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4. Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus

Author

Baggen, Jim, Hurdiss, Daniel L., Zocher, Georg, Mistry, Nitesh, Roberts, Richard W., Slager, Jasper J., Guo, Hongbo, van Vliet, Arno L. W., Wahedi, Maryam, Benschop, Kimberley, Duizer, Erwin, de Haan, Cornelis A. M., de Vries, Erik, Casasnovas, José M., de Groot, Raoul J., Arnberg, Niklas, Stehle, Thilo, Ranson, Neil A., Thibaut, Hendrik Jan, and van Kuppeveld, Frank J. M.

Published
2018

5. Enterovirus D68 receptor requirements unveiled by haploid genetics

Author

Baggen, Jim, Thibaut, Hendrik Jan, Staring, Jacqueline, Jae, Lucas T., Liu, Yue, Guo, Hongbo, Slager, Jasper J., de Bruin, Jost W., van Vliet, Arno L. W., Blomen, Vincent A., Overduin, Pieter, Sheng, Ju, de Haan, Cornelis A. M., de Vries, Erik, Meijer, Adam, Rossmann, Michael G., Brummelkamp, Thijn R., and van Kuppeveld, Frank J. M.

Published
2016

6. Bypassing pan-enterovirus host factor PLA2G16

Author

Baggen, Jim, Liu, Yue, Lyoo, Heyrhyoung, van Vliet, Arno L. W., Wahedi, Maryam, de Bruin, Jost W., Roberts, Richard W., Overduin, Pieter, Meijer, Adam, Rossmann, Michael G., Thibaut, Hendrik Jan, and van Kuppeveld, Frank J. M.

Published
2019
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9. Inhibition of the integrated stress response by viral proteins that block p-eIF2-eIF2B association

Author

Rabouw, Huib H, Visser, Linda J, Passchier, Tim C, Langereis, Martijn A, Liu, Fan, Giansanti, Piero, van Vliet, Arno L W, Dekker, José G, van der Grein, Susanne G, Saucedo, Jesús G, Anand, Aditya A, Trellet, Mikael E, Bonvin, Alexandre M J J, Walter, Peter, Heck, Albert J R, de Groot, Raoul J, van Kuppeveld, Frank J M, LS Virologie, dI&I I&I-1, Sub Biomol.Mass Spectrometry & Proteom., Virologie, dB&C I&I, Sub NMR Spectroscopy, Afd Biomol.Mass Spect. and Proteomics, and Biomolecular Mass Spectrometry and Proteomics

Subjects
Taverne
Abstract

Eukaryotic cells, when exposed to environmental or internal stress, activate the integrated stress response (ISR) to restore homeostasis and promote cell survival. Specific stress stimuli prompt dedicated stress kinases to phosphorylate eukaryotic initiation factor 2 (eIF2). Phosphorylated eIF2 (p-eIF2) in turn sequesters the eIF2-specific guanine exchange factor eIF2B to block eIF2 recycling, thereby halting translation initiation and reducing global protein synthesis. To circumvent stress-induced translational shutdown, viruses encode ISR antagonists. Those identified so far prevent or reverse eIF2 phosphorylation. We now describe two viral proteins-one from a coronavirus and the other from a picornavirus-that have independently acquired the ability to counteract the ISR at its very core by acting as a competitive inhibitor of p-eIF2-eIF2B interaction. This allows continued formation of the eIF2-GTP-Met-tRNAi ternary complex and unabated global translation at high p-eIF2 levels that would otherwise cause translational arrest. We conclude that eIF2 and p-eIF2 differ in their interaction with eIF2B to such effect that p-eIF2-eIF2B association can be selectively inhibited.

Published
2020

10. Enterocytes, fibroblasts and myeloid cells synergize in anti-bacterial and anti-viral pathways with IL22 as the central cytokine

Author

IRAS OH Toxicology, dIRAS RA-1, Virologie, dI&I I&I-1, Klooster, Jean Paul Ten, Bol-Schoenmakers, Marianne, van Summeren, Kitty, van Vliet, Arno L W, de Haan, Cornelis A M, van Kuppeveld, Frank J M, Verkoeijen, Saertje, Pieters, Raymond, IRAS OH Toxicology, dIRAS RA-1, Virologie, dI&I I&I-1, Klooster, Jean Paul Ten, Bol-Schoenmakers, Marianne, van Summeren, Kitty, van Vliet, Arno L W, de Haan, Cornelis A M, van Kuppeveld, Frank J M, Verkoeijen, Saertje, and Pieters, Raymond

Published
2021

11. Identification of the Cell-Surface Protease ADAM9 as an Entry Factor for Encephalomyocarditis Virus

Author

Baggen, Jim, Thibaut, Hendrik Jan, Hurdiss, Daniel L, Wahedi, Maryam, Marceau, Caleb D, van Vliet, Arno L W, Carette, Jan E, van Kuppeveld, Frank J M, LS Virologie, dI&I I&I-1, LS Virologie, and dI&I I&I-1

