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Kunová N, Ondrovičová G, Bauer JA, Krajčovičová V, Pinkas M, Stojkovičová B, Havalová H, Lukáčová V, Kohútová L, Košťan J, Martináková L, Baráth P, Nováček J, Zoll S, Kereϊche S, Kutejová E, Pevala V. Polyphosphate and tyrosine phosphorylation in the N-terminal domain of the human mitochondrial Lon protease disrupts its functions. Sci Rep 2024; 14:9923. [PMID: 38688959 PMCID: PMC11061198 DOI: 10.1038/s41598-024-60030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/18/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Phosphorylation plays a crucial role in the regulation of many fundamental cellular processes. Phosphorylation levels are increased in many cancer cells where they may promote changes in mitochondrial homeostasis. Proteomic studies on various types of cancer identified 17 phosphorylation sites within the human ATP-dependent protease Lon, which degrades misfolded, unassembled and oxidatively damaged proteins in mitochondria. Most of these sites were found in Lon's N-terminal (NTD) and ATPase domains, though little is known about the effects on their function. By combining the biochemical and cryo-electron microscopy studies, we show the effect of Tyr186 and Tyr394 phosphorylations in Lon's NTD, which greatly reduce all Lon activities without affecting its ability to bind substrates or perturbing its tertiary structure. A substantial reduction in Lon's activities is also observed in the presence of polyphosphate, whose amount significantly increases in cancer cells. Our study thus provides an insight into the possible fine-tuning of Lon activities in human diseases, which highlights Lon's importance in maintaining proteostasis in mitochondria.
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Grants
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- BIOMEDIRES - II. stage, ITMS: 313011W428 European Regional Development Fund
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
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Affiliation(s)
- Nina Kunová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Gabriela Ondrovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Jacob A Bauer
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Veronika Krajčovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Laboratory of Clinical and Molecular Genetics, National Institute of Children's Diseases, Limbová 1, 833 40, Bratislava, Slovakia
| | - Matyáš Pinkas
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Barbora Stojkovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Henrieta Havalová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | | | - Lenka Kohútová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Július Košťan
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna, Biocenter 5, 1030, Vienna, Austria
| | - Lucia Martináková
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Peter Baráth
- Medirex Group Academy, Nitra, Slovakia
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jiří Nováček
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic
| | - Sami Kereϊche
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic.
| | - Eva Kutejová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
| | - Vladimír Pevala
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
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Sülzen H, Volkov AN, Geens R, Zahedifard F, Stijlemans B, Zoltner M, Magez S, Sterckx YGJ, Zoll S. Beyond the VSG layer: Exploring the role of intrinsic disorder in the invariant surface glycoproteins of African trypanosomes. PLoS Pathog 2024; 20:e1012186. [PMID: 38648216 PMCID: PMC11065263 DOI: 10.1371/journal.ppat.1012186] [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] [Received: 12/18/2023] [Revised: 05/02/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
In the bloodstream of mammalian hosts, African trypanosomes face the challenge of protecting their invariant surface receptors from immune detection. This crucial role is fulfilled by a dense, glycosylated protein layer composed of variant surface glycoproteins (VSGs), which undergo antigenic variation and provide a physical barrier that shields the underlying invariant surface glycoproteins (ISGs). The protective shield's limited permeability comes at the cost of restricted access to the extracellular host environment, raising questions regarding the specific function of the ISG repertoire. In this study, we employ an integrative structural biology approach to show that intrinsically disordered membrane-proximal regions are a common feature of members of the ISG super-family, conferring the ability to switch between compact and elongated conformers. While the folded, membrane-distal ectodomain is buried within the VSG layer for compact conformers, their elongated counterparts would enable the extension beyond it. This dynamic behavior enables ISGs to maintain a low immunogenic footprint while still allowing them to engage with the host environment when necessary. Our findings add further evidence to a dynamic molecular organization of trypanosome surface antigens wherein intrinsic disorder underpins the characteristics of a highly flexible ISG proteome to circumvent the constraints imposed by the VSG coat.
