PreprintCited by 28Enzyme Structure and FunctionInsect Resistance and GeneticsEntomopathogenic Microorganisms in Pest Control

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De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

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Preprint — published as 10.1038/s41467-022-31746-x · Paper page

Abstract

Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan , respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo -grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.

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Research works printed but not linked: 98

  1. 10.1016/j.ibmb.2011.02.006 · DOI
  2. 10.1016/j.jip.2012.05.001 · DOI
  3. 1995, Cloning and expression of a novel toxin gene from Bacillus thuringiensis subsp. jegathesan encoding a highly mosquitocidal protein, Appl Env. Microbiol, 61, 4230, 10.1128/aem.61.12.4230-4235.1995 · DOI
  4. 10.1007/7171_008/Published · DOI
  5. 10.1128/JB.188.9.3391-3401.2006 · DOI
  6. 10.1016/j.jmb.2005.02.013 · DOI
  7. 10.1016/j.jmb.2011.09.021 · DOI
  8. 2001, A theoretical model of the tridimensional structure of Bacillus thuringiensis subsp. medellin Cry 11Bb toxin deduced by homology modelling, Mem Inst Oswaldo Cruz, 96, 357, 10.1590/S0074-02762001000300013 · DOI
  9. 10.1038/nature09750 · DOI
  10. 10.1107/S205225251402702X · DOI
  11. Boutet, S. , Fromme, P. & Hunter, M. S. X-ray Free Electron Lasers - A Revolution in Structural Biology. vol. 1 (Springer International Publishing, 2018). · DOI
  12. 10.1038/s41467-020-14894-w · DOI
  13. 10.1038/353815a0 · DOI
  14. 10.1016/S0969-2126(01)00601-3 · DOI
  15. 10.1006/jmbi.1995.0630 · DOI
  16. 2017, Crystallophore: a versatile lanthanide complex for protein crystallography combining nucleating effects, phasing properties, and luminescence, Chem. Sci, 8, 5909, 10.1039/C7SC00758B · DOI
  17. 2019, Protein crystal structure determination with the crystallophore, a nucleating and phasing agent, J. Appl. Crystallogr, 52, 722, 10.1107/S1600576719006381 · DOI
  18. 2014, Structural insights into Bacillus thuringiensis Cry, Cyt and parasporin toxins, Toxins, 6, 2732, 10.3390/toxins6092732 · DOI
  19. 10.1093/bioinformatics/16.10.915 · DOI
  20. 10.1016/0097-8485(93)85006-X · DOI
  21. 10.1107/S160057751500449X · DOI
  22. 10.1038/nmeth.3667 · DOI
  23. 2008, Gas dynamic virtual nozzle for generation of microscopic droplet streams, J. Phys.-Appl. Phys, 41, 7
  24. 10.1016/B978-0-12-381270-4.00019-6 · DOI
  25. 10.1093/nar/27.1.49 · DOI
  26. 10.1111/j.1574-6976.2012.00341.x · DOI
  27. 2018, Distributed computing for macromolecular crystallography, Acta Crystallogr. Sect. Struct. Biol, 74, 143, 10.1107/S2059798317014565 · DOI
  28. 10.1038/nature19825 · DOI
  29. 10.1128/AEM.01056-06 · DOI
  30. 2014, Functional Analysis of Two Processed Fragments of Bacillus thuringiensis Cry11A Toxin, Biosci. Biotechnol. Biochem, 68, 523
  31. 10.1128/AEM.01303-09 · DOI
  32. 10.1016/j.febslet.2005.05.032 · DOI
  33. 10.1371/journal.pone.0019952 · DOI
  34. 10.1042/bj3380185 · DOI
  35. 10.1093/nar/gkz730 · DOI
  36. 2011, The adaptive gain integrating pixel detector AGIPD a detector for the European XFEL, Nucl. Instrum. Methods Phys. Res. Sect. Accel. Spectrometers Detect. Assoc. Equip, 633, S11, 10.1016/j.nima.2010.06.107 · DOI
  37. 10.1021/jf1036189 · DOI
  38. 10.1042/BJ20051517 · DOI
  39. 10.1111/1462-2920.12263 · DOI
  40. 10.1073/pnas.0505494102 · DOI
  41. 10.1073/pnas.1413456111 · DOI
  42. 10.1107/S0907444901008186 · DOI
  43. Adalat, R. , Saleem, F. , Crickmore, N. , Naz, S. & Shakoori, A. R. In Vivo Crystallization of Three-Domain Cry Toxins. Toxins Basel 9, (2017). · DOI
  44. 10.1126/science.aan6398 · DOI
  45. 10.1038/s41467-018-05490-0 · DOI
  46. 2013, Construction and characterization of the interdomain chimeras using Cry11Aa and Cry11Ba from Bacillus thuringiensis and identification of a possible novel toxic chimera, Biotechnol. Lett, 36, 105
