Structure of the hexagonal surface layer on Caulobacter crescentus cells (original) (raw)

• Albers, S. V. & Meyer, B. H. The archaeal cell envelope. Nat. Rev. Microbiol. 9, 414–426 (2011).
  Article CAS Google Scholar
• Fagan, R. P. & Fairweather, N. F. Biogenesis and functions of bacterial S-layers. Nat. Rev. Microbiol. 12, 211–222 (2014).
  Article CAS Google Scholar
• Glauert, A. M. The fine structure of bacteria. Br. Med. Bull. 18, 245–250 (1962).
  Article CAS Google Scholar
• Sara, M. & Sleytr, U. B. S-layer proteins. J. Bacteriol. 182, 859–868 (2000).
  Article CAS Google Scholar
• Zhu, C. et al. Diversity in S-layers. Prog. Biophys. Mol. Biol. 123, 1–15 (2017).
  Article Google Scholar
• Kirk, J. A., Banerji, O. & Fagan, R. P. Characteristics of the Clostridium difficile cell envelope and its importance in therapeutics. Microb. Biotechnol. 10, 76–90 (2016).
  Article Google Scholar
• Sleytr, U. B. & Beveridge, T. J. Bacterial S-layers. Trends Microbiol. 7, 253–260 (1999).
  Article CAS Google Scholar
• Houwink, A. L. A macromolecular mono-layer in the cell wall of Spirillum spec. Biochim. Biophys. Acta 10, 360–366 (1953).
  Article CAS Google Scholar
• Sleytr, U. B. & Glauert, A. M. Ultrastructure of the cell walls of two closely related Clostridia that possess different regular arrays of surface subunits. J. Bacteriol. 126, 869–882 (1976).
  CAS PubMed PubMed Central Google Scholar
• Baumeister, W., Wildhaber, I. & Phipps, B. M. Principles of organization in eubacterial and archaebacterial surface proteins. Can. J. Microbiol. 35, 215–227 (1989).
  Article CAS Google Scholar
• Kessel, M., Wildhaber, I., Cohen, S. & Baumeister, W. Three-dimensional structure of the regular surface glycoprotein layer of Halobacterium volcanii from the Dead Sea. EMBO J. 7, 1549–1554 (1988).
  Article CAS Google Scholar
• Lupas, A. et al. Domain structure of the Acetogenium kivui surface layer revealed by electron crystallography and sequence analysis. J. Bacteriol. 176, 1224–1233 (1994).
  Article CAS Google Scholar
• Baranova, E. et al. SbsB structure and lattice reconstruction unveil Ca2+ triggered S-layer assembly. Nature 487, 119–122 (2012).
  Article CAS Google Scholar
• Arbing, M. A. et al. Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans. Proc. Natl Acad. Sci. USA 109, 11812–11817 (2012).
  Article CAS Google Scholar
• Jing, H. et al. Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins. Structure 10, 1453–1464 (2002).
  Article CAS Google Scholar
• Kern, J. et al. Structure of surface layer homology (SLH) domains from Bacillus anthracis surface array protein. J. Biol. Chem. 286, 26042–26049 (2011).
  Article CAS Google Scholar
• Jiang, C., Brown, P. J., Ducret, A. & Brun, Y. V. Sequential evolution of bacterial morphology by co-option of a developmental regulator. Nature 506, 489–493 (2014).
  Article CAS Google Scholar
• Wagner, J. K. & Brun, Y. V. Out on a limb: how the Caulobacter stalk can boost the study of bacterial cell shape. Mol. Microbiol. 64, 28–33 (2007).
  Article CAS Google Scholar
• Amat, F. et al. Analysis of the intact surface layer of Caulobacter crescentus by cryo-electron tomography. J. Bacteriol. 192, 5855–5865 (2010).
  Article CAS Google Scholar
• Smit, J., Engelhardt, H., Volker, S., Smith, S. H. & Baumeister, W. The S-layer of Caulobacter crescentus: three-dimensional image reconstruction and structure analysis by electron microscopy. J. Bacteriol. 174, 6527–6538 (1992).
  Article CAS Google Scholar
• Ford, M. J., Nomellini, J. F. & Smit, J. S-layer anchoring and localization of an S-layer-associated protease in Caulobacter crescentus. J. Bacteriol. 189, 2226–2237 (2007).
