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Front Mol Biosci. 2021 May 10;8:653148. doi: 10.3389/fmolb.2021.653148. eCollection 2021.

Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications.

Frontiers in molecular biosciences

Nadide Altincekic, Sophie Marianne Korn, Nusrat Shahin Qureshi, Marie Dujardin, Martí Ninot-Pedrosa, Rupert Abele, Marie Jose Abi Saad, Caterina Alfano, Fabio C L Almeida, Islam Alshamleh, Gisele Cardoso de Amorim, Thomas K Anderson, Cristiane D Anobom, Chelsea Anorma, Jasleen Kaur Bains, Adriaan Bax, Martin Blackledge, Julius Blechar, Anja Böckmann, Louis Brigandat, Anna Bula, Matthias Bütikofer, Aldo R Camacho-Zarco, Teresa Carlomagno, Icaro Putinhon Caruso, Betül Ceylan, Apirat Chaikuad, Feixia Chu, Laura Cole, Marquise G Crosby, Vanessa de Jesus, Karthikeyan Dhamotharan, Isabella C Felli, Jan Ferner, Yanick Fleischmann, Marie-Laure Fogeron, Nikolaos K Fourkiotis, Christin Fuks, Boris Fürtig, Angelo Gallo, Santosh L Gande, Juan Atilio Gerez, Dhiman Ghosh, Francisco Gomes-Neto, Oksana Gorbatyuk, Serafima Guseva, Carolin Hacker, Sabine Häfner, Bing Hao, Bruno Hargittay, K Henzler-Wildman, Jeffrey C Hoch, Katharina F Hohmann, Marie T Hutchison, Kristaps Jaudzems, Katarina Jović, Janina Kaderli, Gints Kalniņš, Iveta Kaņepe, Robert N Kirchdoerfer, John Kirkpatrick, Stefan Knapp, Robin Krishnathas, Felicitas Kutz, Susanne Zur Lage, Roderick Lambertz, Andras Lang, Douglas Laurents, Lauriane Lecoq, Verena Linhard, Frank Löhr, Anas Malki, Luiza Mamigonian Bessa, Rachel W Martin, Tobias Matzel, Damien Maurin, Seth W McNutt, Nathane Cunha Mebus-Antunes, Beat H Meier, Nathalie Meiser, Miguel Mompeán, Elisa Monaca, Roland Montserret, Laura Mariño Perez, Celine Moser, Claudia Muhle-Goll, Thais Cristtina Neves-Martins, Xiamonin Ni, Brenna Norton-Baker, Roberta Pierattelli, Letizia Pontoriero, Yulia Pustovalova, Oliver Ohlenschläger, Julien Orts, Andrea T Da Poian, Dennis J Pyper, Christian Richter, Roland Riek, Chad M Rienstra, Angus Robertson, Anderson S Pinheiro, Raffaele Sabbatella, Nicola Salvi, Krishna Saxena, Linda Schulte, Marco Schiavina, Harald Schwalbe, Mara Silber, Marcius da Silva Almeida, Marc A Sprague-Piercy, Georgios A Spyroulias, Sridhar Sreeramulu, Jan-Niklas Tants, Kaspars Tārs, Felix Torres, Sabrina Töws, Miguel Á Treviño, Sven Trucks, Aikaterini C Tsika, Krisztina Varga, Ying Wang, Marco E Weber, Julia E Weigand, Christoph Wiedemann, Julia Wirmer-Bartoschek, Maria Alexandra Wirtz Martin, Johannes Zehnder, Martin Hengesbach, Andreas Schlundt

Affiliations

  1. Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany.
  2. Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany.
  3. Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
  4. Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France.
  5. Institute for Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
  6. Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland.
  7. Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy.
  8. National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
  9. Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
  10. Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil.
  11. Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States.
  12. Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
  13. Department of Chemistry, University of California, Irvine, CA, United States.
  14. LCP, NIDDK, NIH, Bethesda, MD, United States.
  15. Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.
  16. Latvian Institute of Organic Synthesis, Riga, Latvia.
  17. BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany.
  18. Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany.
  19. Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil.
  20. Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
  21. Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany.
  22. Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States.
  23. Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States.
  24. Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy.
  25. Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy.
  26. Department of Pharmacy, University of Patras, Patras, Greece.
  27. Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil.
  28. Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States.
  29. Signals GmbH & Co. KG, Frankfurt am Main, Germany.
  30. Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany.
  31. Latvian Biomedical Research and Study Centre, Riga, Latvia.
  32. "Rocasolano" Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain.
  33. Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
  34. IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany.
  35. Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, United States.
  36. Department of Biology, Technical University of Darmstadt, Darmstadt, Germany.
  37. Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany.