  47. 10.1016/j.febslet.2005.05.032 · DOI
  48. 2018, Protein crystallization in living cells, Biol Chem, 399, 751, 10.1515/hsz-2018-0158 · DOI
  49. 10.1126/science.abj8754 · DOI · Paper page
  50. 10.1107/S0907444911039655 · DOI
  51. 10.1107/S0907444911001314 · DOI
  52. Banneville, A.-S. et al. Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction | bioRxiv. https://www.biorxiv.org/content/10.1101/2021.10.27.466113v1?rss=1. · DOI
  53. 10.1006/jipa.2001.5038 · DOI
  54. 10.1007/s002530050316 · DOI
  55. 10.1093/bioinformatics/btv115 · DOI
  56. 2004, Affordable image analysis using NIH Image/ImageJ, Indian J Cancer, 41, 47, 10.4103/0019-509X.12345 · DOI
  57. 10.2478/s11534-011-0096-2 · DOI
  58. 2011, DeStripe: frequency-based algorithm for removing stripe noises from AFM images, BMC Struct. Biol, 11, 7, 10.1186/1472-6807-11-7 · DOI
  59. 10.1038/nmeth.3667 · DOI
  60. 10.1107/S160057751500449X · DOI
  61. 2016, Diffraction-geometry refinement in the DIALS framework, Acta Crystallogr. Sect. Struct. Biol, 72, 558, 10.1107/S2059798316002187 · DOI
  62. 10.1107/S0907444913000863 · DOI
  63. 10.1038/nmeth.2887 · DOI
  64. 2018, DIALS: implementation and evaluation of a new integration package, Acta Crystallogr. Sect. Struct. Biol, 74, 85, 10.1107/S2059798317017235 · DOI
  65. 10.1107/S0021889897006766 · DOI
  66. 10.1016/B978-0-12-381270-4.00019-6 · DOI
  67. 10.1107/S0021889807021206 · DOI · Paper page
  68. 10.1107/S1399004715004514 · DOI
  69. 10.1016/j.cpc.2012.04.023 · DOI
  70. 10.1107/S0907444913013620 · DOI
  71. 10.1038/ncomms3701 · DOI
  72. 10.1107/S0907444910045749 · DOI · Paper page
  73. 2019, XGANDALF - extended gradient descent algorithm for lattice finding, Acta Crystallogr. Sect. Found. Adv, 75, 694, 10.1107/S2053273319010593 · DOI
  74. 10.1107/S0021889891010634 · DOI
  75. 2016, it TakeTwo: an indexing algorithm suited to still images with known crystal parameters, Acta Crystallogr. Sect. D, 72, 956, 10.1107/S2059798316010706 · DOI
  76. 10.1107/S0907444905039107 · DOI
  77. 10.1107/S0021889812002312 · DOI
  78. 2018, Distributed computing for macromolecular crystallography, Acta Crystallogr. Sect. Struct. Biol, 74, 143, 10.1107/S2059798317014565 · DOI
  79. 10.1107/S090744490705024X · DOI · Paper page
  80. 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr Biol Crystallogr, 60, 2126, 10.1107/S0907444904019158 · DOI · Paper page
  81. 10.1107/S0907444912001308 · DOI · Paper page
  82. Uervirojnangkoorn, M. et al. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. eLife 4, (2015). · DOI
  83. 10.1107/S0907444904016427 · DOI
  84. 2009, ALINE: a WYSIWYG protein-sequence alignment editor for publication-quality alignments, Acta Crystallogr Biol Crystallogr, 65, 510, 10.1107/S0907444909007835 · DOI
  85. 10.1016/j.jmb.2007.05.022 · DOI
  86. 10.1093/nar/gkz268 · DOI · Paper page
  87. 2004, Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallogr Biol Crystallogr, 60, 225
  88. 10.1093/bioinformatics/17.4.377 · DOI
  89. 10.1093/nar/gku400 · DOI
  90. 2021, Fast and sensitive taxonomic assignment to metagenomic contigs, Bioinformatics, 37, 3029, 10.1093/bioinformatics/btab184 · DOI
  91. 2017, MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets, Nat. Biotechnol, 35, 1026, 10.1038/nbt.3988 · DOI · Paper page
  92. Prakash, A. , Jeffryes, M. , Bateman, A. & Finn, R. D. The HMMER Web Server for Protein Sequence Similarity Search. Curr. Protoc. Bioinforma. 60, 3.15.1-3.15.23 (2017). · DOI
  93. 10.1093/nar/gky448 · DOI · Paper page
  94. Savi, M. K. , Mangamana, E. T. , Deguenon, J. M. , Hounmenou, C. G. & Kakaï, R. G. Determination of Lethal Concentrations Using an R Software Function Integrating the Abbott Correction. J. Agric. Sci. Technol. A 7, (2017). · DOI
  95. 10.1897/05-320R.1 · DOI
  96. 10.1016/0003-2697(92)90061-B · DOI
  97. 10.1038/nprot.2013.024 · DOI · Paper page
  98. 10.1021/acs.analchem.5b00140 · DOI · Paper page

