Thomas W Hercher
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Research and Infection Biology (HKI), Beutenbergstrasse 11a, Faculty of Biological Sciences, Friedrich Schiller University Jena, D-07743, Jena, Germany
| | - Lena van den Hout
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
| | - Lars Knüppel
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
| | - Simon Sivov
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
| | - Jutta Schulze
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
| | - Ralf-R Mendel
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
| | - Robert Hänsch
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany.
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, , Southwest University, Tiansheng Road No. 2, 400715, Chongqing, Beibei District, PR China.
| | - David Kaufholdt
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstrasse 1, D-38106, Braunschweig, Germany
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4
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Gupta MN, Uversky VN. Moonlighting enzymes: when cellular context defines specificity. Cell Mol Life Sci 2023; 80:130. [PMID: 37093283 PMCID: PMC11073002 DOI: 10.1007/s00018-023-04781-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 04/15/2023] [Indexed: 04/25/2023]
Abstract
It is not often realized that the absolute protein specificity is an exception rather than a rule. Two major kinds of protein multi-specificities are promiscuity and moonlighting. This review discusses the idea of enzyme specificity and then focusses on moonlighting. Some important examples of protein moonlighting, such as crystallins, ceruloplasmin, metallothioniens, macrophage migration inhibitory factor, and enzymes of carbohydrate metabolism are discussed. How protein plasticity and intrinsic disorder enable the removing the distinction between enzymes and other biologically active proteins are outlined. Finally, information on important roles of moonlighting in human diseases is updated.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612-4799, USA.
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5
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Byron A, Griffith BGC, Herrero A, Loftus AEP, Koeleman ES, Kogerman L, Dawson JC, McGivern N, Culley J, Grimes GR, Serrels B, von Kriegsheim A, Brunton VG, Frame MC. Characterisation of a nucleo-adhesome. Nat Commun 2022; 13:3053. [PMID: 35650196 PMCID: PMC9160004 DOI: 10.1038/s41467-022-30556-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 05/02/2022] [Indexed: 11/09/2022] Open
Abstract
In addition to central functions in cell adhesion signalling, integrin-associated proteins have wider roles at sites distal to adhesion receptors. In experimentally defined adhesomes, we noticed that there is clear enrichment of proteins that localise to the nucleus, and conversely, we now report that nuclear proteomes contain a class of adhesome components that localise to the nucleus. We here define a nucleo-adhesome, providing experimental evidence for a remarkable scale of nuclear localisation of adhesion proteins, establishing a framework for interrogating nuclear adhesion protein functions. Adding to nuclear FAK's known roles in regulating transcription, we now show that nuclear FAK regulates expression of many adhesion-related proteins that localise to the nucleus and that nuclear FAK binds to the adhesome component and nuclear protein Hic-5. FAK and Hic-5 work together in the nucleus, co-regulating a subset of genes transcriptionally. We demonstrate the principle that there are subcomplexes of nuclear adhesion proteins that cooperate to control transcription.
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Affiliation(s)
- Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK.
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.
