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Optical and force nanoscopy in microbiology.

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Xiao, Jie Dufrêne, Yves [UCL]

Microbial cells have developed sophisticated multicomponent structures and machineries to govern basic cellular processes, such as chromosome segregation, gene expression, cell division, mechanosensing, cell adhesion and biofilm formation. Because of the small cell sizes, subcellular structures have long been difficult to visualize using diffraction-limited light microscopy. During the last three decades, optical and force nanoscopy techniques have been developed to probe intracellular and extracellular structures with unprecedented resolutions, enabling researchers to study their organization, dynamics and interactions in individual cells, at the single-molecule level, from the inside out, and all the way up to cell-cell interactions in microbial communities. In this Review, we discuss the principles, advantages and limitations of the main optical and force nanoscopy techniques available in microbiology, and we highlight some outstanding questions that these new tools may help to answer.

Document type Article de périodique (Journal article) – Article de recherche
Access type Accès interdit
Publication date 2016
Language Anglais
Journal information "Nature microbiology" - Vol. 1, no.11, p. 16186 (2016)
Peer reviewed yes
e-issn 2058-5276
Publication status Publié
Affiliations UCL - SST/ISV - Institut des sciences de la vie
UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology
Links
  1. Ghosal D., Lo we J., Collaborative protein filaments, 10.15252/embj.201591756
  2. Cloud-Hansen Karen A., Peterson S. Brook, Stabb Eric V., Goldman William E., McFall-Ngai Margaret J., Handelsman Jo, Breaching the great wall: peptidoglycan and microbial interactions, 10.1038/nrmicro1486
  3. Kolter Roberto, Greenberg E. Peter, Microbial sciences: The superficial life of microbes, 10.1038/441300a
  4. Müller Daniel J., Dufrêne Yves F., Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology, 10.1038/nnano.2008.100
  5. Dufrêne Yves F., Towards nanomicrobiology using atomic force microscopy, 10.1038/nrmicro1948
  6. Engel Andreas, Müller Daniel J., 10.1038/78929
  7. Engel Andreas, Gaub Hermann E., Structure and Mechanics of Membrane Proteins, 10.1146/annurev.biochem.77.062706.154450
  8. Ando Toshio, Uchihashi Takayuki, Scheuring Simon, Filming Biomolecular Processes by High-Speed Atomic Force Microscopy, 10.1021/cr4003837
  9. Hinterdorfer Peter, Dufrêne Yves F, Detection and localization of single molecular recognition events using atomic force microscopy, 10.1038/nmeth871
  10. Müller Daniel J, Helenius Jonne, Alsteens David, Dufrêne Yves F, Force probing surfaces of living cells to molecular resolution, 10.1038/nchembio.181
  11. Strunz T., Oroszlan K., Schafer R., Guntherodt H.-J., Dynamic force spectroscopy of single DNA molecules, 10.1073/pnas.96.20.11277
  12. Dupres Vincent, Menozzi Franco D, Locht Camille, Clare Brian H, Abbott Nicholas L, Cuenot Stéphane, Bompard Coralie, Raze Dominique, Dufrêne Yves F, Nanoscale mapping and functional analysis of individual adhesins on living bacteria, 10.1038/nmeth769
  13. Alsteens D., Garcia M. C., Lipke P. N., Dufrene Y. F., Force-induced formation and propagation of adhesion nanodomains in living fungal cells, 10.1073/pnas.1013893107
  14. Dupres Vincent, Alsteens David, Wilk Sabrina, Hansen Benjamin, Heinisch Jürgen J, Dufrêne Yves F, The yeast Wsc1 cell surface sensor behaves like a nanospring in vivo, 10.1038/nchembio.220
  15. Helenius J., Heisenberg C.-P., Gaub H. E., Muller D. J., Single-cell force spectroscopy, 10.1242/jcs.030999
  16. Beaussart Audrey, El-Kirat-Chatel Sofiane, Herman Philippe, Alsteens David, Mahillon Jacques, Hols Pascal, Dufrêne Yves F., Single-Cell Force Spectroscopy of Probiotic Bacteria, 10.1016/j.bpj.2013.03.046
  17. Beaussart Audrey, Baker Amy E., Kuchma Sherry L., El-Kirat-Chatel Sofiane, O’Toole George A., Dufrêne Yves F., Nanoscale Adhesion Forces of Pseudomonas aeruginosa Type IV Pili, 10.1021/nn5044383
  18. Dufrêne Yves F, Martínez-Martín David, Medalsy Izhar, Alsteens David, Müller Daniel J, Multiparametric imaging of biological systems by force-distance curve–based AFM, 10.1038/nmeth.2602