Subjects
Picornavirus, viruses, ved/biology.organism_classification_rank.species, disintegrin and metalloproteinase domain-containing protein 9 (adam9), Virus Attachment, Virus Replication, Microbiology, Virus, Host-Microbe Biology, Gene Knockout Techniques, Mice, 03 medical and health sciences, 0302 clinical medicine, Cell Line, Tumor, Virology, INFECTION, Cardiovirus Infections, Animals, Humans, PIGS, Model organism, Receptor, Pathogen, haploid genetic screen, 030304 developmental biology, REQUIRES, 0303 health sciences, METALLOPROTEASE-DISINTEGRIN MDC9, Science & Technology, biology, RECEPTOR, Genome, Human, ved/biology, Fibroblast growth factor receptor 1, Cell Membrane, Membrane Proteins, Virus Internalization, biology.organism_classification, encephalomyocarditis virus, QR1-502, 3. Good health, ADAM Proteins, disintegrin and metalloproteinase domain-containing protein 9 (ADAM9), 030220 oncology & carcinogenesis, Signal transduction, Life Sciences & Biomedicine, Research Article, Genetic screen
Abstract

EMCV is an animal pathogen that causes acute viral infections, usually myocarditis or encephalitis. It is thought to circulate mainly among rodents, from which it is occasionally transmitted to other animal species, including humans. EMCV causes fatal outbreaks of myocarditis and encephalitis in pig farms and zoos, making it an important veterinary pathogen. Although EMCV has been widely used as a model to study mechanisms of viral disease in mice, little is known about its entry mechanism. Here, we employ a haploid genetic screen for EMCV host factors and identify an essential role for ADAM9 in EMCV entry., Encephalomyocarditis virus (EMCV) is an animal pathogen and an important model organism, whose receptor requirements are poorly understood. Here, we employed a genome-wide haploid genetic screen to identify novel EMCV host factors. In addition to the previously described picornavirus receptors sialic acid and glycosaminoglycans, this screen unveiled important new host factors for EMCV. These factors include components of the fibroblast growth factor (FGF) signaling pathway, such as the potential receptors FGFR1 and ADAM9, a cell-surface metalloproteinase. By employing various knockout cells, we confirmed the importance of the identified host factors for EMCV infection. The largest reduction in infection efficiency was observed in cells lacking ADAM9. Pharmacological inhibition of the metalloproteinase activity of ADAM9 did not affect virus infection. Moreover, reconstitution of inactive ADAM9 in knockout cells restored susceptibility to EMCV, pointing to a proteinase-independent role of ADAM9 in mediating EMCV infection. Using neutralization assays with ADAM9-specific antiserum and soluble receptor proteins, we provided evidence for a role of ADAM9 in EMCV entry. Finally, binding assays showed that ADAM9 facilitates attachment of EMCV to the cell surface. Together, our findings reveal a role for ADAM9 as a novel receptor or cofactor for EMCV.

Published
2019

12. Translation and Replication Dynamics of Single RNA Viruses

Author

Boersma, Sanne, Rabouw, Huib H, Bruurs, Lucas J M, Pavlovič, Tonja, van Vliet, Arno L W, Beumer, Joep, Clevers, Hans, van Kuppeveld, Frank J M, Tanenbaum, Marvin E, Boersma, Sanne, Rabouw, Huib H, Bruurs, Lucas J M, Pavlovič, Tonja, van Vliet, Arno L W, Beumer, Joep, Clevers, Hans, van Kuppeveld, Frank J M, and Tanenbaum, Marvin E

Abstract

RNA viruses are among the most prevalent pathogens and are a major burden on society. Although RNA viruses have been studied extensively, little is known about the processes that occur during the first several hours of infection because of a lack of sensitive assays. Here we develop a single-molecule imaging assay, virus infection real-time imaging (VIRIM), to study translation and replication of individual RNA viruses in live cells. VIRIM uncovered a striking heterogeneity in replication dynamics between cells and revealed extensive coordination between translation and replication of single viral RNAs. Furthermore, using VIRIM, we identify the replication step of the incoming viral RNA as a major bottleneck of successful infection and identify host genes that are responsible for inhibition of early virus replication. Single-molecule imaging of virus infection is a powerful tool to study virus replication and virus-host interactions that may be broadly applicable to RNA viruses.