| | - Billie G C Griffith
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Ana Herrero
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria, 39011, Santander, Spain
| | - Alexander E P Loftus
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Emma S Koeleman
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120, Heidelberg, Germany
| | - Linda Kogerman
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - John C Dawson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Niamh McGivern
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- Almac Diagnostic Services, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Jayne Culley
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Bryan Serrels
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
- NanoString Technologies, Inc., Seattle, WA, 98109, USA
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Valerie G Brunton
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Margaret C Frame
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
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6
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Cain JA, Dale AL, Cordwell SJ. Exploiting pglB Oligosaccharyltransferase-Positive and -Negative Campylobacter jejuni and a Multiprotease Digestion Strategy to Identify Novel Sites Modified by N-Linked Protein Glycosylation. J Proteome Res 2021; 20:4995-5009. [PMID: 34677046 DOI: 10.1021/acs.jproteome.1c00482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Campylobacter jejuni is a bacterial pathogen encoding a unique N-linked glycosylation (pgl) system that mediates attachment of a heptasaccharide to N-sequon-containing membrane proteins by the PglB oligosaccharyltransferase (OST). Many targets of PglB are known, yet only a fraction of sequons are experimentally confirmed, and site occupancy remains elusive. We exploited pglB-positive (wild-type; WT) and -negative (ΔpglB) proteomes to identify potential glycosites. The nonglycosylated forms of known glycopeptides were typically increased in protein normalized abundance in ΔpglB relative to WT and restored by pglB reintroduction (ΔpglB::pglB). Sequon-containing peptide abundances were thus consistent with significant site occupancy in the presence of the OST. Peptides with novel sequons were either unaltered (likely not glycosylated) or showed abundance consistent with known glycopeptides. Topology analysis revealed that unaltered sequons often displayed cytoplasmic localization, despite originating from membrane proteins. Novel glycosites were confirmed using parallel multiprotease digestion, LC-MS/MS, and FAIMS-MS to define the glycoproteomes of WT and ΔpglB::pglB C. jejuni. We identified 142 glycosites, of which 32 were novel, and 83% of sites predicted by proteomics were validated. There are now 166 experimentally verified C. jejuni glycosites and evidence for occupancy or nonoccupancy of 31 additional sites. This study serves as a model for the use of OST-negative cells and proteomics for highlighting novel glycosites and determining occupancy in a range of organisms.
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Affiliation(s)
- Joel A Cain
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Ashleigh L Dale
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
| | - Stuart J Cordwell
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia.,Sydney Mass Spectrometry, The University of Sydney, Sydney 2006, Australia
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7
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Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence. Biochem Soc Trans 2021; 49:1905-1926. [PMID: 34374408 DOI: 10.1042/bst20191088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022]
Abstract
Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.
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8
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Addressing Antiretroviral Drug Resistance with Host-Targeting Drugs-First Steps towards Developing a Host-Targeting HIV-1 Assembly Inhibitor. Viruses 2021; 13:v13030451. [PMID: 33802145 PMCID: PMC8001593 DOI: 10.3390/v13030451] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
The concerning increase in HIV-1 resistance argues for prioritizing the development of host-targeting antiviral drugs because such drugs can offer high genetic barriers to the selection of drug-resistant viral variants. Targeting host proteins could also yield drugs that act on viral life cycle events that have proven elusive to inhibition, such as intracellular events of HIV-1 immature capsid assembly. Here, we review small molecule inhibitors identified primarily through HIV-1 self-assembly screens and describe how all act either narrowly post-entry or broadly on early and late events of the HIV-1 life cycle. We propose that a different screening approach could identify compounds that specifically inhibit HIV-1 Gag assembly, as was observed when a potent rabies virus inhibitor was identified using a host-catalyzed rabies assembly screen. As an example of this possibility, we discuss an antiretroviral small molecule recently identified using a screen that recapitulates the host-catalyzed HIV-1 capsid assembly pathway. This chemotype potently blocks HIV-1 replication in T cells by specifically inhibiting immature HIV-1 capsid assembly but fails to select for resistant viral variants over 37 passages, suggesting a host protein target. Development of such small molecules could yield novel host-targeting antiretroviral drugs and provide insight into chronic diseases resulting from dysregulation of host machinery targeted by these drugs.
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9
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Müller-Schiffmann A, Trossbach SV, Lingappa VR, Korth C. Viruses as 'Truffle Hounds': Molecular Tools for Untangling Brain Cellular Pathology. Trends Neurosci 2020; 44:352-365. [PMID: 33317827 DOI: 10.1016/j.tins.2020.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/06/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022]
Abstract
The ability of viruses to evolve several orders of magnitude faster than their host cells has enabled them to exploit host cellular machinery by selectively recruiting multiprotein complexes (MPCs) for their catalyzed assembly and replication. This hijacking may depend on alternative, 'moonlighting' functions of host proteins that deviate from their canonical functions thereby inducing cellular pathology. Here, we posit that if virus-induced cellular pathology is similar to that of other, unknown (non-viral) causes, the identification and molecular characterization of the host proteins involved in virus-mediated cellular pathology can be leveraged to decipher the non-viral disease-relevant mechanisms. We focus on how virus-induced aberrant proteostasis and protein aggregation resemble the cellular pathology of sporadic neurodegenerative diseases (NDs) and how this can be exploited for drug discovery.
