Single-molecule super-resolution imaging in bacteria

Current Opinion in Microbiology

Volumn 15, Issue 6, 2012, Pages 758-763

  Cattoni, D I ^a   Fiche, J B ^a   Nollmann M ^a  

^a CENTRE DE BIOCHIMIE STRUCTURALE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

BACTERIUM; BACTERIUM COMPETENCE; BACTERIUM CONJUGATION; CELL DIVISION; CELL MIGRATION; CELL SEPARATION; CELLULAR SECRETION; DIFFRACTION; DNA REPLICATION; DNA TRANSCRIPTION; FLUORESCENCE MICROSCOPY; MOLECULAR DYNAMICS; MOLECULAR IMAGING; NONHUMAN; OPTICAL RESOLUTION; REVIEW; SINGLE MOLECULE SUPER RESOLUTION MICROSCOPY;

BACTERIA; BACTERIAL PROTEINS; MICROSCOPY; MULTIPROTEIN COMPLEXES;

EID: 84872273211     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2012.10.007     Document Type: Review

References (53)

1. Schermelleh L., Heintzmann R., Leonhardt H. A guide to super-resolution fluorescence microscopy. J Cell Biol 2010, 190:165-175.
2. Huang B., Bates M., Zhuang X. Super-resolution fluorescence microscopy. Annu Rev Biochem 2009, 78:993-1016.
3. 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. Science 2006, 313:1642-1645.
4. Hess S.T., Girirajan T.P., Mason M.D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 2006, 91:4258-4272.
5. Rust M.J., Bates M., Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 2006, 3:793-795.
6. Heilemann M., van de Linde S., Mukherjee A., Sauer M. Super-resolution imaging with small organic fluorophores. Angew Chem Int Ed Engl 2009, 48:6903-6908.
7. Lemmer P., Gunkel M., Weiland Y., Müller P., Baddeley D., Kaufmann R., Urich A., Eipel H., Amberger R., Hausmann M., et al. Using conventional fluorescent markers for far-field fluorescence localization nanoscopy allows resolution in the 10-nm range. J Microsc 2009, 235:163-171.
8. Biteen J.S., Thompson M.A., Tselentis N.K., Bowman G.R., Shapiro L., Moerner W.E. Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP. Nat Methods 2008, 5:947-949.
9. Shroff H., Galbraith C.G., Galbraith J.A., White H., Gillette J., Olenych S., Davidson M.W., Betzig E. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc Natl Acad Sci USA 2007, 104:20308-20313.
10. Subach F.V., Patterson G.H., Renz M., Lippincott-Schwartz J., Verkhusha V.V. Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells. J Am Chem Soc 2010, 132:6481-6491.
11. van de Linde S., Loschberger A., Klein T., Heidbreder M., Wolter S., Heilemann M., Sauer M. Direct stochastic optical reconstruction microscopy with standard fluorescent probes. Nat Protoc 2011, 6:991-1009.
12. Steinhauer C., Forthmann C., Vogelsang J., Tinnefeld P. Superresolution microscopy on the basis of engineered dark states. J Am Chem Soc 2008, 130:16840-16841.
13. Bates M., Huang B., Dempsey G.T., Zhuang X. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 2007, 317:1749-1753.
14. Dempsey G.T., Vaughan J.C., Chen K.H., Bates M., Zhuang X. Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat Methods 2011, 8:1027-1036.
15. Wombacher R., Heidbreder M., van de Linde S., Sheetz M.P., Heilemann M., Cornish V.W., Sauer M. Live-cell super-resolution imaging with trimethoprim conjugates. Nat Methods 2010, 7:717-719.
16. Klein T., Loschberger A., Proppert S., Wolter S., van de Linde S., Sauer M. Live-cell dSTORM with SNAP-tag fusion proteins. Nat Methods 2011, 8:7-9.
17. Sharonov A., Hochstrasser R.M. Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Proc Natl Acad Sci USA 2006, 103:18911-18916.
18. 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. Proc Natl Acad Sci USA 2011, 108:E1102-E1110.
19. Giannone G., Hosy E., Levet F., Constals A., Schulze K., Sobolevsky A.I., Rosconi M.P., Gouaux E., Tampe R., Choquet D., et al. Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density. Biophys J 2010, 99:1303-1310.
20. Yildiz A., Forkey J.N., McKinney S.A., Ha T., Goldman Y.E., Selvin P.R. Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization. Science 2003, 300:2061-2065.
21. Thompson R.E., Larson D.R., Webb W.W. Precise nanometer localization analysis for individual fluorescent probes. Biophys J 2002, 82:2775-2783.