Published
2020

13. Inhibition of the integrated stress response by viral proteins that block p-eIF2-eIF2B association

Author

LS Virologie, dI&I I&I-1, Sub Biomol.Mass Spectrometry & Proteom., Virologie, dB&C I&I, Sub NMR Spectroscopy, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Rabouw, Huib H, Visser, Linda J, Passchier, Tim C, Langereis, Martijn A, Liu, Fan, Giansanti, Piero, van Vliet, Arno L W, Dekker, José G, van der Grein, Susanne G, Saucedo, Jesús G, Anand, Aditya A, Trellet, Mikael E, Bonvin, Alexandre M J J, Walter, Peter, Heck, Albert J R, de Groot, Raoul J, van Kuppeveld, Frank J M, LS Virologie, dI&I I&I-1, Sub Biomol.Mass Spectrometry & Proteom., Virologie, dB&C I&I, Sub NMR Spectroscopy, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Rabouw, Huib H, Visser, Linda J, Passchier, Tim C, Langereis, Martijn A, Liu, Fan, Giansanti, Piero, van Vliet, Arno L W, Dekker, José G, van der Grein, Susanne G, Saucedo, Jesús G, Anand, Aditya A, Trellet, Mikael E, Bonvin, Alexandre M J J, Walter, Peter, Heck, Albert J R, de Groot, Raoul J, and van Kuppeveld, Frank J M

Published
2020

14. Translation and Replication Dynamics of Single RNA Viruses

Author

LS Algemene Literatuurwetenschap, LS Virologie, Virologie, dI&I I&I-1, Faculteit Diergeneeskunde, Boersma, Sanne, Rabouw, Huib H, Bruurs, Lucas J M, Pavlovič, Tonja, van Vliet, Arno L W, Beumer, Joep, Clevers, Hans, van Kuppeveld, Frank J M, Tanenbaum, Marvin E, LS Algemene Literatuurwetenschap, LS Virologie, Virologie, dI&I I&I-1, Faculteit Diergeneeskunde, Boersma, Sanne, Rabouw, Huib H, Bruurs, Lucas J M, Pavlovič, Tonja, van Vliet, Arno L W, Beumer, Joep, Clevers, Hans, van Kuppeveld, Frank J M, and Tanenbaum, Marvin E

Published
2020

15. Translation and Replication Dynamics of Single RNA Viruses

Author

CMM Sectie Molecular Cancer Research, Child Health, Regenerative Medicine and Stem Cells, Cancer, Hubrecht Institute with UMC, Boersma, Sanne, Rabouw, Huib H, Bruurs, Lucas J M, Pavlovič, Tonja, van Vliet, Arno L W, Beumer, Joep, Clevers, Hans, van Kuppeveld, Frank J M, Tanenbaum, Marvin E, CMM Sectie Molecular Cancer Research, Child Health, Regenerative Medicine and Stem Cells, Cancer, Hubrecht Institute with UMC, Boersma, Sanne, Rabouw, Huib H, Bruurs, Lucas J M, Pavlovič, Tonja, van Vliet, Arno L W, Beumer, Joep, Clevers, Hans, van Kuppeveld, Frank J M, and Tanenbaum, Marvin E

Published
2020

17. Complexity and Diversity of the Mammalian Sialome Revealed by Nidovirus Virolectins

Author

Langereis, Martijn A, Bakkers, Mark J G, Deng, Lingquan, Padler-Karavani, Vered, Vervoort, Stephin J, Hulswit, Ruben J G, van Vliet, Arno L W, Gerwig, Gerrit J, de Poot, Stefanie A H, Boot, Willemijn, van Ederen, Anne Marie, Heesters, Balthasar A, van der Loos, Chris M, van Kuppeveld, Frank J M, Yu, Hai, Huizinga, Eric G, Chen, Xi, Varki, Ajit, Kamerling, Johannis P, de Groot, Raoul J, Bio organic Chemistry, Crystal and Structural Chemistry, dI&I I&I-1, LS Virologie, Sub Membrane Biochemistry & Biophysics, Afd Chemical Biology and Drug Discovery, Sub Crystal and Structural Chemistry, Bio organic Chemistry, Crystal and Structural Chemistry, dI&I I&I-1, LS Virologie, Sub Membrane Biochemistry & Biophysics, Afd Chemical Biology and Drug Discovery, and Sub Crystal and Structural Chemistry

Subjects
Medical Physiology, Nidovirales, Biochemistry, Genome, Viral, Non-U.S. Gov't, lcsh:QH301-705.5, Mammals, Regulation of gene expression, 0303 health sciences, biology, Research Support, Non-U.S. Gov't, 030302 biochemistry & molecular biology, Acetylation, Lipids, 3. Good health, Cell biology, Hemagglutinins, Sialome, Glycan, 1.1 Normal biological development and functioning, Hemagglutinins, Viral, Research Support, Article, General Biochemistry, Genetics and Molecular Biology, N.I.H, 03 medical and health sciences, Species Specificity, Research Support, N.I.H., Extramural, Underpinning research, Journal Article, Animals, Humans, Differential expression, 030304 developmental biology, Biochemistry, Genetics and Molecular Biology(all), Cell growth, Proteins, Extramural, N-Acetylneuraminic Acid, lcsh:Biology (General), Gene Expression Regulation, Sialic Acids, biology.protein, Acetylesterase, Generic health relevance, Biochemistry and Cell Biology, Viral Fusion Proteins, Function (biology), Genetics and Molecular Biology(all)
Abstract