Metadata

Authors
Tetreau, G., Sawaya, M. R., De Zitter, E., Andreeva, E. A., Banneville, A.-S., Schibrowsky, N., Coquelle, N., Brewster, A. S., Grünbein, M. L., Kovacs, G. N., Hunter, M. S., Kloos, M., Sierra, R. G., Schiro, G., Qiao, P., Stricker, M., Bideshi, D., Young, I. D., Zala, N., Engilberge, S., Gorel, A., Signor, L., Teulon, J.-M., Hilpert, M., Foucar, L., Bielecki, J., Bean, R., de Wijn, R., Sato, T., Kirkwood, H., Letrun, R., Batyuk, A., Snigireva, I., Fenel, D., Schubert, R., Canfield, E. J., Alba, M. M., Laporte, F., Després, L., Bacia, M., Roux, A., Chapelle, C., Riobé, F., Maury, O., Ling, W. L., Boutet, S., Mancuso, A., Gutsche, I., Girard, E., Barends, T. R. M., Pellequer, J.-L., Park, H.-W., Laganowsky, A. D., Rodriguez, J., Burghammer, M., Shoeman, R. L., Doak, R. B., Weik, M., Sauter, N. K., Federici, B., Cascio, D., Schlichting, I., & Colletier, J.-P.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • University of California, Los Angeles (US)
  • Institut Laue-Langevin (FR)
  • Lawrence Berkeley National Laboratory (US)
  • Max Planck Institute for Medical Research (DE)
  • SLAC National Accelerator Laboratory (US)
  • Texas A&M University (US)
  • University of California, Riverside (US)
  • European X-Ray Free-Electron Laser (DE)
  • European Synchrotron Radiation Facility (FR)
  • University of Southern California (US)
  • Lyon 1 Université (FR)
Corresponding author
Colletier, Jacques-Philippe
Venue
Nature Communications
Publisher
openRxiv
Published
2021-12-16
Volume
13
Issue
1
Pages
4376-4376
ISSN
2041-1723 (ISSN-L)
OpenAlex
W4288096555
Cited by
28
References
1
Citations by year
2026: 4 · 2025: 6 · 2024: 8 · 2023: 9 · 2022: 1
FWCI
1.68
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • HAL (submittedVersion, other-oa)
  • HAL (submittedVersion, cc-by-nc)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
  • European XFEL (submittedVersion)
Funders
  • U.S. Department of Energy (76SF00515, DE–AC02–76SF00515, P41GM103393, AC02‐76SF00515, DE-AC02-)
  • U.S. Department of Health and Human Services (P41RR001209, P41GM103393, 1U01CK000516, GM117126)
  • Infrastructures en Biologie Santé et Agronomie (ANR-17-EURE-0003, ANR-10-INBS-05-02)
  • Agence Nationale de la Recherche (UAR 3518 CNRS-CEA-UGA-EMBL, ANR-17-EURE-0003, ANR-10-INBS-05-02, ANR-10- INBS-05, ANR-17-EURE-, ANR-2018CE11-0005-02, ANR-17-CE11-0018, ANR-15-CE32-0004, DE-AC02-76SF00515, ANR-17, ANR-10, UMS 3518 CNRS-CEA-UGA-EMBL)
  • Centre National de la Recherche Scientifique (DE-AC02-76SF00515, ANR‐10‐INBS‐05‐02, UMS 3518 CNRS‐CEA‐UGA‐EMBL, ANR‐17‐EURE‐0003, UAR 3518 CNRS-CEA-UGA-EMBL)
  • Région Auvergne-Rhône-Alpes (ANR-17-EURE-0003, ANR-10-INBS-05-02)
  • French Infrastructure for Integrated Structural Biology (UAR 3518 CNRS-CEA-UGA-EMBL, ANR-17-EURE-0003, ANR-10-INBS-05–02, UMS 3518, ANR-10-INBS-0.5, UMS 3518 CNRS-CEA-UGA-EMBL, ANR-10-INBS)
  • National Institutes of Health (1U01CK000516, DE-AC02-76SF00515)
  • Centers for Disease Control and Prevention (1U01CK000516, U01CK000516)
  • Office of Science (AC02-76SF00515, P41GM103393, DE-AC02-76SF0051 5, DE-AC02, 76SF00515)
  • National Institute of General Medical Sciences (R01GM117126, T32GM007185, P41GM103393)
  • National Center for Research Resources (P41RR001209)
  • Basic Energy Sciences (DE-AC02, P41GM103393, 76SF00515, AC02-76SF00515, DE-AC-02-76SF00515)
  • SLAC National Accelerator Laboratory (DEAC02−76SF00515, AC02‐76SF00515, P41GM103393)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Insect Resistance and Genetics
  • Life Sciences › Agricultural and Biological Sciences › Insect Science › Entomopathogenic Microorganisms in Pest Control
Keywords
Cry11Aa, mosquitocidal toxin, Bacillus thuringiensis var. israelensis, nanocrystals, serial femtosecond crystallography, de novo structure determination, single-wavelength anomalous dispersion, protoxin, mosquito control, toxin toxicity
MeSH terms
Animals, Bacillus thuringiensis, Bacterial Proteins, Endotoxins, Hemolysin Proteins, Larva, Mosquito Control, Nanoparticles

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