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Affiliation(s)
- Hagen Sülzen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Rob Geens
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Center of Excellence, Department of Pharmaceutical Sciences, Universiteit of Antwerp, Wilrijk, Belgium
| | - Farnaz Zahedifard
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Benoit Stijlemans
- Brussels Center for Immunology (BCIM), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Stefan Magez
- Brussels Center for Immunology (BCIM), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Incheon, South Korea
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Center of Excellence, Department of Pharmaceutical Sciences, Universiteit of Antwerp, Wilrijk, Belgium
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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Dhillon A, Persson BD, Volkov AN, Sülzen H, Kádek A, Pompach P, Kereïche S, Lepšík M, Danskog K, Uetrecht C, Arnberg N, Zoll S. Structural insights into the interaction between adenovirus C5 hexon and human lactoferrin. J Virol 2024; 98:e0157623. [PMID: 38323814 PMCID: PMC10949841 DOI: 10.1128/jvi.01576-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/10/2023] [Accepted: 01/13/2024] [Indexed: 02/08/2024] Open
Abstract
Adenovirus (AdV) infection of the respiratory epithelium is common but poorly understood. Human AdV species C types, such as HAdV-C5, utilize the Coxsackie-adenovirus receptor (CAR) for attachment and subsequently integrins for entry. CAR and integrins are however located deep within the tight junctions in the mucosa where they would not be easily accessible. Recently, a model for CAR-independent AdV entry was proposed. In this model, human lactoferrin (hLF), an innate immune protein, aids the viral uptake into epithelial cells by mediating interactions between the major capsid protein, hexon, and yet unknown host cellular receptor(s). However, a detailed understanding of the molecular interactions driving this mechanism is lacking. Here, we present a new cryo-EM structure of HAdV-5C hexon at high resolution alongside a hybrid structure of HAdV-5C hexon complexed with human lactoferrin (hLF). These structures reveal the molecular determinants of the interaction between hLF and HAdV-C5 hexon. hLF engages hexon primarily via its N-terminal lactoferricin (Lfcin) region, interacting with hexon's hypervariable region 1 (HVR-1). Mutational analyses pinpoint critical Lfcin contacts and also identify additional regions within hLF that critically contribute to hexon binding. Our study sheds more light on the intricate mechanism by which HAdV-C5 utilizes soluble hLF/Lfcin for cellular entry. These findings hold promise for advancing gene therapy applications and inform vaccine development. IMPORTANCE Our study delves into the structural aspects of adenovirus (AdV) infections, specifically HAdV-C5 in the respiratory epithelium. It uncovers the molecular details of a novel pathway where human lactoferrin (hLF) interacts with the major capsid protein, hexon, facilitating viral entry, and bypassing traditional receptors such as CAR and integrins. The study's cryo-EM structures reveal how hLF engages hexon, primarily through its N-terminal lactoferricin (Lfcin) region and hexon's hypervariable region 1 (HVR-1). Mutational analyses identify critical Lfcin contacts and other regions within hLF vital for hexon binding. This structural insight sheds light on HAdV-C5's mechanism of utilizing soluble hLF/Lfcin for cellular entry, holding promise for gene therapy and vaccine development advancements in adenovirus research.
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Affiliation(s)
- Arun Dhillon
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Hagen Sülzen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Alan Kádek
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Petr Pompach
- Biotechnology and Biomedical Center of the Academy of Sciences and Charles University in Vestec, Vestec, Czech Republic
| | - Sami Kereïche
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katarina Danskog
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Charlotte Uetrecht
- Department of Health Sciences and Biomedicine, Faculty V: School of Life Sciences, CSSB Centre for Structural Systems Biology, Deutsches Elektronen Synchrotron DESY and Leibniz Institute of Virology, Hamburg, University of Siegen, Siegen, Germany
| | - Niklas Arnberg
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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4
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Sülzen H, Began J, Dhillon A, Kereïche S, Pompach P, Votrubova J, Zahedifard F, Šubrtova A, Šafner M, Hubalek M, Thompson M, Zoltner M, Zoll S. Cryo-EM structures of Trypanosoma brucei gambiense ISG65 with human complement C3 and C3b and their roles in alternative pathway restriction. Nat Commun 2023; 14:2403. [PMID: 37105991 PMCID: PMC10140031 DOI: 10.1038/s41467-023-37988-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
African Trypanosomes have developed elaborate mechanisms to escape the adaptive immune response, but little is known about complement evasion particularly at the early stage of infection. Here we show that ISG65 of the human-infective parasite Trypanosoma brucei gambiense is a receptor for human complement factor C3 and its activation fragments and that it takes over a role in selective inhibition of the alternative pathway C5 convertase and thus abrogation of the terminal pathway. No deposition of C4b, as part of the classical and lectin pathway convertases, was detected on trypanosomes. We present the cryo-electron microscopy (EM) structures of native C3 and C3b in complex with ISG65 which reveal a set of modes of complement interaction. Based on these findings, we propose a model for receptor-ligand interactions as they occur at the plasma membrane of blood-stage trypanosomes and may facilitate innate immune escape of the parasite.