SUMMARY Sialic acids (Sias), 9-carbon-backbone sugars, are among the most complex and versatile molecules of life. As terminal residues of glycans on proteins and lipids, Sias are key elements of glycotopes of both cellular and microbial lectins and thus act as important molecular tags in cell recognition and signaling events. Their functions in such interactions can be regulated by post-synthetic modifications, the most common of which is differential Sia-O-acetylation (O-Ac-Sias). The biology of O-Ac-Sias remains mostly unexplored, largely because of limitations associated with their specific in situ detection. Here, we show that dual-function hemagglutinin-esterase envelope proteins of nidoviruses distinguish between a variety of closely related O-Ac-Sias. By using soluble forms of hemagglutinin-esterases as lectins and sialate-O-acetylesterases, we demonstrate differential expression of distinct O-Ac-sialoglycan populations in an organ-, tissue- and cell-specific fashion. Our findings indicate that programmed Sia-O-acetylation/de-O-acetylation may be critical to key aspects of cell development, homeostasis, and/or function., Graphical Abstract

Published
2015
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19. Bypassing pan-enterovirus host factor PLA2G16

Author

LS Virologie, dI&I I&I-1, Baggen, Jim, Liu, Yue, Lyoo, Heyrhyoung, van Vliet, Arno L W, Wahedi, Maryam, de Bruin, Jost W, Roberts, Richard W, Overduin, Pieter, Meijer, Adam, Rossmann, Michael G, Thibaut, Hendrik Jan, van Kuppeveld, Frank J M, LS Virologie, dI&I I&I-1, Baggen, Jim, Liu, Yue, Lyoo, Heyrhyoung, van Vliet, Arno L W, Wahedi, Maryam, de Bruin, Jost W, Roberts, Richard W, Overduin, Pieter, Meijer, Adam, Rossmann, Michael G, Thibaut, Hendrik Jan, and van Kuppeveld, Frank J M

Published
2019

20. Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus

Author

Baggen, Jim, Hurdiss, Daniel L, Zocher, Georg, Mistry, Nitesh, Roberts, Richard W, Slager, Jasper J, Guo, Hongbo, van Vliet, Arno L W, Wahedi, Maryam, Benschop, Kimberley, Duizer, Erwin, de Haan, Cornelis A M, de Vries, Erik, Casasnovas, José M, de Groot, Raoul J, Arnberg, Niklas, Stehle, Thilo, Ranson, Neil A, Thibaut, Hendrik Jan, van Kuppeveld, Frank J M, LS Virologie, Virologie, dI&I I&I-1, LS Virologie, Virologie, and dI&I I&I-1

Subjects
0301 basic medicine, ICAM-1, receptor, viruses, 030106 microbiology, Coronacrisis-Taverne, Coxsackievirus, Virus, Disease Outbreaks, 03 medical and health sciences, Pandemic, conjunctivitis, medicine, Humans, Amino Acid Sequence, Receptor, Pandemics, Phylogeny, Multidisciplinary, biology, Sequence Homology, Amino Acid, Cryoelectron Microscopy, Acute hemorrhagic conjunctivitis, Outbreak, Biological Sciences, medicine.disease, biology.organism_classification, Intercellular Adhesion Molecule-1, Virology, N-Acetylneuraminic Acid, Enterovirus C, Human, Viral Tropism, 030104 developmental biology, coxsackievirus A24v, Capsid, sialic acid, Mutation, Tissue tropism, Receptors, Virus, Capsid Proteins, Conjunctivitis, Acute Hemorrhagic, Protein Binding
Abstract

Acute hemorrhagic conjunctivitis (AHC) is a painful, contagious eye disease, with millions of cases in the last decades. Coxsackievirus A24 (CV-A24) was not originally associated with human disease, but in 1970 a pathogenic "variant" (CV-A24v) emerged, which is now the main cause of AHC. Initially, this variant circulated only in Southeast Asia, but it later spread worldwide, accounting for numerous AHC outbreaks and two pandemics. While both CV-A24 variant and nonvariant strains still circulate in humans, only variant strains cause AHC for reasons that are yet unknown. Since receptors are important determinants of viral tropism, we set out to map the CV-A24 receptor repertoire and establish whether changes in receptor preference have led to the increased pathogenicity and rapid spread of CV-A24v. Here, we identify ICAM-1 as an essential receptor for both AHC-causing and non-AHC strains. We provide a high-resolution cryo-EM structure of a virus-ICAM-1 complex, which revealed critical ICAM-1-binding residues. These data could help identify a possible conserved mode of receptor engagement among ICAM-1-binding enteroviruses and rhinoviruses. Moreover, we identify a single capsid substitution that has been adopted by all pandemic CV-A24v strains and we reveal that this adaptation enhances the capacity of CV-A24v to bind sialic acid. Our data elucidate the CV-A24v receptor repertoire and point to a role of enhanced receptor engagement in the adaptation to the eye, possibly enabling pandemic spread.