PMID: 34041264 PMCID: PMC8141814 DOI: 10.3389/fmolb.2021.653148

Abstract

The highly infectious disease COVID-19 caused by the

Copyright © 2021 Altincekic, Korn, Qureshi, Dujardin, Ninot-Pedrosa, Abele, Abi Saad, Alfano, Almeida, Alshamleh, de Amorim, Anderson, Anobom, Anorma, Bains, Bax, Blackledge, Blechar, Böckmann, Brigandat, Bula, Bütikofer, Camacho-Zarco, Carlomagno, Caruso, Ceylan, Chaikuad, Chu, Cole, Crosby, de Jesus, Dhamotharan, Felli, Ferner, Fleischmann, Fogeron, Fourkiotis, Fuks, Fürtig, Gallo, Gande, Gerez, Ghosh, Gomes-Neto, Gorbatyuk, Guseva, Hacker, Häfner, Hao, Hargittay, Henzler-Wildman, Hoch, Hohmann, Hutchison, Jaudzems, Jović, Kaderli, Kalniņš, Kaņepe, Kirchdoerfer, Kirkpatrick, Knapp, Krishnathas, Kutz, zur Lage, Lambertz, Lang, Laurents, Lecoq, Linhard, Löhr, Malki, Bessa, Martin, Matzel, Maurin, McNutt, Mebus-Antunes, Meier, Meiser, Mompeán, Monaca, Montserret, Mariño Perez, Moser, Muhle-Goll, Neves-Martins, Ni, Norton-Baker, Pierattelli, Pontoriero, Pustovalova, Ohlenschläger, Orts, Da Poian, Pyper, Richter, Riek, Rienstra, Robertson, Pinheiro, Sabbatella, Salvi, Saxena, Schulte, Schiavina, Schwalbe, Silber, Almeida, Sprague-Piercy, Spyroulias, Sreeramulu, Tants, Tārs, Torres, Töws, Treviño, Trucks, Tsika, Varga, Wang, Weber, Weigand, Wiedemann, Wirmer-Bartoschek, Wirtz Martin, Zehnder, Hengesbach and Schlundt.

Keywords: COVID-19; NMR spectroscopy; SARS-CoV-2; accessory proteins; cell-free protein synthesis; intrinsically disordered region; nonstructural proteins; structural proteins

Conflict of interest statement

CH was employed by Signals GmbH & Co. KG. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potenti