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Affiliation(s)
- Andreas Müller-Schiffmann
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Svenja V Trossbach
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | | | - Carsten Korth
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany.
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10
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Satala D, Satala G, Karkowska-Kuleta J, Bukowski M, Kluza A, Rapala-Kozik M, Kozik A. Structural Insights into the Interactions of Candidal Enolase with Human Vitronectin, Fibronectin and Plasminogen. Int J Mol Sci 2020; 21:ijms21217843. [PMID: 33105833 PMCID: PMC7660097 DOI: 10.3390/ijms21217843] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Significant amounts of enolase—a cytosolic enzyme involved in the glycolysis pathway—are exposed on the cell surface of Candida yeast. It has been hypothesized that this exposed enolase form contributes to infection-related phenomena such as fungal adhesion to human tissues, and the activation of fibrinolysis and extracellular matrix degradation. The aim of the present study was to characterize, in structural terms, the protein-protein interactions underlying these moonlighting functions of enolase. The tight binding of human vitronectin, fibronectin and plasminogen by purified C. albicans and C. tropicalis enolases was quantitatively analyzed by surface plasmon resonance measurements, and the dissociation constants of the formed complexes were determined to be in the 10−7–10−8 M range. In contrast, the binding of human proteins by the S.cerevisiae enzyme was much weaker. The chemical cross-linking method was used to map the sites on enolase molecules that come into direct contact with human proteins. An internal motif 235DKAGYKGKVGIAMDVASSEFYKDGK259 in C. albicans enolase was suggested to contribute to the binding of all three human proteins tested. Models for these interactions were developed and revealed the sites on the enolase molecule that bind human proteins, extensively overlap for these ligands, and are well-separated from the catalytic activity center.
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Affiliation(s)
- Dorota Satala
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, 30-387 Kraków, Poland; (D.S.); (M.B.)
| | - Grzegorz Satala
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Kraków, Poland;
| | - Justyna Karkowska-Kuleta
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, 30-387 Kraków, Poland; (J.K.-K.); (A.K.); (M.R.-K.)
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, 30-387 Kraków, Poland; (D.S.); (M.B.)
| | - Anna Kluza
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, 30-387 Kraków, Poland; (J.K.-K.); (A.K.); (M.R.-K.)
| | - Maria Rapala-Kozik
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, 30-387 Kraków, Poland; (J.K.-K.); (A.K.); (M.R.-K.)
| | - Andrzej Kozik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, 30-387 Kraków, Poland; (D.S.); (M.B.)
- Correspondence:
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Kumar S, Koehn JT, Gonzalez-Juarrero M, Crans DC, Crick DC. Mycobacterium tuberculosis Survival in J774A.1 Cells Is Dependent on MenJ Moonlighting Activity, Not Its Enzymatic Activity. ACS Infect Dis 2020; 6:2661-2671. [PMID: 32866371 DOI: 10.1021/acsinfecdis.0c00312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MenJ, a flavoprotein oxidoreductase, is responsible for the saturation of the β-isoprene unit of mycobacterial menaquinone, resulting in the conversion of menaquinone with nine isoprene units (MK-9) to menaquinone with nine isoprene units where the double bond in the second unit is reduced [MK-9(II-H2)]. The hydrogenation of MK-9 increases the efficiency of the mycobacterial electron transport system, whereas the deletion of MenJ results in decreased survival of the bacteria inside J774A.1 macrophage-like cells but is not required for growth in culture. Thus, it was suggested that MenJ may represent a contextual drug target in M. tuberculosis, that is, a drug target that is valid only in the context of an infected macrophage. However, it was unclear if the conversion of MK-9 to MK-9(II-H2) or the MenJ protein itself was responsible for bacterial survival. In order to resolve this issue, a plasmid expressing folded, full-length, inactive MenJ was engineered. Primary sequence analysis data revealed that MenJ shares conserved FAD binding, NADH binding, and catalytic and C-terminal motifs with archaeal geranylgeranyl reductases. A MenJ mutant deficient in any one of these motifs is devoid of reductase activity. Therefore, point mutations of highly conserved amino acids in the conserved motifs were generated and the recombinant proteins were monitored for conformational changes by circular