Published
2017

21. Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus

Author

LS Virologie, Virologie, dI&I I&I-1, Baggen, Jim, Hurdiss, Daniel L, Zocher, Georg, Mistry, Nitesh, Roberts, Richard W, Slager, Jasper J, Guo, Hongbo, van Vliet, Arno L W, Wahedi, Maryam, Benschop, Kimberley, Duizer, Erwin, de Haan, Cornelis A M, de Vries, Erik, Casasnovas, José M, de Groot, Raoul J, Arnberg, Niklas, Stehle, Thilo, Ranson, Neil A, Thibaut, Hendrik Jan, van Kuppeveld, Frank J M, LS Virologie, Virologie, dI&I I&I-1, Baggen, Jim, Hurdiss, Daniel L, Zocher, Georg, Mistry, Nitesh, Roberts, Richard W, Slager, Jasper J, Guo, Hongbo, van Vliet, Arno L W, Wahedi, Maryam, Benschop, Kimberley, Duizer, Erwin, de Haan, Cornelis A M, de Vries, Erik, Casasnovas, José M, de Groot, Raoul J, Arnberg, Niklas, Stehle, Thilo, Ranson, Neil A, Thibaut, Hendrik Jan, and van Kuppeveld, Frank J M

Published
2018

23. Betacoronavirus Adaptation to Humans Involved Progressive Loss of Hemagglutinin-Esterase Lectin Activity

Author

dI&I I&I-1, LS Virologie, Bakkers, Mark J G, Lang, Yifei, Feitsma, Louris J, Hulswit, Ruben J G, de Poot, Stefanie A H, van Vliet, Arno L W, Margine, Irina, de Groot-Mijnes, Jolanda D F, van Kuppeveld, Frank J M, Langereis, Martijn A, Huizinga, Eric G, de Groot, Raoul J, dI&I I&I-1, LS Virologie, Bakkers, Mark J G, Lang, Yifei, Feitsma, Louris J, Hulswit, Ruben J G, de Poot, Stefanie A H, van Vliet, Arno L W, Margine, Irina, de Groot-Mijnes, Jolanda D F, van Kuppeveld, Frank J M, Langereis, Martijn A, Huizinga, Eric G, and de Groot, Raoul J

Published
2017

24. Betacoronavirus Adaptation to Humans Involved Progressive Loss of Hemagglutinin-Esterase Lectin Activity

Author

Bakkers, Mark J G, Lang, Yifei, Feitsma, Louris J, Hulswit, Ruben J G, de Poot, Stefanie A H, van Vliet, Arno L W, Margine, Irina, de Groot-Mijnes, Jolanda D F, van Kuppeveld, Frank J M, Langereis, Martijn A, Huizinga, Eric G, de Groot, Raoul J, dI&I I&I-1, LS Virologie, dI&I I&I-1, and LS Virologie

Subjects
0301 basic medicine, Viral protein, viruses, Adaptation, Biological, Hemagglutinins, Viral, Virus Attachment, Host tropism, medicine.disease_cause, Microbiology, Article, Coronavirus OC43, Human, 03 medical and health sciences, chemistry.chemical_compound, Lectins, Virology, medicine, Influenza A virus, Animals, Humans, Receptor, biology, Hemagglutinin esterase, Lectin, biology.organism_classification, Sialic acid, 030104 developmental biology, chemistry, Mutation, biology.protein, Receptors, Virus, Parasitology, Viral Fusion Proteins, Betacoronavirus, Protein Binding
Abstract

Summary Human beta1-coronavirus (β1CoV) OC43 emerged relatively recently through a single zoonotic introduction. Like related animal β1CoVs, OC43 uses 9-O-acetylated sialic acid as receptor determinant. β1CoV receptor binding is typically controlled by attachment/fusion spike protein S and receptor-binding/receptor-destroying hemagglutinin-esterase protein HE. We show that following OC43’s introduction into humans, HE-mediated receptor binding was selected against and ultimately lost through progressive accumulation of mutations in the HE lectin domain. Consequently, virion-associated receptor-destroying activity toward multivalent glycoconjugates was reduced and altered such that some clustered receptor populations are no longer cleaved. Loss of HE lectin function was also observed for another respiratory human coronavirus, HKU1. This thus appears to be an adaptation to the sialoglycome of the human respiratory tract and for replication in human airways. The findings suggest that the dynamics of virion-glycan interactions contribute to host tropism. Our observations are relevant also to other human respiratory viruses of zoonotic origin, particularly influenza A virus., Graphical Abstract, Highlights • Adaption of coronaviruses OC43 and HKU1 to humans involved loss of HE lectin function • OC43 HE receptor binding site was lost via progressive accumulation of mutations • Loss of HE receptor binding alters sialate-9-O-acetylesterase receptor destroying activity • Balance of receptor binding and receptor destruction contributes to host tropism, Coronavirus OC43 entered the human population relatively recently. Bakkers et al. report that as an adaptation to replication in human airways, the OC43 hemagglutinin-esterase lost its receptor-binding function. Consequently, virion-associated receptor-destroying activity toward clustered sialoglycan-based receptor determinants was reduced. Suggestive of convergent evolution, human respiratory coronavirus HKU1 underwent similar changes.