  19. Medalsy Izhar, Hensen Ulf, Muller Daniel J., Imaging and Quantifying Chemical and Physical Properties of Native Proteins at Molecular Resolution by Force-Volume AFM, 10.1002/anie.201103991
  20. Rico Felix, Su Chanmin, Scheuring Simon, Mechanical Mapping of Single Membrane Proteins at Submolecular Resolution, 10.1021/nl202351t
  21. Alsteens David, Trabelsi Heykel, Soumillion Patrice, Dufrêne Yves F., Multiparametric atomic force microscopy imaging of single bacteriophages extruding from living bacteria, 10.1038/ncomms3926
  22. Formosa Cécile, Schiavone Marion, Boisrame Anita, Richard Mathias L., Duval Raphaël E., Dague Etienne, Multiparametric imaging of adhesive nanodomains at the surface of Candida albicans by atomic force microscopy, 10.1016/j.nano.2014.07.008
  23. Formosa-Dague Cécile, Speziale Pietro, Foster Timothy J., Geoghegan Joan A., Dufrêne Yves F., Zinc-dependent mechanical properties ofStaphylococcus aureusbiofilm-forming surface protein SasG, 10.1073/pnas.1519265113
  24. Formosa-Dague Cécile, Feuillie Cécile, Beaussart Audrey, Derclaye Sylvie, Kucharíková Soňa, Lasa Iñigo, Van Dijck Patrick, Dufrêne Yves F., Sticky Matrix: Adhesion Mechanism of the Staphylococcal Polysaccharide Intercellular Adhesin, 10.1021/acsnano.5b07515
  25. Hell Stefan W., Wichmann Jan, Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy, 10.1364/ol.19.000780
  26. Klar T. A., Jakobs S., Dyba M., Egner A., Hell S. W., Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission, 10.1073/pnas.97.15.8206
  27. Schneider Jale, Zahn Jasmin, Maglione Marta, Sigrist Stephan J, Marquard Jonas, Chojnacki Jakub, Kräusslich Hans-Georg, Sahl Steffen J, Engelhardt Johann, Hell Stefan W, Ultrafast, temporally stochastic STED nanoscopy of millisecond dynamics, 10.1038/nmeth.3481
  28. Schmidt Roman, Wurm Christian A., Punge Annedore, Egner Alexander, Jakobs Stefan, Hell Stefan W., Mitochondrial Cristae Revealed with Focused Light, 10.1021/nl901398t
  29. Betzig E., Patterson G. H., Sougrat R., Lindwasser O. W., Olenych S., Bonifacino J. S., Davidson M. W., Lippincott-Schwartz J., Hess H. F., Imaging Intracellular Fluorescent Proteins at Nanometer Resolution, 10.1126/science.1127344
  30. Hess Samuel T., Girirajan Thanu P.K., Mason Michael D., Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy, 10.1529/biophysj.106.091116
  31. Rust Michael J, Bates Mark, Zhuang Xiaowei, Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM), 10.1038/nmeth929
  32. Heilemann Mike, van de Linde Sebastian, Schüttpelz Mark, Kasper Robert, Seefeldt Britta, Mukherjee Anindita, Tinnefeld Philip, Sauer Markus, Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes, 10.1002/anie.200802376
  33. van Oijen A.M, Köhler J, Schmidt J, Müller M, Brakenhoff G.J, 3-Dimensional super-resolution by spectrally selective imaging, 10.1016/s0009-2614(98)00673-3
  34. Thompson Russell E., Larson Daniel R., Webb Watt W., Precise Nanometer Localization Analysis for Individual Fluorescent Probes, 10.1016/s0006-3495(02)75618-x
  35. Chozinski Tyler J., Gagnon Lauren A., Vaughan Joshua C., Twinkle, twinkle little star: Photoswitchable fluorophores for super-resolution imaging, 10.1016/j.febslet.2014.06.043
  36. Pavani S. R. P., Thompson M. A., Biteen J. S., Lord S. J., Liu N., Twieg R. J., Piestun R., Moerner W. E., Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function, 10.1073/pnas.0900245106
  37. Juette Manuel F, Gould Travis J, Lessard Mark D, Mlodzianoski Michael J, Nagpure Bhupendra S, Bennett Brian T, Hess Samuel T, Bewersdorf Joerg, Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples, 10.1038/nmeth.1211
  38. Tang J., Akerboom J., Vaziri A., Looger L. L., Shank C. V., Near-isotropic 3D optical nanoscopy with photon-limited chromophores, 10.1073/pnas.1004899107
  39. Huang B., Wang W., Bates M., Zhuang X., Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy, 10.1126/science.1153529
  40. Shtengel G., Galbraith J. A., Galbraith C. G., Lippincott-Schwartz J., Gillette J. M., Manley S., Sougrat R., Waterman C. M., Kanchanawong P., Davidson M. W., Fetter R. D., Hess H. F., Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure, 10.1073/pnas.0813131106
