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Structural basis for receptor recognition by Lujo virus

Abstract

Lujo virus (LUJV) has emerged as a highly fatal human pathogen. Despite its membership among the Arenaviridae, LUJV does not classify with the known Old and New World groups of that viral family. Likewise, LUJV was recently found to use neuropilin-2 (NRP2) as a cellular receptor instead of the canonical receptors used by Old World and New World arenaviruses. The emergence of a deadly pathogen into human populations using an unprecedented entry route raises many questions regarding the mechanism of cell recognition. To provide the basis for combating LUJV in particular, and to increase our general understanding of the molecular changes that accompany an evolutionary switch to a new receptor for arenaviruses, we used X-ray crystallography to reveal how the GP1 receptor-binding domain of LUJV (LUJVGP1) recognizes NRP2. Structural data show that LUJVGP1 is more similar to Old World than to New World arenaviruses. Structural analysis supported by experimental validation further suggests that NRP2 recognition is metal-ion dependent and that the complete NRP2 binding site is formed in the context of the trimeric spike. Taken together, our data provide the mechanism for the cell attachment step of LUJV and present indispensable information for combating this phatogen.

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Fig. 1: Crystal structure of the GP1 receptor-binding domain from LUJV.
Fig. 2: NRP2 recognition by LUJVGP1.
Fig. 3: Experimental validations for the NRP2 recognition mode by LUJVGP1.
Fig. 4: The NRP2 binding site on LUJVGP1 is located closer to the α-DG binding site than to the TfR1 binding site.
Fig. 5: Binding to NRP2 involves a quaternary site that is composed of two copies of LUJVGP1 in the context of the spike.
Fig. 6: The sole histidine residue at the interface cannot account for acidic-induced dissociation of the complex.

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References

  1. Moraz, M. L. & Kunz, S. Pathogenesis of arenavirus hemorrhagic fevers. Expert Rev. Anti. Infect. Ther. 9, 49–59 (2011).

    Article  PubMed  Google Scholar 

  2. Geisbert, T. W. & Jahrling, P. B. Exotic emerging viral diseases: progress and challenges. Nat. Med. 10, S110–S121 (2004).

    Article  CAS  PubMed  Google Scholar 

  3. Nunberg, J. H. & York, J. The curious case of arenavirus entry, and its inhibition. Viruses 4, 83–101 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Cao, W. et al. Identification of alpha-dystroglycan as a receptor for lymphocytic choriomeningitis virus and Lassa fever virus. Science 282, 2079–2081 (1998).

    Article  CAS  PubMed  Google Scholar 

  5. Kunz, S., Rojek, J. M., Perez, M., Spiropoulou, C. F. & Oldstone, M. B. Characterization of the interaction of lassa fever virus with its cellular receptor alpha-dystroglycan. J. Virol. 79, 5679–5987 (2005).

    Google Scholar 

  6. Radoshitzky, S. R. et al. Transferrin receptor 1 is a cellular receptor for New World haemorrhagic fever arenaviruses. Nature 446, 92–96 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Flanagan, M. L. et al. New world clade B arenaviruses can use transferrin receptor 1 (TfR1)-dependent and -independent entry pathways, and glycoproteins from human pathogenic strains are associated with the use of TfR1. J. Virol. 82, 938–948 (2008).

    Article  CAS  PubMed  Google Scholar 

  8. Eschli, B. et al. Identification of an N-terminal trimeric coiled-coil core within arenavirus glycoprotein 2 permits assignment to class I viral fusion proteins. J. Virol. 80, 5897–5907 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Rojek, J. M. & Kunz, S. Cell entry by human pathogenic arenaviruses. Cell. Microbiol. 10, 828–835 (2008).

    Article  CAS  PubMed  Google Scholar 

  10. Bowden, T. A. et al. Unusual molecular architecture of the machupo virus attachment glycoprotein. J. Virol. 83, 8259–8265 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Cohen-Dvashi, H., Cohen, N., Israeli, H. & Diskin, R. Molecular mechanism for LAMP1 recognition by Lassa virus. J. Virol. 89, 7584–7592 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Israeli, H., Cohen-Dvashi, H., Shulman, A., Shimon, A. & Diskin, R. Mapping of the Lassa virus LAMP1 binding site reveals unique determinants not shared by other old world arenaviruses. PLoS Pathog 13, e1006337 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Shimon, A., Shani, O. & Diskin, R. Structural basis for receptor selectivity by the Whitewater Arroyo mammarenavirus. J. Mol. Biol. 429, 2825–2839 (2017).