Published
2017

25. Enterovirus D68 receptor requirements unveiled by haploid genetics

Author

dI&I I&I-1, LS Virologie, Baggen, Jim, Thibaut, Hendrik Jan, Staring, Jacqueline, Jae, Lucas T, Liu, Yue, Guo, Hongbo, Slager, Jasper J, de Bruin, Jost W, van Vliet, Arno L W, Blomen, Vincent A, Overduin, Pieter, Sheng, Ju, de Haan, Xander, de Vries, Erik, Meijer, Adam, Rossmann, Michael G, Brummelkamp, Thijn R, van Kuppeveld, Frank J M, dI&I I&I-1, LS Virologie, Baggen, Jim, Thibaut, Hendrik Jan, Staring, Jacqueline, Jae, Lucas T, Liu, Yue, Guo, Hongbo, Slager, Jasper J, de Bruin, Jost W, van Vliet, Arno L W, Blomen, Vincent A, Overduin, Pieter, Sheng, Ju, de Haan, Xander, de Vries, Erik, Meijer, Adam, Rossmann, Michael G, Brummelkamp, Thijn R, and van Kuppeveld, Frank J M

Published
2016

26. Molecular basis for the acid-initiated uncoating of human enterovirus D68.

Author

Yue Liu, Ju Sheng, van Vliet, Arno L. W., Buda, Geeta, van Kuppeveld, Frank J. M., and Rossmann, Michael G.

Subjects
ENTEROVIRUSES, ACIDIFICATION, ORGANIC coatings, CAPSIDS, RNA, CRYOELECTRONICS, MICROSCOPY, MOLECULES
Abstract

Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes respiratory infections and is acid-labile. The molecular mechanism by which the acid-sensitive EV-D68 virions uncoat and deliver their genome into a host cell is unknown. Using cryoelectron microscopy (cryo-EM), we have determined the structures of the full native virion and an uncoating intermediate [the A (altered) particle] of EV-D68 at 2.2- and 2.7-Å resolution, respectively. These structures showed that acid treatment of EVD68 leads to particle expansion, externalization of the viral protein VP1 N termini from the capsid interior, and formation of pores around the icosahedral twofold axes through which the viral RNA can exit. Moreover, because of the low stability of EV-D68, cryo-EM analyses of a mixed population of particles at neutral pH and following acid treatment demonstrated the involvement of multiple structural intermediates during virus uncoating. Among these, a previously undescribed state, the expanded 1 ("E1") particle, shows a majority of internal regions (e.g., the VP1 N termini) to be ordered as in the full native virion. Thus, the E1 particle acts as an intermediate in the transition from full native virions to A particles. Together, the present work delineates the pathway of EV-D68 uncoating and provides the molecular basis for the acid lability of EV-D68 and of the related common cold viruses. [ABSTRACT FROM AUTHOR]

Published
2018
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27. Complexity and Diversity of the Mammalian Sialome Revealed by Nidovirus Virolectins

Author

Langereis, Martijn A., Bakkers, Mark J G, Deng, Lingquan, Padler-Karavani, Vered, Vervoort, Stephin J., Hulswit, Ruben J G, van Vliet, Arno L W, Gerwig, Gerrit J., de Poot, Stefanie A H, Boot, Willemijn, van Ederen, Anne Marie, Heesters, Balthasar A., van der Loos, Chris M., van Kuppeveld, Frank J M, Yu, Hai, Huizinga, Eric G., Chen, Xi, Varki, Ajit, Kamerling, Johannis P., de Groot, Raoul J., Langereis, Martijn A., Bakkers, Mark J G, Deng, Lingquan, Padler-Karavani, Vered, Vervoort, Stephin J., Hulswit, Ruben J G, van Vliet, Arno L W, Gerwig, Gerrit J., de Poot, Stefanie A H, Boot, Willemijn, van Ederen, Anne Marie, Heesters, Balthasar A., van der Loos, Chris M., van Kuppeveld, Frank J M, Yu, Hai, Huizinga, Eric G., Chen, Xi, Varki, Ajit, Kamerling, Johannis P., and de Groot, Raoul J.