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Affiliation(s)
- Hagen Sülzen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
- Faculty of Science, Charles University, Albertov 6, 12800, Prague 2, Czech Republic
| | - Jakub Began
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, 1066, Epalinges, Switzerland
| | - Arun Dhillon
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Sami Kereïche
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Albertov 4, 12800, Prague, Czech Republic
| | - Petr Pompach
- Institute of Biotechnology of the Czech Academy of Sciences, 25250, Vestec, Czech Republic
| | - Jitka Votrubova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Farnaz Zahedifard
- Department of Parasitology, Faculty of Science, Charles University Prague, Biocev, 25250, Vestec, Czech Republic
| | - Adriana Šubrtova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Marie Šafner
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Maaike Thompson
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
- University of Antwerp, Antwerp, Belgium
- Agidens, Industrial Machinery Manufacturing, Zwijndrecht, Antwerp, Belgium
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University Prague, Biocev, 25250, Vestec, Czech Republic
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic.
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Makarov A, Began J, Mautone IC, Pinto E, Ferguson L, Zoltner M, Zoll S, Field MC. The role of invariant surface glycoprotein 75 in xenobiotic acquisition by African trypanosomes. Microb Cell 2023; 10:18-35. [PMID: 36789350 PMCID: PMC9896412 DOI: 10.15698/mic2023.02.790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/02/2023] [Accepted: 01/13/2023] [Indexed: 02/05/2023]
Abstract
The surface proteins of parasitic protozoa mediate functions essential to survival within a host, including nutrient accumulation, environmental sensing and immune evasion. Several receptors involved in nutrient uptake and defence from the innate immune response have been described in African trypanosomes and, together with antigenic variation, contribute towards persistence within vertebrate hosts. Significantly, a superfamily of invariant surface glycoproteins (ISGs) populates the trypanosome surface, one of which, ISG75, is implicated in uptake of the century-old drug suramin. By CRISPR/Cas9 knockout and biophysical analysis, we show here that ISG75 directly binds suramin and mediates uptake of additional naphthol-related compounds, making ISG75 a conduit for entry of at least one structural class of trypanocidal compounds. However, ISG75 null cells present only modest attenuation of suramin sensitivity, have unaltered viability in vivo and in vitro and no alteration to suramin-invoked proteome responses. While ISG75 is demonstrated as a valid suramin cell entry pathway, we suggest the presence of additional mechanisms for suramin accumulation, further demonstrating the complexity of trypanosomatid drug interactions and potential for evolution of resistance.
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Affiliation(s)
- Alexandr Makarov
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Jakub Began
- Laboratory of Structural Parasitology, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Ileana Corvo Mautone
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, Universidad de la República, Paysandú 60000, Uruguay
| | - Erika Pinto
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Liam Ferguson
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Charles University, Faculty of Science, Department of Parasitology, Vestec, Czech Republic
| | - Sebastian Zoll
- Laboratory of Structural Parasitology, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic
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Magez S, Li Z, Nguyen HTT, Pinto Torres JE, Van Wielendaele P, Radwanska M, Began J, Zoll S, Sterckx YGJ. The History of Anti-Trypanosome Vaccine Development Shows That Highly Immunogenic and Exposed Pathogen-Derived Antigens Are Not Necessarily Good Target Candidates: Enolase and ISG75 as Examples. Pathogens 2021; 10:pathogens10081050. [PMID: 34451514 PMCID: PMC8400590 DOI: 10.3390/pathogens10081050] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 12/02/2022] Open
Abstract
Salivarian trypanosomes comprise a group of extracellular anthroponotic and zoonotic parasites. The only sustainable method for global control of these infection is through vaccination of livestock animals. Despite multiple reports describing promising laboratory results, no single field-applicable solution has been successful so far. Conventionally, vaccine research focusses mostly on exposed immunogenic antigens, or the structural molecular knowledge of surface exposed invariant immunogens. Unfortunately, extracellular parasites (or parasites with extracellular life stages) have devised efficient defense systems against host antibody attacks, so they can deal with the mammalian humoral immune response. In the case of trypanosomes, it appears that these mechanisms have been perfected, leading to vaccine failure in natural hosts. Here, we provide two examples of potential vaccine candidates that, despite being immunogenic and accessible to the immune system, failed to induce a functionally protective memory response. First, trypanosomal enolase was tested as a vaccine candidate, as it was recently characterized as a highly conserved enzyme that is readily recognized during infection by the host antibody response. Secondly, we re-addressed a vaccine approach towards the Invariant Surface Glycoprotein ISG75, and showed that despite being highly immunogenic, trypanosomes can avoid anti-ISG75 mediated parasitemia control.