  Article CAS Google Scholar
• Nomellini, J. F., Kupcu, S., Sleytr, U. B. & Smit, J. Factors controlling in vitro recrystallization of the Caulobacter crescentus paracrystalline S-layer. J. Bacteriol. 179, 6349–6354 (1997).
  Article CAS Google Scholar
• Garnham, C. P., Campbell, R. L. & Davies, P. L. Anchored clathrate waters bind antifreeze proteins to ice. Proc. Natl Acad. Sci. USA 108, 7363–7367 (2011).
  Article CAS Google Scholar
• Ireland, M. M., Karty, J. A., Quardokus, E. M., Reilly, J. P. & Brun, Y. V. Proteomic analysis of the Caulobacter crescentus stalk indicates competence for nutrient uptake. Mol. Microbiol. 45, 1029–1041 (2002).
  Article CAS Google Scholar
• Bharat, T. A. M. & Scheres, S. H. W. Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION. Nat. Protoc. 11, 2054–2065 (2016).
  Article CAS Google Scholar
• Schur, F. K. M. et al. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Science 353, 506–508 (2016).
  Article CAS Google Scholar
• Howorka, S. Rationally engineering natural protein assemblies in nanobiotechnology. Curr. Opin. Biotechnol. 22, 485–491 (2011).
  Article CAS Google Scholar
• Mark, S. S. et al. Bionanofabrication of metallic and semiconductor nanoparticle arrays using S-layer protein lattices with different lateral spacings and geometries. Langmuir 22, 3763–3774 (2006).
  Article CAS Google Scholar
• Chang, Y.-W. et al. Architecture of the type IVa pilus machine. Science 351, aad2001 (2016).
  Article Google Scholar
• Poindexter, J. S. Biological properties and classification of the Caulobacter group. Bacteriol. Rev. 28, 231–295 (1964).
  CAS PubMed PubMed Central Google Scholar
• Stock, D., Perisic, O. & Löwe, J. Robotic nanolitre protein crystallisation at the MRC Laboratory of Molecular Biology. Prog. Biophys. Mol. Biol. 88, 311–327 (2005).
  Article CAS Google Scholar
• Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010).
  Article CAS Google Scholar
• Evans, P. R. An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr. D 67, 282–292 (2011).
  Article CAS Google Scholar
• Sheldrick, G. M. in Direct Methods for Solving Macromolecular Structures (ed. Fortier, S. ) 401–411 (Springer, 1998).
  Book Google Scholar
• McCoy, A. J. Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D 63, 32–41 (2007).
  Article CAS Google Scholar
• Cowtan, K. Recent developments in classical density modification. Acta Crystallogr. D 66, 470–478 (2010).
  Article CAS Google Scholar
• Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D 62, 1002–1011 (2006).
  Article Google Scholar
• Turk, D. MAIN software for density averaging, model building, structure refinement and validation. Acta Crystallogr. D 69, 1342–1357 (2013).
  Article CAS Google Scholar
• Adams, P. D. et al. PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
  Article CAS Google Scholar
• Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997).
  Article CAS Google Scholar
• Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
  Article Google Scholar
• Hagen, W. J. H., Wan, W. & Briggs, J. A. G. Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J. Struct. Biol. 197, 191–198 (2016).
  Article Google Scholar
• Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).
  Article CAS Google Scholar
• Bharat, T. A. M. et al. Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells. PLoS Biol. 9, e1001196 (2011).
  Article CAS Google Scholar
• Bharat, T. A. M., Russo, C. J., Löwe, J., Passmore, L. A. & Scheres, S. H. W. Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging. Structure 23, 1743–1753 (2015).
  Article CAS Google Scholar
• Mindell, J. A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003).
  Article Google Scholar
• Briggs, J. A. et al. Structure and assembly of immature HIV. Proc. Natl Acad. Sci. USA 106, 11090–11095 (2009).
  Article CAS Google Scholar
• Förster, F., Medalia, O., Zauberman, N., Baumeister, W. & Fass, D. Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc. Natl Acad. Sci. USA 102, 4729–4734 (2005).
  Article Google Scholar
• Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
  Article CAS Google Scholar
• Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
  Article CAS Google Scholar
• Söding, J., Biegert, A. & Lupas, A. N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244–W248 (2005).
  Article Google Scholar