Published
2015

28. Complexity and Diversity of the Mammalian Sialome Revealed by Nidovirus Virolectins

Author

Bio organic Chemistry, Crystal and Structural Chemistry, dI&I I&I-1, LS Virologie, Sub Membrane Biochemistry & Biophysics, Afd Chemical Biology and Drug Discovery, Sub Crystal and Structural Chemistry, Langereis, Martijn A, Bakkers, Mark J G, Deng, Lingquan, Padler-Karavani, Vered, Vervoort, Stephin J, Hulswit, Ruben J G, van Vliet, Arno L W, Gerwig, Gerrit J, de Poot, Stefanie A H, Boot, Willemijn, van Ederen, Anne Marie, Heesters, Balthasar A, van der Loos, Chris M, van Kuppeveld, Frank J M, Yu, Hai, Huizinga, Eric G, Chen, Xi, Varki, Ajit, Kamerling, Johannis P, de Groot, Raoul J, Bio organic Chemistry, Crystal and Structural Chemistry, dI&I I&I-1, LS Virologie, Sub Membrane Biochemistry & Biophysics, Afd Chemical Biology and Drug Discovery, Sub Crystal and Structural Chemistry, Langereis, Martijn A, Bakkers, Mark J G, Deng, Lingquan, Padler-Karavani, Vered, Vervoort, Stephin J, Hulswit, Ruben J G, van Vliet, Arno L W, Gerwig, Gerrit J, de Poot, Stefanie A H, Boot, Willemijn, van Ederen, Anne Marie, Heesters, Balthasar A, van der Loos, Chris M, van Kuppeveld, Frank J M, Yu, Hai, Huizinga, Eric G, Chen, Xi, Varki, Ajit, Kamerling, Johannis P, and de Groot, Raoul J

Published
2015

29. Complexity and Diversity of the Mammalian Sialome Revealed by Nidovirus Virolectins

Author

CMM Groep Coffer, Orthopaedie Onderzoek, MMB, Langereis, Martijn A., Bakkers, Mark J G, Deng, Lingquan, Padler-Karavani, Vered, Vervoort, Stephin J., Hulswit, Ruben J G, van Vliet, Arno L W, Gerwig, Gerrit J., de Poot, Stefanie A H, Boot, Willemijn, van Ederen, Anne Marie, Heesters, Balthasar A., van der Loos, Chris M., van Kuppeveld, Frank J M, Yu, Hai, Huizinga, Eric G., Chen, Xi, Varki, Ajit, Kamerling, Johannis P., de Groot, Raoul J., CMM Groep Coffer, Orthopaedie Onderzoek, MMB, Langereis, Martijn A., Bakkers, Mark J G, Deng, Lingquan, Padler-Karavani, Vered, Vervoort, Stephin J., Hulswit, Ruben J G, van Vliet, Arno L W, Gerwig, Gerrit J., de Poot, Stefanie A H, Boot, Willemijn, van Ederen, Anne Marie, Heesters, Balthasar A., van der Loos, Chris M., van Kuppeveld, Frank J M, Yu, Hai, Huizinga, Eric G., Chen, Xi, Varki, Ajit, Kamerling, Johannis P., and de Groot, Raoul J.

Published
2015

34. Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution.

Author

Qinghong Zeng, Langereis, Martijn A., van Vliet, Arno L. W., Huizinga, Eric G., and de Groot, Raoul J.

Subjects
CORONAVIRUSES, HEMAGGLUTININ, ESTERASES, INFLUENZA viruses, GLYCOPROTEINS, LECTINS, ENZYMES, ANTIVIRAL agents
Abstract

The hemagglutinin-esterases (HE5) are a family of viral envelope glycoproteins that mediate reversible attachment to O-acetylated sialic acids by acting both as lectins and as receptor-destroying enzymes (RDEs). Related HEs occur in influenza C, toro-, and coronaviruses, apparently as a result of relatively recent lateral gene transfer events. Here, we report the crystal structure of a coronavirus (CoV) HE in complex with its receptor. We show that CoV HE arose from an influenza C-like HE fusion protein (HEF). In the process, HE was transformed from a trimer into a dimer, whereas remnants of the fusion domain were adapted to establish novel monomer-monomer contacts. Whereas the structural design of the RDE-acetylesterase domain remained unaltered, the HE receptor-binding domain underwent remodeling to such extent that the ligand is now bound in opposite orientation. This is surprising, because the architecture of the HEF site was preserved in influenza A HA over a much larger evolutionary distance, a switch in receptor specificity and extensive antigenic variation notwithstanding. Apparently, HA and HEF are under more stringent selective constraints than HE, limiting their exploration of alternative binding-site topologies. We attribute the plasticity of the Coy HE receptor-binding site to evolutionary flexibility conferred by functional redundancy between HE and its companion spike protein S. Our findings offer unique insights into the structural and functional consequences of independent protein evolution after interviral gene exchange and open potential avenues to broad-spectrum antiviral drug design. [ABSTRACT FROM AUTHOR]

Published
2008
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35. Nidovirus Sialate-O-Acetylesterases.

Author

Smits, Saskia L., Gerwig, Gerrit J., van Vliet, Arno L. W., Lissenberg, Arjen, Briza, Peter, Kamerling, Johannis P., Vlasak, Reinhard, and de Groot, Raoul J.