  41. Shroff Hari, Galbraith Catherine G, Galbraith James A, Betzig Eric, Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics, 10.1038/nmeth.1202
  42. Coltharp Carla, Kessler Rene P., Xiao Jie, Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements, 10.1371/journal.pone.0051725
  43. Endesfelder Ulrike, Malkusch Sebastian, Fricke Franziska, Heilemann Mike, A simple method to estimate the average localization precision of a single-molecule localization microscopy experiment, 10.1007/s00418-014-1192-3
  44. Huang Fang, Hartwich Tobias M P, Rivera-Molina Felix E, Lin Yu, Duim Whitney C, Long Jane J, Uchil Pradeep D, Myers Jordan R, Baird Michelle A, Mothes Walther, Davidson Michael W, Toomre Derek, Bewersdorf Joerg, Video-rate nanoscopy using sCMOS camera–specific single-molecule localization algorithms, 10.1038/nmeth.2488
  45. Gustafsson M. G. L., Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. SHORT COMMUNICATION, 10.1046/j.1365-2818.2000.00710.x
  46. Schermelleh L., Carlton P. M., Haase S., Shao L., Winoto L., Kner P., Burke B., Cardoso M. C., Agard D. A., Gustafsson M. G. L., Leonhardt H., Sedat J. W., Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy, 10.1126/science.1156947
  47. Gustafsson M. G. L., Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution, 10.1073/pnas.0406877102
  48. Li D., Shao L., Chen B.-C., Zhang X., Zhang M., Moses B., Milkie D. E., Beach J. R., Hammer J. A., Pasham M., Kirchhausen T., Baird M. A., Davidson M. W., Xu P., Betzig E., Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics, 10.1126/science.aab3500
  49. Hell Stefan W, Microscopy and its focal switch, 10.1038/nmeth.1291
  50. Hell S. W., Kroug M., Ground-state-depletion fluorscence microscopy: A concept for breaking the diffraction resolution limit, 10.1007/bf01081333
  51. Hofmann M., Eggeling C., Jakobs S., Hell S. W., Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins, 10.1073/pnas.0506010102
  52. Sharonov A., Hochstrasser R. M., Wide-field subdiffraction imaging by accumulated binding of diffusing probes, 10.1073/pnas.0609643104
  53. Jungmann Ralf, Steinhauer Christian, Scheible Max, Kuzyk Anton, Tinnefeld Philip, Simmel Friedrich C., Single-Molecule Kinetics and Super-Resolution Microscopy by Fluorescence Imaging of Transient Binding on DNA Origami, 10.1021/nl103427w
  54. Schoen Ingmar, Ries Jonas, Klotzsch Enrico, Ewers Helge, Vogel Viola, Binding-Activated Localization Microscopy of DNA Structures, 10.1021/nl2025954
  55. Huang Bo, Babcock Hazen, Zhuang Xiaowei, Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells, 10.1016/j.cell.2010.12.002
  56. Dempsey Graham T, Vaughan Joshua C, Chen Kok Hao, Bates Mark, Zhuang Xiaowei, Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging, 10.1038/nmeth.1768
  57. Durisic Nela, Laparra-Cuervo Lara, Sandoval-Álvarez Ángel, Borbely Joseph Steven, Lakadamyali Melike, Single-molecule evaluation of fluorescent protein photoactivation efficiency using an in vivo nanotemplate, 10.1038/nmeth.2784
  58. Gahlmann Andreas, Moerner W. E., Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging, 10.1038/nrmicro3154
  59. Coltharp Carla, Xiao Jie, Superresolution microscopy for microbiology : Superresolution microscopy for microbiology, 10.1111/cmi.12024
  60. Coltharp Carla, Yang Xinxing, Xiao Jie, Quantitative analysis of single-molecule superresolution images, 10.1016/j.sbi.2014.08.008
  61. Small Alexander R., Parthasarathy Raghuveer, Superresolution Localization Methods, 10.1146/annurev-physchem-040513-103735
  62. Dame Remus T, Tark-Dame Mariliis, Bacterial chromatin: converging views at different scales, 10.1016/j.ceb.2016.02.015
  63. Spahn Christoph, Endesfelder Ulrike, Heilemann Mike, Super-resolution imaging of Escherichia coli nucleoids reveals highly structured and asymmetric segregation during fast growth, 10.1016/j.jsb.2014.01.007
  64. Spahn Christoph, Cella-Zannacchi Francesca, Endesfelder Ulrike, Heilemann Mike, Correlative super-resolution imaging of RNA polymerase distribution and dynamics, bacterial membrane and chromosomal structure in Escherichia coli, 10.1088/2050-6120/3/1/014005
  65. Foo Yong Hwee, Spahn Christoph, Zhang Hongfang, Heilemann Mike, Kenney Linda J., Single cell super-resolution imaging of E. coli OmpR during environmental stress, 10.1039/c5ib00077g