References

  1. Biomol NMR Assign. 2021 Apr;15(1):173-176 - PubMed
  2. J Biol Chem. 2019 Sep 13;294(37):13606-13618 - PubMed
  3. PLoS Pathog. 2010 Apr 22;6(4):e1000863 - PubMed
  4. Protein Sci. 2020 Jul;29(7):1596-1605 - PubMed
  5. Antiviral Res. 2014 Sep;109:97-109 - PubMed
  6. Protein Expr Purif. 2015 Dec;116:1-6 - PubMed
  7. J Infect Dis. 2016 Feb 15;213(4):579-83 - PubMed
  8. J Mol Biol. 2010 Jul 23;400(4):724-42 - PubMed
  9. Virology. 2015 Oct;484:313-322 - PubMed
  10. Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4251-E4260 - PubMed
  11. Emerg Microbes Infect. 2020 Dec;9(1):221-236 - PubMed
  12. Proc Natl Acad Sci U S A. 2004 Mar 16;101(11):3792-6 - PubMed
  13. J Mol Biol. 2003 Aug 29;331(5):991-1004 - PubMed
  14. Biochim Biophys Acta Biomembr. 2018 Jun;1860(6):1309-1317 - PubMed
  15. J Virol. 2009 Oct;83(19):10314-8 - PubMed
  16. Nature. 1997 Jul 24;388(6640):343-9 - PubMed
  17. Biochemistry. 2020 Oct 6;59(39):3741-3756 - PubMed
  18. J Virol. 2009 Mar;83(5):2368-73 - PubMed
  19. Oral Dis. 2020 May 31;: - PubMed
  20. Biomol NMR Assign. 2021 Apr;15(1):219-227 - PubMed
  21. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W460-4 - PubMed
  22. Cell Res. 2020 Dec;30(12):1143-1145 - PubMed
  23. Elife. 2020 Oct 01;9: - PubMed
  24. Mol Cell. 2020 Sep 3;79(5):710-727 - PubMed
  25. Nat Commun. 2020 Jul 24;11(1):3717 - PubMed
  26. J Virol. 2008 May;82(9):4471-9 - PubMed
  27. Nature. 2020 Aug;584(7819):154-156 - PubMed
  28. Science. 2020 Sep 11;369(6509):1395-1398 - PubMed
  29. Antiviral Res. 2016 Nov;135:97-107 - PubMed
  30. Biomol NMR Assign. 2021 Apr;15(1):65-71 - PubMed
  31. Front Microbiol. 2020 Sep 03;11:2086 - PubMed
  32. Acta Pharm Sin B. 2020 Jul;10(7):1228-1238 - PubMed
  33. J Virol. 2009 Dec;83(24):12998-3008 - PubMed
  34. Protein J. 2020 Jun;39(3):198-216 - PubMed
  35. J Virol. 2009 Apr;83(7):3007-18 - PubMed
  36. Virus Res. 2015 Apr 16;202:89-100 - PubMed
  37. Nat Protoc. 2010 Feb;5(2):227-38 - PubMed
  38. Biochemistry. 2020 Jul 21;59(28):2608-2615 - PubMed
  39. Protein Sci. 2020 Sep;29(9):1890-1901 - PubMed
  40. EMBO J. 1996 Apr 15;15(8):2020-8 - PubMed
  41. Nat Struct Mol Biol. 2020 Dec;27(12):1202-1208 - PubMed
  42. Protein Expr Purif. 2009 Mar;64(1):16-23 - PubMed
  43. Nature. 2020 Nov;587(7835):657-662 - PubMed
  44. Nat Commun. 2019 May 28;10(1):2342 - PubMed
  45. J Struct Biol. 2020 Aug 1;211(2):107548 - PubMed
  46. Biomol NMR Assign. 2020 Oct;14(2):329-333 - PubMed
  47. Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12885-90 - PubMed
  48. Biochemistry. 2006 Oct 3;45(39):11827-35 - PubMed
  49. Biophys J. 2007 Feb 15;92(4):1374-83 - PubMed
  50. Structure. 2004 Feb;12(2):341-53 - PubMed
  51. Antiviral Res. 2014 Mar;103:39-50 - PubMed
  52. Arch Microbiol. 2021 Jan;203(1):59-66 - PubMed
  53. Nat Commun. 2020 Jul 14;11(1):3581 - PubMed
  54. Nucleic Acids Res. 2019 Jul 9;47(12):6538-6550 - PubMed
  55. Methods Mol Biol. 2017;1635:91-108 - PubMed
  56. Science. 2003 Jun 13;300(5626):1763-7 - PubMed
  57. Angew Chem Int Ed Engl. 2018 Apr 16;57(17):4787-4791 - PubMed