Subjects
*VIRUSES, *ENZYMES, *CELL receptors, *CORONAVIRUSES, *ORTHOMYXOVIRUSES, *BIOCHEMISTRY
Abstract

Many viruses achieve reversible attachment to sialic acid (Sia) by encoding envelope glycoproteins with receptor-binding and receptor-destroying activities. Toroviruses and group 2 coronaviruses bind to O-acetylated Sias, presumably via their spike proteins (S), whereas other glycoproteins, the hemagglutinin-esterases (HE), destroy Sia receptors by de-O-acetylation. Here, we present a comprehensive study of these enzymes. Sialate-9-O-acetylesterases specific for 5-N-acetyl-9-O-acetylneuraminic acid, described for bovine and human coronaviruses, also occur in equine coronaviruses and in porcine toroviruses. Bovine toroviruses, however, express novel sialate-9-O-acetylesterases, which prefer the di-O-acetylated substrate 5-N-acetyl-7 (8)9-di-O-acetylneuraminic acid. Whereas most rodent coronaviruses express sialate-4-O-acetylesterases, the HE of murine coronavirus DVIM cleaves 9-O-acetylated Sias. Under the premise that HE specificity reflects receptor usage, we propose that two types of Sias serve as initial attachment factors for coronaviruses in mice. There are striking parallels between orthomyxo- and nidovirus biology. Reminiscent of antigenic shifts in orthomyxoviruses, rodent coronaviruses exchanged S and HE sequences through recombination to extents not appreciated before. As for orthomyxovirus reassortants, the fitness of nidovirus recombinant offspring probably depends both on antigenic properties and on compatibility of receptor-binding and receptor-destroying activities. [ABSTRACT FROM AUTHOR]

Published
2005
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36. Fluoxetine targets an allosteric site in the enterovirus 2C AAA+ ATPase and stabilizes a ring-shaped hexameric complex.

Author

Hurdiss, Daniel L., El Kazzi, Priscila, Bauer, Lisa, Papageorgiou, Nicolas, Ferron, François P., Donselaar, Tim, van Vliet, Arno L. W., Shamorkina, Tatiana M., Snijder, Joost, Canard, Bruno, Decroly, Etienne, Brancale, Andrea, Zeev-Ben-Mordehai, Tzviya, Förster, Friedrich, van Kuppeveld, Frank J. M., and Coutard, Bruno

Subjects
*ADENOSINE triphosphatase, *FLUOXETINE, *GUANIDINIUM chlorides, *DRUG repositioning, *STRUCTURAL engineering, *VIRAL nonstructural proteins, *BENZIMIDAZOLES, *DNA helicases, *DNA replication
Abstract

Enteroviruses are globally prevalent human pathogens responsible for many diseases. The nonstructural protein 2C is a AAA+ helicase and plays a key role in enterovirus replication. Drug repurposing screens identified 2C-targeting compounds such as fluoxetine and dibucaine, but how they inhibit 2C is unknown. Here, we present a crystal structure of the soluble and monomeric fragment of coxsackievirus B3 2C protein in complex with (S)-fluoxetine (SFX), revealing an allosteric binding site. To study the functional consequences of SFX binding, we engineered an adenosine triphosphatase (ATPase)-competent, hexameric 2C protein. Using this system, we show that SFX, dibucaine, HBB [2-(?-hydroxybenzyl)-benzimidazole], and guanidine hydrochloride inhibit 2C ATPase activity. Moreover, cryo-electron microscopy analysis demonstrated that SFX and dibucaine lock 2C in a defined hexameric state, rationalizing their mode of inhibition. Collectively, these results provide important insights into 2C inhibition and a robust engineering strategy for structural, functional, and drug-screening analysis of 2C proteins. [ABSTRACT FROM AUTHOR]

Published
2022
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37. Translation and Replication Dynamics of Single RNA Viruses.

Author

Boersma S, Rabouw HH, Bruurs LJM, Pavlovič T, van Vliet ALW, Beumer J, Clevers H, van Kuppeveld FJM, and Tanenbaum ME

Subjects
Cell Line, Tumor, Cell Survival, HEK293 Cells, Host-Pathogen Interactions, Humans, Interferons metabolism, RNA Transport, RNA, Viral genetics, Reproducibility of Results, Single Molecule Imaging, Time Factors, Protein Biosynthesis, RNA Viruses physiology, Virus Replication physiology
Abstract

RNA viruses are among the most prevalent pathogens and are a major burden on society. Although RNA viruses have been studied extensively, little is known about the processes that occur during the first several hours of infection because of a lack of sensitive assays. Here we develop a single-molecule imaging assay, virus infection real-time imaging (VIRIM), to study translation and replication of individual RNA viruses in live cells. VIRIM uncovered a striking heterogeneity in replication dynamics between cells and revealed extensive coordination between translation and replication of single viral RNAs. Furthermore, using VIRIM, we identify the replication step of the incoming viral RNA as a major bottleneck of successful infection and identify host genes that are responsible for inhibition of early virus replication. Single-molecule imaging of virus infection is a powerful tool to study virus replication and virus-host interactions that may be broadly applicable to RNA viruses., Competing Interests: Declaration of Interests H.C. is the inventor of several patents related to organoid technology; his full disclosure is given at https://www.uu.nl/staff/JCClevers/., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)

Published
2020
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