  66. Kolb Hartmuth C., Finn M. G., Sharpless K. Barry, Click Chemistry: Diverse Chemical Function from a Few Good Reactions, 10.1002/1521-3773(20010601)40:11<2004::aid-anie2004>3.3.co;2-x
  67. Marbouty Martial, Le Gall Antoine, Cattoni Diego I., Cournac Axel, Koh Alan, Fiche Jean-Bernard, Mozziconacci Julien, Murray Heath, Koszul Romain, Nollmann Marcelo, Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging, 10.1016/j.molcel.2015.07.020
  68. Stracy Mathew, Lesterlin Christian, Garza de Leon Federico, Uphoff Stephan, Zawadzki Pawel, Kapanidis Achillefs N., Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid, 10.1073/pnas.1507592112
  69. Lee Steven F., Thompson Michael A., Schwartz Monica A., Shapiro Lucy, Moerner W.E., Super-Resolution Imaging of the Nucleoid-Associated Protein HU in Caulobacter crescentus, 10.1016/j.bpj.2011.02.022
  70. Wang W., Li G.-W., Chen C., Xie X. S., Zhuang X., Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria, 10.1126/science.1204697
  71. Straight Aaron F., Belmont Andrew S., Robinett Carmen C., Murray Andrew W., GFP tagging of budding yeast chromosomes reveals that protein–protein interactions can mediate sister chromatid cohesion, 10.1016/s0960-9822(02)70783-5
  72. Hensel Zach, Weng Xiaoli, Lagda Arvin Cesar, Xiao Jie, Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells, 10.1371/journal.pbio.1001591
  73. Liao Yi, Schroeder Jeremy W., Gao Burke, Simmons Lyle A., Biteen Julie S., Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair, 10.1073/pnas.1507386112
  74. Uphoff S., Reyes-Lamothe R., Garza de Leon F., Sherratt D. J., Kapanidis A. N., Single-molecule DNA repair in live bacteria, 10.1073/pnas.1301804110
  75. Tang M., Shen X., Frank E. G., O'Donnell M., Woodgate R., Goodman M. F., UmuD'2C is an error-prone DNA polymerase, Escherichia coli pol V, 10.1073/pnas.96.16.8919
  76. Robinson Andrew, McDonald John P., Caldas Victor E. A., Patel Meghna, Wood Elizabeth A., Punter Christiaan M., Ghodke Harshad, Cox Michael M., Woodgate Roger, Goodman Myron F., van Oijen Antoine M., Regulation of Mutagenic DNA Polymerase V Activation in Space and Time, 10.1371/journal.pgen.1005482
  77. Lesterlin Christian, Ball Graeme, Schermelleh Lothar, Sherratt David J., RecA bundles mediate homology pairing between distant sisters during DNA break repair, 10.1038/nature12868
  78. Rajendram Manohary, Zhang Leili, Reynolds Bradley J., Auer George K., Tuson Hannah H., Ngo Khanh V., Cox Michael M., Yethiraj Arun, Cui Qiang, Weibel Douglas B., Anionic Phospholipids Stabilize RecA Filament Bundles in Escherichia coli, 10.1016/j.molcel.2015.09.009
  79. Bakshi Somenath, Dalrymple Renée M., Li Wenting, Choi Heejun, Weisshaar James C., Partitioning of RNA Polymerase Activity in Live Escherichia coli from Analysis of Single-Molecule Diffusive Trajectories, 10.1016/j.bpj.2013.10.024
  80. Bakshi Somenath, Siryaporn Albert, Goulian Mark, Weisshaar James C., Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells : Superresolution imaging of ribosome and RNAP, 10.1111/j.1365-2958.2012.08081.x
  81. Endesfelder Ulrike, Finan Kieran, Holden Seamus J., Cook Peter R., Kapanidis Achillefs N., Heilemann Mike, Multiscale Spatial Organization of RNA Polymerase in Escherichia coli, 10.1016/j.bpj.2013.05.048
  82. Cagliero Cedric, Zhou Yan Ning, Jin Ding Jun, Spatial organization of transcription machinery and its segregation from the replisome in fast-growing bacterial cells, 10.1093/nar/gku1103
  83. Jin D. J., Front. Microbiol., 6, 497 (2015)
  84. Bath J., Role of Bacillus subtilis SpoIIIE in DNA Transport Across the Mother Cell-Prespore Division Septum, 10.1126/science.290.5493.995
  85. Yen Shin J., eLife, 4, e06474 (2015)
  86. Fiche Jean-Bernard, Cattoni Diego I., Diekmann Nele, Langerak Julio Mateos, Clerte Caroline, Royer Catherine A., Margeat Emmanuel, Doan Thierry, Nöllmann Marcelo, Recruitment, Assembly, and Molecular Architecture of the SpoIIIE DNA Pump Revealed by Superresolution Microscopy, 10.1371/journal.pbio.1001557
  87. Ptacin J. L., Gahlmann A., Bowman G. R., Perez A. M., von Diezmann A. R. S., Eckart M. R., Moerner W. E., Shapiro L., Bacterial scaffold directs pole-specific centromere segregation, 10.1073/pnas.1405188111