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Affiliation(s)
- Stefan Magez
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
- Department of Biochemistry and Microbiology, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Songdomunhwa-Ro 119-5, Yeonsu-Gu, Incheon 406-840, Korea;
- Correspondence:
| | - Zeng Li
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium; (P.V.W.); (Y.G.-J.S.)
| | - Hang Thi Thu Nguyen
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
- Department of Biochemistry and Microbiology, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Songdomunhwa-Ro 119-5, Yeonsu-Gu, Incheon 406-840, Korea;
| | - Joar Esteban Pinto Torres
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
| | - Pieter Van Wielendaele
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium; (P.V.W.); (Y.G.-J.S.)
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Songdomunhwa-Ro 119-5, Yeonsu-Gu, Incheon 406-840, Korea;
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark Zwijnaarde 71, 9000 Ghent, Belgium
| | - Jakub Began
- Laboratory of Structural Parasitology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo Namesti 2, 16610 Prague 6, Czech Republic; (J.B.); (S.Z.)
| | - Sebastian Zoll
- Laboratory of Structural Parasitology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo Namesti 2, 16610 Prague 6, Czech Republic; (J.B.); (S.Z.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium; (P.V.W.); (Y.G.-J.S.)
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7
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Zoll S, Stanchev S, Began J, Skerle J, Lepšík M, Peclinovská L, Majer P, Strisovsky K. Substrate binding and specificity of rhomboid intramembrane protease revealed by substrate-peptide complex structures. EMBO J 2014; 33:2408-21. [PMID: 25216680 PMCID: PMC4253528 DOI: 10.15252/embj.201489367] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [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] [Indexed: 01/01/2023] Open
Abstract
The mechanisms of intramembrane proteases are incompletely understood due to the lack of structural data on substrate complexes. To gain insight into substrate binding by rhomboid proteases, we have synthesised a series of novel peptidyl-chloromethylketone (CMK) inhibitors and analysed their interactions with Escherichia coli rhomboid GlpG enzymologically and structurally. We show that peptidyl-CMKs derived from the natural rhomboid substrate TatA from bacterium Providencia stuartii bind GlpG in a substrate-like manner, and their co-crystal structures with GlpG reveal the S1 to S4 subsites of the protease. The S1 subsite is prominent and merges into the 'water retention site', suggesting intimate interplay between substrate binding, specificity and catalysis. Unexpectedly, the S4 subsite is plastically formed by residues of the L1 loop, an important but hitherto enigmatic feature of the rhomboid fold. We propose that the homologous region of members of the wider rhomboid-like protein superfamily may have similar substrate or client-protein binding function. Finally, using molecular dynamics, we generate a model of the Michaelis complex of the substrate bound in the active site of GlpG.
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Affiliation(s)
- Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Stancho Stanchev
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jakub Began
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic Department of Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Skerle
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Peclinovská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Büttner FM, Zoll S, Nega M, Götz F, Stehle T. Structure-function analysis of Staphylococcus aureus amidase reveals the determinants of peptidoglycan recognition and cleavage. J Biol Chem 2014; 289:11083-11094. [PMID: 24599952 DOI: 10.1074/jbc.m114.557306] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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: 11/06/2022] Open
Abstract
The bifunctional major autolysin AtlA of Staphylococcus aureus cleaves the bacterium's peptidoglycan network (PGN) at two distinct sites during cell division. Deletion of the enzyme results in large cell clusters with disordered division patterns, indicating that AtlA could be a promising target for the development of new antibiotics. One of the two functions of AtlA is performed by the N-acetylmuramyl-l-alanine amidase AmiA, which cleaves the bond between the carbohydrate and the peptide moieties of PGN. To establish the structural requirements of PGN recognition and the enzymatic mechanism of cleavage, we solved the crystal structure of the catalytic domain of AmiA (AmiA-cat) in complex with a peptidoglycan-derived ligand at 1.55 Å resolution. The peptide stem is clearly visible in the structure, forming extensive contacts with protein residues by docking into an elongated groove. Less well defined electron density and the analysis of surface features indicate likely positions of the carbohydrate backbone and the pentaglycine bridge. Substrate specificity analysis supports the importance of the pentaglycine bridge for fitting into the binding cleft of AmiA-cat. PGN of S. aureus with l-lysine tethered with d-alanine via a pentaglycine bridge is completely hydrolyzed, whereas PGN of Bacillus subtilis with meso-diaminopimelic acid directly tethered with d-alanine is not hydrolyzed. An active site mutant, H370A, of AmiA-cat was completely inactive, providing further support for the proposed catalytic mechanism of AmiA. The structure reported here is not only the first of any bacterial amidase in which both the PGN component and the water molecule that carries out the nucleophilic attack on the carbonyl carbon of the scissile bond are present; it is also the first peptidoglycan amidase complex structure of an important human pathogen.