  58. J Virol. 2008 Jun;82(11):5279-94 - PubMed
  59. mBio. 2020 May 29;11(3): - PubMed
  60. PLoS Pathog. 2007 Aug 10;3(8):e109 - PubMed
  61. J Struct Biol. 2011 Apr;174(1):11-22 - PubMed
  62. Cell Rep. 2020 Sep 22;32(12):108185 - PubMed
  63. Protein Sci. 2003 Jun;12(6):1216-21 - PubMed
  64. Nature. 2021 Jan;589(7840):125-130 - PubMed
  65. Biomol NMR Assign. 2021 Apr;15(1):73-77 - PubMed
  66. Nat Struct Mol Biol. 2020 Oct;27(10):959-966 - PubMed
  67. Bioorg Med Chem Lett. 2020 Sep 1;30(17):127377 - PubMed
  68. J Virol. 2006 Aug;80(16):7894-901 - PubMed
  69. Science. 2020 Apr 24;368(6489):409-412 - PubMed
  70. Science. 2020 May 15;368(6492):779-782 - PubMed
  71. J Virol. 2007 Apr;81(7):3151-61 - PubMed
  72. Protein Expr Purif. 2015 Jan;105:39-46 - PubMed
  73. Biomol NMR Assign. 2021 Mar 17;: - PubMed
  74. Front Mol Biosci. 2019 Aug 08;6:67 - PubMed
  75. Chembiochem. 2020 May 15;21(10):1453-1460 - PubMed
  76. J Mol Biol. 2008 Jul 18;380(4):608-22 - PubMed
  77. J Biol Chem. 2015 Oct 16;290(42):25293-306 - PubMed
  78. Science. 2020 Jun 26;368(6498):1499-1504 - PubMed
  79. J Virol. 2019 May 29;93(12): - PubMed
  80. Molecules. 2020 Jun 28;25(13): - PubMed
  81. ACS Infect Dis. 2020 Dec 11;6(12):3174-3189 - PubMed
  82. J Biomol NMR. 2011 Dec;51(4):467-76 - PubMed
  83. Angew Chem Int Ed Engl. 2021 Mar 1;60(10):5339-5347 - PubMed
  84. Nature. 2020 Jun;582(7811):289-293 - PubMed
  85. Virology. 2014 Jun;458-459:125-35 - PubMed
  86. J Virol. 2007 Nov;81(21):12049-60 - PubMed
  87. J Virol. 2004 Nov;78(22):12557-65 - PubMed
  88. J Biomol NMR. 2016 Jun;65(2):87-98 - PubMed
  89. PLoS Pathog. 2020 Dec 2;16(12):e1009100 - PubMed
  90. J Biol Chem. 2005 Sep 2;280(35):31257-66 - PubMed
  91. Virology. 2020 Jul;546:51-66 - PubMed
  92. Biomol NMR Assign. 2021 Mar 23;: - PubMed
  93. J Virol. 2013 Aug;87(16):9159-72 - PubMed
  94. Biomol NMR Assign. 2021 Mar 26;: - PubMed
  95. Biomol NMR Assign. 2021 Apr;15(1):85-89 - PubMed
  96. Nature. 2020 Jul;583(7816):469-472 - PubMed
  97. J Virol. 2008 Dec;82(24):12392-405 - PubMed
  98. Protein Expr Purif. 2020 Oct;174:105686 - PubMed
  99. Nucleic Acids Res. 2020 Dec 16;48(22):12415-12435 - PubMed
  100. PLoS Biol. 2005 Jan;3(1):e5 - PubMed
  101. Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):9436-41 - PubMed
  102. Biomol NMR Assign. 2020 Oct;14(2):339-346 - PubMed
  103. Nature. 2020 Jul;583(7816):459-468 - PubMed
  104. J Virol. 2007 Nov;81(22):12323-36 - PubMed
  105. PLoS Pathog. 2009 May;5(5):e1000428 - PubMed
  106. Antiviral Res. 2018 Jan;149:58-74 - PubMed
  107. Biomol NMR Assign. 2021 Apr;15(1):129-135 - PubMed
  108. J Biochem Mol Biol. 2007 Sep 30;40(5):649-55 - PubMed
  109. Proc Natl Acad Sci U S A. 2021 Jan 12;118(2): - PubMed
  110. Science. 2020 Sep 4;369(6508):1249-1255 - PubMed
  111. Cell. 2020 Sep 17;182(6):1560-1573.e13 - PubMed
  112. iScience. 2020 Jul 24;23(7):101258 - PubMed
  113. Nature. 2020 Mar;579(7798):265-269 - PubMed
  114. J Virol. 2005 Nov;79(21):13399-411 - PubMed

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