  88. de Boer Piet, Crossley Robin, Rothfield Lawrence, The essential bacterial cell-division protein FtsZ is a GTPase, 10.1038/359254a0
  89. RayChaudhuri Debabrata, Park James T., Escherichia coli cell-division gene ftsZ encodes a novel GTP-binding protein, 10.1038/359251a0
  90. Gong Yan, Bourhis Eric, Chiu Cecilia, Stawicki Scott, DeAlmeida Venita I., Liu Bob Y., Phamluong Khanhky, Cao Tim C., Carano Richard A. D., Ernst James A., Solloway Mark, Rubinfeld Bonnee, Hannoush Rami N., Wu Yan, Polakis Paul, Costa Mike, Wnt Isoform-Specific Interactions with Coreceptor Specify Inhibition or Potentiation of Signaling by LRP6 Antibodies, 10.1371/journal.pone.0012682
  91. Strauss Michael P., Liew Andrew T. F., Turnbull Lynne, Whitchurch Cynthia B., Monahan Leigh G., Harry Elizabeth J., 3D-SIM Super Resolution Microscopy Reveals a Bead-Like Arrangement for FtsZ and the Division Machinery: Implications for Triggering Cytokinesis, 10.1371/journal.pbio.1001389
  92. Holden S. J., Pengo T., Meibom K. L., Fernandez Fernandez C., Collier J., Manley S., High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization, 10.1073/pnas.1313368111
  93. Fleurie Aurore, Lesterlin Christian, Manuse Sylvie, Zhao Chao, Cluzel Caroline, Lavergne Jean-Pierre, Franz-Wachtel Mirita, Macek Boris, Combet Christophe, Kuru Erkin, VanNieuwenhze Michael S., Brun Yves V., Sherratt David, Grangeasse Christophe, MapZ marks the division sites and positions FtsZ rings in Streptococcus pneumoniae, 10.1038/nature13966
  94. Jacq Maxime, Adam Virgile, Bourgeois Dominique, Moriscot Christine, Di Guilmi Anne-Marie, Vernet Thierry, Morlot Cécile, Remodeling of the Z-Ring Nanostructure during theStreptococcus pneumoniaeCell Cycle Revealed by Photoactivated Localization Microscopy, 10.1128/mbio.01108-15
  95. Leisch Nikolaus, Verheul Jolanda, Heindl Niels R., Gruber-Vodicka Harald R., Pende Nika, den Blaauwen Tanneke, Bulgheresi Silvia, Growth in width and FtsZ ring longitudinal positioning in a gammaproteobacterial symbiont, 10.1016/j.cub.2012.08.033
  96. Grangeon Romain, Zupan John R., Anderson-Furgeson James, Zambryski Patricia C., PopZ identifies the new pole, and PodJ identifies the old pole during polar growth inAgrobacterium tumefaciens, 10.1073/pnas.1515544112
  97. Coltharp Carla, Buss Jackson, Plumer Trevor M., Xiao Jie, Defining the rate-limiting processes of bacterial cytokinesis, 10.1073/pnas.1514296113
  98. Rowlett Veronica Wells, Margolin William, 3D-SIM Super-resolution of FtsZ and Its Membrane Tethers in Escherichia coli Cells, 10.1016/j.bpj.2014.08.024
  99. Biteen Julie S., Goley Erin D., Shapiro Lucy, Moerner W. E., Three-Dimensional Super-Resolution Imaging of the Midplane Protein FtsZ in LiveCaulobacter crescentusCells Using Astigmatism, 10.1002/cphc.201100686
  100. Lyu Zhixin, Coltharp Carla, Yang Xinxing, Xiao Jie, Influence of FtsZ GTPase activity and concentration on nanoscale Z-ring structurein vivorevealed by three-dimensional Superresolution imaging : In vivo Influence of FtsZ GTPase Activity and Concentration, 10.1002/bip.22895
  101. Eswaramoorthy P., Erb M. L., Gregory J. A., Silverman J., Pogliano K., Pogliano J., Ramamurthi K. S., Cellular Architecture Mediates DivIVA Ultrastructure and Regulates Min Activity in Bacillus subtilis, 10.1128/mbio.00257-11
  102. Buss Jackson, Coltharp Carla, Huang Tao, Pohlmeyer Chris, Wang Shih-Chin, Hatem Christine, Xiao Jie, In vivoorganization of the FtsZ-ring by ZapA and ZapB revealed by quantitative super-resolution microscopy : PALM reveals ZapA and ZapB organizing FtsZ clusters, 10.1111/mmi.12331
  103. Buss Jackson, Coltharp Carla, Shtengel Gleb, Yang Xinxing, Hess Harald, Xiao Jie, A Multi-layered Protein Network Stabilizes the Escherichia coli FtsZ-ring and Modulates Constriction Dynamics, 10.1371/journal.pgen.1005128
  104. Olshausen Philipp v., Defeu Soufo Hervé Joël, Wicker Kai, Heintzmann Rainer, Graumann Peter L., Rohrbach Alexander, Superresolution Imaging of Dynamic MreB Filaments in B. subtilis—A Multiple-Motor-Driven Transport?, 10.1016/j.bpj.2013.07.038
  105. Reimold C., Defeu Soufo H. J., Dempwolff F., Graumann P. L., Motion of variable-length MreB filaments at the bacterial cell membrane influences cell morphology, 10.1091/mbc.e12-10-0728