    Article  CAS  PubMed  Google Scholar 

  14. Mahmutovic, S. et al. Molecular basis for antibody-mediated neutralization of New World hemorrhagic fever mammarenaviruses. Cell Host Microbe 18, 705–713 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Hastie, K. M. et al. Structural basis for antibody-mediated neutralization of Lassa virus. Science 356, 923–928 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Jae, L.T. et al. Virus entry. Lassa virus entry requires a trigger-induced receptor switch. Science 344, 1506–1510 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Cohen-Dvashi, H., Israeli, H., Shani, O., Katz, A. & Diskin, R. Role of LAMP1 binding and pH sensing by the spike complex of Lassa virus. J. Virol. 90, 10329–10338 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Briese, T. et al. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog. 5, e1000455 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Raaben, M. et al. NRP2 and CD63 are host factors for Lujo virus cell entry. Cell Host Microbe 22, 688–696 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Appleton, B. A. et al. Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding. EMBO J. 26, 4902–4912 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Hastie, K. M. et al. Crystal structure of the prefusion surface glycoprotein of the prototypic arenavirus LCMV. Nat. Struct. Mol. Biol. 23, 513–521 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Abraham, J., Corbett, K. D., Farzan, M., Choe, H. & Harrison, S. C. Structural basis for receptor recognition by New World hemorrhagic fever arenaviruses. Nat. Struct. Mol. Biol. 17, 438–444 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Sullivan, B. M. et al. Point mutation in the glycoprotein of lymphocytic choriomeningitis virus is necessary for receptor binding, dendritic cell infection, and long-term persistence. Proc. Natl Acad. Sci. USA 108, 2969–2974 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Smelt, S. C. et al. Differences in affinity of binding of lymphocytic choriomeningitis virus strains to the cellular receptor alpha-dystroglycan correlate with viral tropism and disease kinetics. J. Virol. 75, 448–457 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Scott, C. C. & Gruenberg, J. Ion flux and the function of endosomes and lysosomes: pH is just the start: the flux of ions across endosomal membranes influences endosome function not only through regulation of the luminal pH. Bioessays 33, 103–110 (2011).

    Article  CAS  PubMed  Google Scholar 

  26. Winter, G. xia2: an expert system for macromolecular crystallography data reduction. J. Appl. Crystallogr. 43, 186–190 (2010).

    Article  CAS  Google Scholar 

  27. Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution?. Acta Crystallogr. D Biol. Crystallogr. 69, 1204–1214 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Winter, G. et al. DIALS: implementation and evaluation of a new integration package. Acta Crystallogr. D Struct. Biol. 74, 85–97 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D Biol. Crystallogr. 62, 72–82 (2006).

    Article  CAS  PubMed  Google Scholar 

  31. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Sims, J. J. et al. Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling. Nat. Methods 9, 303–309 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Jurrus, E. et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 27, 112–128 (2018).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Diffraction experiments were performed in beamline ID23-2 at the European Synchrotron Radiation Facility (ESRF), Grenoble, France. We are grateful to C. Zubieta at the ESRF for providing assistance in using beamline ID23-2. We thank R. Read from the University of Cambridge for his invaluable advice and contribution to the analysis of our crystallographic data. We thank D. Fass for providing critical comments and suggestions. Ron Diskin is an incumbent of the Tauro career development chair in biomedical research. Research in the Diskin lab is supported by a research grant from the Enoch Foundation, a research grant from the Abramson Family Center for Young Scientists, a research grant from Ms Rudolfine Steindling, by the Minerva Foundation with funding from the Federal German Ministry for Education and Research and by a grant from the Israel Science Foundation (grant No. 682/16).

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H.C.D. together with I.K. produced, purified and crystallized the LUJVGP1/NRP2 complex. H.C.D. and R.D. collected diffraction data. R.D. solved and analysed the structure. H.C.D. conducted structure/function studies. R.D. wrote the manuscript with the help of H.C.D.

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Correspondence to Ron Diskin.

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Supplementary Results, Supplementary Tables 1 and 2, Supplementary Figures 1–13, Supplementary References.

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Cohen-Dvashi, H., Kilimnik, I. & Diskin, R. Structural basis for receptor recognition by Lujo virus. Nat Microbiol 3, 1153–1160 (2018). https://doi.org/10.1038/s41564-018-0224-5

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