dichroism and oxidoreductase activity. The mutational analysis indicates that amino acids tryptophan 215 (W215) and cysteine 46 (C46) of M. tuberculosis MenJ, conserved in known archaeal geranylgeranyl reductases and putative menaquinone saturases, are essential to the hydrogenation of MK-9. The mutation of either C46 to serine (C46S) or W215 to leucine (W215L) in MenJ completely abolishes the catalytic activity in vitro, and menJ knockout strains of M. tuberculosis expressing either the C46S or W215L mutant protein are unable to convert MK-9 to MK-9(II-H2) but survive inside the J774A.1 cells. Thus, surprisingly, the survival of M. tuberculosis in J774A.1 cells is dependent on the expression of MenJ rather than its oxidoreductase activity, the conversion of MK-9 to MK-9(II-H2) as previously hypothesized. Overall, the current data suggest that MenJ is a moonlighting protein.
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Wygrecka M, Kosanovic D, Kwapiszewska G, Preissner KT. Editorial: Multitasking Biomolecules in Human Pathologies: Known Players on Their Unexpected Journeys. Front Med (Lausanne) 2020; 7:478. [PMID: 32974371 PMCID: PMC7471247 DOI: 10.3389/fmed.2020.00478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/15/2020] [Indexed: 01/01/2023] Open
Affiliation(s)
- Malgorzata Wygrecka
- Department of Biochemistry, Universities of Giessen and Marburg Lung Center, Giessen, Germany
| | - Djuro Kosanovic
- Department of Pulmonology, I. M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | - Klaus T Preissner
- Department of Biochemistry, Universities of Giessen and Marburg Lung Center, Giessen, Germany
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13
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Moonlighting Proteins at the Candidal Cell Surface. Microorganisms 2020; 8:microorganisms8071046. [PMID: 32674422 PMCID: PMC7409194 DOI: 10.3390/microorganisms8071046] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/11/2020] [Accepted: 07/12/2020] [Indexed: 12/31/2022] Open
Abstract
The cell wall in Candida albicans is not only a tight protective envelope but also a point of contact with the human host that provides a dynamic response to the constantly changing environment in infection niches. Particularly important roles are attributed to proteins exposed at the fungal cell surface. These include proteins that are stably and covalently bound to the cell wall or cell membrane and those that are more loosely attached. Interestingly in this regard, numerous loosely attached proteins belong to the class of “moonlighting proteins” that are originally intracellular and that perform essentially different functions in addition to their primary housekeeping roles. These proteins also demonstrate unpredicted interactions with non-canonical partners at an a priori unexpected extracellular location, achieved via non-classical secretion routes. Acting both individually and collectively, the moonlighting proteins contribute to candidal virulence and pathogenicity through their involvement in mechanisms critical for successful host colonization and infection, such as the adhesion to host cells, interactions with plasma homeostatic proteolytic cascades, responses to stress conditions and molecular mimicry. The documented knowledge of the roles of these proteins in C. albicans pathogenicity has utility for assisting the design of new therapeutic, diagnostic and preventive strategies against candidiasis.
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Cronan JE. Progress in the Enzymology of the Mitochondrial Diseases of Lipoic Acid Requiring Enzymes. Front Genet 2020; 11:510. [PMID: 32508887 PMCID: PMC7253636 DOI: 10.3389/fgene.2020.00510] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Three human mitochondrial diseases that directly affect lipoic acid metabolism result from heterozygous missense and nonsense mutations in the LIAS, LIPT1, and LIPT2 genes. However, the functions of the proteins encoded by these genes in lipoic acid metabolism remained uncertain due to a lack of biochemical analysis at the enzyme level. An exception was the LIPT1 protein for which a perplexing property had been reported, a ligase lacking the ability to activate its substrate. This led to several models, some contradictory, to accommodate the role of LIPT1 protein activity in explaining the phenotypes of the afflicted neonatal patients. Recent evidence indicates that this LIPT1 protein activity is a misleading evolutionary artifact and that the physiological role of LIPT1 is in transfer of lipoic acid moieties from one protein to another. This and other new biochemical data now define a straightforward pathway that fully explains each of the human disorders specific to the assembly of lipoic acid on its cognate enzyme proteins.