  106. Kim S. Y., Gitai Z., Kinkhabwala A., Shapiro L., Moerner W. E., Single molecules of the bacterial actin MreB undergo directed treadmilling motion in Caulobacter crescentus, 10.1073/pnas.0604503103
  107. Biteen Julie S, Thompson Michael A, Tselentis Nicole K, Bowman Grant R, Shapiro Lucy, Moerner W E, Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP, 10.1038/nmeth.1258
  108. Ptacin Jerod L., Lee Steven F., Garner Ethan C., Toro Esteban, Eckart Michael, Comolli Luis R., Moerner W.E., Shapiro Lucy, A spindle-like apparatus guides bacterial chromosome segregation, 10.1038/ncb2083
  109. Ausmees Nora, Kuhn Jeffrey R, Jacobs-Wagner Christine, The Bacterial Cytoskeleton, 10.1016/s0092-8674(03)00935-8
  110. Lew M. D., Lee S. F., Ptacin J. L., Lee M. K., Twieg R. J., Shapiro L., Moerner W. E., Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus, 10.1073/pnas.1114444108
  111. Greenfield Derek, McEvoy Ann L., Shroff Hari, Crooks Gavin E., Wingreen Ned S., Betzig Eric, Liphardt Jan, Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy, 10.1371/journal.pbio.1000137
  112. Fredlund Jennifer, Broder Dan, Fleming Tinya, Claussin Clémence, Pogliano Kit, The SpoIIQ landmark protein has different requirements for septal localization and immobilization : Localization and immobilization of SpoIIQ, 10.1111/mmi.12333
  113. Haas Beth L., Matson Jyl S., DiRita Victor J., Biteen Julie S., Single-molecule tracking in liveVibrio choleraereveals that ToxR recruits the membrane-bound virulence regulator TcpP to thetoxTpromoter : Super-resolvingV. choleraevirulence regulation, 10.1111/mmi.12834
  114. Llorente-Garcia Isabel, Lenn Tchern, Erhardt Heiko, Harriman Oliver L., Liu Lu-Ning, Robson Alex, Chiu Sheng-Wen, Matthews Sarah, Willis Nicky J., Bray Christopher D., Lee Sang-Hyuk, Shin Jae Yen, Bustamante Carlos, Liphardt Jan, Friedrich Thorsten, Mullineaux Conrad W., Leake Mark C., Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation, 10.1016/j.bbabio.2014.01.020
  115. Karunatilaka Krishanthi S., Cameron Elizabeth A., Martens Eric C., Koropatkin Nicole M., Biteen Julie S., Superresolution Imaging Captures Carbohydrate Utilization Dynamics in Human Gut Symbionts, 10.1128/mbio.02172-14
  116. Dufrene Y. F., J. Bacteriol., 181, 5350 (1999)
  117. Schabert F., Henn C, Engel A, Native Escherichia coli OmpF porin surfaces probed by atomic force microscopy, 10.1126/science.7701347
  118. Kailas L., Terry C., Abbott N., Taylor R., Mullin N., Tzokov S. B., Todd S. J., Wallace B. A., Hobbs J. K., Moir A., Bullough P. A., Surface architecture of endospores of the Bacillus cereus/anthracis/thuringiensis family at the subnanometer scale, 10.1073/pnas.1109419108
  119. Casuso Ignacio, Kodera Noriyuki, Le Grimellec Christian, Ando Toshio, Scheuring Simon, Contact-Mode High-Resolution High-Speed Atomic Force Microscopy Movies of the Purple Membrane, 10.1016/j.bpj.2009.06.019
  120. Shibata Mikihiro, Yamashita Hayato, Uchihashi Takayuki, Kandori Hideki, Ando Toshio, High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin, 10.1038/nnano.2010.7
  121. Yamashita Hayato, Inoue Keiichi, Shibata Mikihiro, Uchihashi Takayuki, Sasaki Jun, Kandori Hideki, Ando Toshio, Role of trimer–trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy, 10.1016/j.jsb.2013.02.011
  122. Casuso Ignacio, Khao Jonathan, Chami Mohamed, Paul-Gilloteaux Perrine, Husain Mohamed, Duneau Jean-Pierre, Stahlberg Henning, Sturgis James N., Scheuring Simon, Characterization of the motion of membrane proteins using high-speed atomic force microscopy, 10.1038/nnano.2012.109
  123. Turner Robert D., Hurd Alexander F., Cadby Ashley, Hobbs Jamie K., Foster Simon J., Cell wall elongation mode in Gram-negative bacteria is determined by peptidoglycan architecture, 10.1038/ncomms2503
  124. Turner Robert D., Vollmer Waldemar, Foster Simon J., Different walls for rods and balls: the diversity of peptidoglycan : The diversity of peptidoglycan, 10.1111/mmi.12513
  125. Hayhurst E. J., Kailas L., Hobbs J. K., Foster S. J., Cell wall peptidoglycan architecture in Bacillus subtilis, 10.1073/pnas.0804138105