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Affiliation(s)
- Felix Michael Büttner
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Sebastian Zoll
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Mulugeta Nega
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany, and
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany, and
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany,; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.
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Stehle T, Zoll S. Bacterial cell wall degradation by a staphylococcal autolysin. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311097819] [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: 11/10/2022] Open
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Zoll S, Pätzold B, Schlag M, Götz F, Kalbacher H, Stehle T. Structural basis of cell wall cleavage by a staphylococcal autolysin. PLoS Pathog 2010; 6:e1000807. [PMID: 20300605 PMCID: PMC2837410 DOI: 10.1371/journal.ppat.1000807] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 02/04/2010] [Indexed: 01/07/2023] Open
Abstract
The major autolysins (Atl) of Staphylococcus epidermidis and S. aureus play an important role in cell separation, and their mutants are also attenuated in virulence. Therefore, autolysins represent a promising target for the development of new types of antibiotics. Here, we report the high-resolution structure of the catalytically active amidase domain AmiE (amidase S. epidermidis) from the major autolysin of S. epidermidis. This is the first protein structure with an amidase-like fold from a bacterium with a gram-positive cell wall architecture. AmiE adopts a globular fold, with several alpha-helices surrounding a central beta-sheet. Sequence comparison reveals a cluster of conserved amino acids that define a putative binding site with a buried zinc ion. Mutations of key residues in the putative active site result in loss of activity, enabling us to propose a catalytic mechanism. We also identified and synthesized muramyltripeptide, the minimal peptidoglycan fragment that can be used as a substrate by the enzyme. Molecular docking and digestion assays with muramyltripeptide derivatives allow us to identify key determinants of ligand binding. This results in a plausible model of interaction of this ligand not only for AmiE, but also for other PGN-hydrolases that share the same fold. As AmiE active-site mutations also show a severe growth defect, our findings provide an excellent platform for the design of specific inhibitors that target staphylococcal cell separation and can thereby prevent growth of this pathogen.
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Affiliation(s)
- Sebastian Zoll
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
| | - Bernhard Pätzold
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
| | - Martin Schlag
- Department of Microbial Genetics, Faculty of Biology, University of Tübingen, Tübingen, Germany
| | - Friedrich Götz
- Department of Microbial Genetics, Faculty of Biology, University of Tübingen, Tübingen, Germany
| | - Hubert Kalbacher
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
- Medical and Natural Sciences Research Center, Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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Schlag M, Biswas R, Krismer B, Kohler T, Zoll S, Yu W, Schwarz H, Peschel A, Götz F. Role of staphylococcal wall teichoic acid in targeting the major autolysin Atl. Mol Microbiol 2010; 75:864-73. [DOI: 10.1111/j.1365-2958.2009.07007.x] [Citation(s) in RCA: 207] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Lützner N, Pätzold B, Zoll S, Stehle T, Kalbacher H. Development of a novel fluorescent substrate for Autolysin E, a bacterial type II amidase. Biochem Biophys Res Commun 2009; 380:554-8. [DOI: 10.1016/j.bbrc.2009.01.140] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 01/22/2009] [Indexed: 10/21/2022]
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Zoll S, Paetzold B, Schlag M, Goetz F, Stehle T. The crystal structure of the staphylococcal amidase AmiE reveals the active site of a metalloenzyme. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308091393] [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: 04/03/2023] Open
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