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Affiliation(s)
- John E Cronan
- B103 Chemical and Life Sciences Laboratory, Departments of Microbiology and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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15
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Gibhardt J, Heidemann JL, Bremenkamp R, Rosenberg J, Seifert R, Kaever V, Ficner R, Commichau FM. An extracytoplasmic protein and a moonlighting enzyme modulate synthesis of c-di-AMP in Listeria monocytogenes. Environ Microbiol 2020; 22:2771-2791. [PMID: 32250026 DOI: 10.1111/1462-2920.15008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/06/2023]
Abstract
The second messenger cyclic di-AMP (c-di-AMP) is essential for growth of many bacteria because it controls osmolyte homeostasis. c-di-AMP can regulate the synthesis of potassium uptake systems in some bacteria and it also directly inhibits and activates potassium import and export systems, respectively. Therefore, c-di-AMP production and degradation have to be tightly regulated depending on the environmental osmolarity. The Gram-positive pathogen Listeria monocytogenes relies on the membrane-bound diadenylate cyclase CdaA for c-di-AMP production and degrades the nucleotide with two phosphodiesterases. While the enzymes producing and degrading the dinucleotide have been reasonably well examined, the regulation of c-di-AMP production is not well understood yet. Here we demonstrate that the extracytoplasmic regulator CdaR interacts with CdaA via its transmembrane helix to modulate c-di-AMP production. Moreover, we show that the phosphoglucosamine mutase GlmM forms a complex with CdaA and inhibits the diadenylate cyclase activity in vitro. We also found that GlmM inhibits c-di-AMP production in L. monocytogenes when the bacteria encounter osmotic stress. Thus, GlmM is the major factor controlling the activity of CdaA in vivo. GlmM can be assigned to the class of moonlighting proteins because it is active in metabolism and adjusts the cellular turgor depending on environmental osmolarity.
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Affiliation(s)
- Johannes Gibhardt
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany.,FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Jana L Heidemann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, University of Goettingen, 37077, Göttingen, Germany
| | - Rica Bremenkamp
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Roland Seifert
- Institute of Pharmacology & Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Volkhard Kaever
- Institute of Pharmacology & Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, University of Goettingen, 37077, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
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16
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McGuire PJ. Chemical individuality in T cells: A Garrodian view of immunometabolism. Immunol Rev 2020; 295:82-100. [PMID: 32236968 DOI: 10.1111/imr.12854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/28/2020] [Accepted: 03/01/2020] [Indexed: 02/06/2023]
Abstract
Metabolically quiescent T cells circulate throughout the body in search of antigen. Following engagement of their cognate receptors, T cells undergo metabolic reprogramming to support their activation, differentiation, and ultimately function. In the spirit of Sir Archibald Garrod, this metabolic reprogramming actually imparts a chemical individuality which confers advantage, while in others confers vulnerability, depending upon the milieu. Studying T cell immunometabolism in the context of inborn errors of metabolism allows one to define essential pathways of intermediary metabolism as well metabolic vulnerabilities and plasticity. Inborn errors of metabolism, a class of diseases first named by Garrod, have a long history of being informative for common physiologic and pathologic processes. This endeavor may be accomplished through the study of patients, animal models, and in vitro models of inborn errors of metabolism. In this review, the basics of intermediary metabolism and core metabolic pathways will be discussed, along with their relationship to T cell immunometabolism. Due to their pleiotropic nature, the reader will be specifically directed toward various inborn errors of metabolism which may be helpful for answering important questions about the role of metabolism in T cells.
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Affiliation(s)
- Peter J McGuire
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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