  126. Turner Robert D., Ratcliffe Emma C., Wheeler Richard, Golestanian Ramin, Hobbs Jamie K., Foster Simon J., Peptidoglycan architecture can specify division planes in Staphylococcus aureus, 10.1038/ncomms1025
  127. Wheeler Richard, Mesnage Stéphane, Boneca Ivo G., Hobbs Jamie K., Foster Simon J., Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria : Ovococcal peptidoglycan architecture and dynamics, 10.1111/j.1365-2958.2011.07871.x
  128. Plomp M., Leighton T. J., Wheeler K. E., Hill H. D., Malkin A. J., In vitro high-resolution structural dynamics of single germinating bacterial spores, 10.1073/pnas.0610626104
  129. Andre Guillaume, Kulakauskas Saulius, Chapot-Chartier Marie-Pierre, Navet Benjamine, Deghorain Marie, Bernard Elvis, Hols Pascal, Dufrêne Yves F., Imaging the nanoscale organization of peptidoglycan in living Lactococcus lactis cells, 10.1038/ncomms1027
  130. LOTAN Reuben, SHARON Nathan, MIRELMAN David, Interaction of Wheat-Germ Agglutinin with Bacterial Cells and Cell-Wall Polymers, 10.1111/j.1432-1033.1975.tb02158.x
  131. Kuru Erkin, Hughes H. Velocity, Brown Pamela J., Hall Edward, Tekkam Srinivas, Cava Felipe, de Pedro Miguel A., Brun Yves V., VanNieuwenhze Michael S., In Situ Probing of Newly Synthesized Peptidoglycan in Live Bacteria with FluorescentD-Amino Acids, 10.1002/anie.201206749
  132. Liechti G. W., Kuru E., Hall E., Kalinda A., Brun Y. V., VanNieuwenhze M., Maurelli A. T., A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis, 10.1038/nature12892
  133. Sheldrick George M., Jones Peter G., Kennard Olga, Williams Dudley H., Smith Gerald A., Structure of vancomycin and its complex with acetyl-D-alanyl-D-alanine, 10.1038/271223a0
  134. Monteiro João M., Fernandes Pedro B., Vaz Filipa, Pereira Ana R., Tavares Andreia C., Ferreira Maria T., Pereira Pedro M., Veiga Helena, Kuru Erkin, VanNieuwenhze Michael S., Brun Yves V., Filipe Sérgio R., Pinho Mariana G., Cell shape dynamics during the staphylococcal cell cycle, 10.1038/ncomms9055
  135. van Teeseling Muriel C.F., Mesman Rob J., Kuru Erkin, Espaillat Akbar, Cava Felipe, Brun Yves V., VanNieuwenhze Michael S., Kartal Boran, van Niftrik Laura, Anammox Planctomycetes have a peptidoglycan cell wall, 10.1038/ncomms7878
  136. Tsui Ho-Ching T., Boersma Michael J., Vella Stephen A., Kocaoglu Ozden, Kuru Erkin, Peceny Julia K., Carlson Erin E., VanNieuwenhze Michael S., Brun Yves V., Shaw Sidney L., Winkler Malcolm E., Pbp2x localizes separately from Pbp2b and other peptidoglycan synthesis proteins during later stages of cell division ofStreptococcus pneumoniae D39 : Separation of pneumococcal Pbp2x from Pbp2b at septa, 10.1111/mmi.12745
  137. Lee T. K., Tropini C., Hsin J., Desmarais S. M., Ursell T. S., Gong E., Gitai Z., Monds R. D., Huang K. C., A dynamically assembled cell wall synthesis machinery buffers cell growth, 10.1073/pnas.1313826111
  138. Land Adrian D., Tsui Ho-Ching T., Kocaoglu Ozden, Vella Stephen A., Shaw Sidney L., Keen Susan K., Sham Lok-To, Carlson Erin E., Winkler Malcolm E., Requirement of essential Pbp2x and GpsB for septal ring closure inStreptococcus pneumoniae D39 : Essential role of GpsB in pneumococcal division, 10.1111/mmi.12408
  139. Kocaoglu Ozden, Calvo Rebecca A., Sham Lok-To, Cozy Loralyn M., Lanning Bryan R., Francis Samson, Winkler Malcolm E., Kearns Daniel B., Carlson Erin E., Selective Penicillin-Binding Protein Imaging Probes Reveal Substructure in Bacterial Cell Division, 10.1021/cb300329r
  140. Bustanji Y., Arciola C. R., Conti M., Mandello E., Montanaro L., Samori B., Dynamics of the interaction between a fibronectin molecule and a living bacterium under mechanical force, 10.1073/pnas.1735343100
  141. Lower S. K., Lamlertthon S., Casillas-Ituarte N. N., Lins R. D., Yongsunthon R., Taylor E. S., DiBartola A. C., Edmonson C., McIntyre L. M., Reller L. B., Que Y.-A., Ros R., Lower B. H., Fowler V. G., Polymorphisms in fibronectin binding protein A of Staphylococcus aureus are associated with infection of cardiovascular devices, 10.1073/pnas.1109071108
  142. Herman Philippe, El-Kirat-Chatel Sofiane, Beaussart Audrey, Geoghegan Joan A., Foster Timothy J., Dufrêne Yves F., The binding force of the staphylococcal adhesin SdrG is remarkably strong : Binding strength of the staphylococcal adhesin SdrG, 10.1111/mmi.12663
  143. Herman-Bausier Philippe, Dufrêne Yves F., Atomic force microscopy reveals a dual collagen-binding activity for the staphylococcal surface protein SdrF : Collagen-binding activity of SdrF, 10.1111/mmi.13254
  144. Herman-Bausier Philippe, El-Kirat-Chatel Sofiane, Foster Timothy J., Geoghegan Joan A., Dufrêne Yves F., Staphylococcus aureusFibronectin-Binding Protein A Mediates Cell-Cell Adhesion through Low-Affinity Homophilic Bonds, 10.1128/mbio.00413-15
  145. Gruszka Dominika T., Whelan Fiona, Farrance Oliver E., Fung Herman K. H., Paci Emanuele, Jeffries Cy M., Svergun Dmitri I., Baldock Clair, Baumann Christoph G., Brockwell David J., Potts Jennifer R., Clarke Jane, Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein, 10.1038/ncomms8271
  146. El-Kirat-Chatel Sofiane, Beaussart Audrey, Vincent Stéphane P., Abellán Flos Marta, Hols Pascal, Lipke Peter N., Dufrêne Yves F., Forces in yeast flocculation, 10.1039/c4nr06315e
  147. El-Kirat-Chatel Sofiane, Dufrêne Yves F., Nanoscale adhesion forces between the fungal pathogen Candida albicans and macrophages, 10.1039/c5nh00049a
  148. Formosa-Dague Cécile, Fu Zhuo-Han, Feuillie Cécile, Derclaye Sylvie, Foster Timothy J., Geoghegan Joan A., Dufrêne Yves F., Forces between Staphylococcus aureus and human skin, 10.1039/c6nh00057f
  149. Berk V., Fong J. C. N., Dempsey G. T., Develioglu O. N., Zhuang X., Liphardt J., Yildiz F. H., Chu S., Molecular Architecture and Assembly Principles of Vibrio cholerae Biofilms, 10.1126/science.1222981
  150. Turnbull Lynne, Toyofuku Masanori, Hynen Amelia L., Kurosawa Masaharu, Pessi Gabriella, Petty Nicola K., Osvath Sarah R., Cárcamo-Oyarce Gerardo, Gloag Erin S., Shimoni Raz, Omasits Ulrich, Ito Satoshi, Yap Xinhui, Monahan Leigh G., Cavaliere Rosalia, Ahrens Christian H., Charles Ian G., Nomura Nobuhiko, Eberl Leo, Whitchurch Cynthia B., Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms, 10.1038/ncomms11220
  151. Ivanov Ivan E., Boyd Chelsea D., Newell Peter D., Schwartz Mary E., Turnbull Lynne, Johnson Michael S., Whitchurch Cynthia B., O'Toole George A., Camesano Terri A., Atomic force and super-resolution microscopy support a role for LapA as a cell-surface biofilm adhesin of Pseudomonas fluorescens, 10.1016/j.resmic.2012.10.001
  152. Fritz J., Translating Biomolecular Recognition into Nanomechanics, 10.1126/science.288.5464.316
  153. Ndieyira Joseph Wafula, Watari Moyu, Barrera Alejandra Donoso, Zhou Dejian, Vögtli Manuel, Batchelor Matthew, Cooper Matthew A., Strunz Torsten, Horton Mike A., Abell Chris, Rayment Trevor, Aeppli Gabriel, McKendry Rachel A., Nanomechanical detection of antibiotic–mucopeptide binding in a model for superbug drug resistance, 10.1038/nnano.2008.275
  154. Longo G., Alonso-Sarduy L., Rio L. Marques, Bizzini A., Trampuz A., Notz J., Dietler G., Kasas S., Rapid detection of bacterial resistance to antibiotics using AFM cantilevers as nanomechanical sensors, 10.1038/nnano.2013.120
  155. Kasas Sandor, Ruggeri Francesco Simone, Benadiba Carine, Maillard Caroline, Stupar Petar, Tournu Hélène, Dietler Giovanni, Longo Giovanni, Detecting nanoscale vibrations as signature of life, 10.1073/pnas.1415348112
  156. Beaussart Audrey, Abellán-Flos Marta, El-Kirat-Chatel Sofiane, Vincent Stéphane P., Dufrêne Yves F., Force Nanoscopy as a Versatile Platform for Quantifying the Activity of Antiadhesion Compounds Targeting Bacterial Pathogens, 10.1021/acs.nanolett.5b04689
  157. Kirat-Chatel S., ACS Nano, 2012, 10792 (2012)
  158. Andre Guillaume, Deghorain Marie, Bron Peter A., van Swam Iris I., Kleerebezem Michiel, Hols Pascal, Dufrêne Yves F., Fluorescence and Atomic Force Microscopy Imaging of Wall Teichoic Acids inLactobacillus plantarum, 10.1021/cb1003509
  159. Odermatt Pascal D., Shivanandan Arun, Deschout Hendrik, Jankele Radek, Nievergelt Adrian P., Feletti Lely, Davidson Michael W., Radenovic Aleksandra, Fantner Georg E., High-Resolution Correlative Microscopy: Bridging the Gap between Single Molecule Localization Microscopy and Atomic Force Microscopy, 10.1021/acs.nanolett.5b00572
Bibliographic reference Xiao, Jie ; Dufrêne, Yves. Optical and force nanoscopy in microbiology.. In: Nature microbiology, Vol. 1, no.11, p. 16186 (2016)
Permanent URL http://hdl.handle.net/2078.1/181015