22. Henriques R., Lelek M., Fornasiero E.F., Valtorta F., Zimmer C., Mhlanga M.M. QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ. Nat Methods 2010, 7:339-340.
23. Parthasarathy R. Rapid, accurate particle tracking by calculation of radial symmetry centers. Nat Methods 2012, 9:724-726.
24. Izeddin I., Boulanger J., Racine V., Specht C.G., Kechkar A., Nair D., Triller A., Choquet D., Dahan M., Sibarita J.B. Wavelet analysis for single molecule localization microscopy. Opt Express 2012, 20:2081-2095.
25. Abraham A.V., Ram S., Chao J., Ward E.S., Ober R.J. Quantitative study of single molecule location estimation techniques. Opt Express 2009, 17:23352-23373.
26. Mortensen K.I., Churchman L.S., Spudich J.A., Flyvbjerg H. Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat Methods 2010, 7:377-381.
27. Huang F., Schwartz S.L., Byars J.M., Lidke K.A. Simultaneous multiple-emitter fitting for single molecule super-resolution imaging. Biomed Opt Express 2011, 2:1377-1393.
28. Smith C.S., Joseph N., Rieger B., Lidke K.A. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat Methods 2010, 7:373-375.
29. Ober R.J., Ram S., Ward E.S. Localization accuracy in single-molecule microscopy. Biophys J 2004, 86:1185-1200.
30. Shroff H., Galbraith C.G., Galbraith J.A., Betzig E. Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat Methods 2008, 5:417-423.
31. van de Linde S., Wolter S., Heilemann M., Sauer M. The effect of photoswitching kinetics and labeling densities on super-resolution fluorescence imaging. J Biotechnol 2010, 149:260-266.
32. Huang B., Wang W., Bates M., Zhuang X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 2008, 319:810-813.
33. Juette M.F., Gould T.J., Lessard M.D., Mlodzianoski M.J., Nagpure B.S., Bennett B.T., Hess S.T., Bewersdorf J. Three-dimensional sub-100nm resolution fluorescence microscopy of thick samples. Nat Methods 2008, 5:527-529.
34. Pavani S.R., 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. Proc Natl Acad Sci USA 2009, 106:2995-2999.
35. 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., et al. Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc Natl Acad Sci USA 2009, 106:3125-3130.
36. Greenfield D., McEvoy A.L., Shroff H., Crooks G.E., Wingreen N.S., Betzig E., Liphardt J. Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Biol 2009, 7:e1000137.
37. Wang W., Li G.W., Chen C., Xie X.S., Zhuang X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 2011, 333:1445-1449.
38. Lee S.F., Thompson M.A., Schwartz M.A., Shapiro L., Moerner W.E. Super-resolution imaging of the nucleoid-associated protein HU in Caulobacter crescentus. Biophys J 2011, 100:L31-L33.
39. Garner E.C., Bernard R., Wang W., Zhuang X., Rudner D.Z., Mitchison T. Coupled, circumferential motions of the cell wall synthesis machinery and MreB filaments in B. subtilis. Science 2011, 333:222-225.
40. Dominguez-Escobar J., Chastanet A., Crevenna A.H., Fromion V., Wedlich-Soldner R., Carballido-Lopez R. Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria. Science 2011, 333:225-228.
41. Fu G., Huang T., Buss J., Coltharp C., Hensel Z., Xiao J. In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM). PLoS ONE 2010, 5:e12682.
42. Ptacin J.L., Lee S.F., Garner E.C., Toro E., Eckart M., Comolli L.R., Moerner W.E., Shapiro L. A spindle-like apparatus guides bacterial chromosome segregation. Nat Cell Biol 2010, 12:791-798.
43. Manley S., Gillette J.M., Patterson G.H., Shroff H., Hess H.F., Betzig E., Lippincott-Schwartz J. High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nat Methods 2008, 5:155-157.
44. Subach F.V., Patterson G.H., Manley S., Gillette J.M., Lippincott-Schwartz J., Verkhusha V.V. Photoactivatable mCherry for high-resolution two-color fluorescence microscopy. Nat Methods 2009, 6:153-159.
45. Subach O.M., Patterson G.H., Ting L.M., Wang Y., Condeelis J.S., Verkhusha V.V. A photoswitchable orange-to-far-red fluorescent protein. PSmOrange. Nat Methods 2011, 8:771-777.
46. Zhang M., Chang H., Zhang Y., Yu J., Wu L., Ji W., Chen J., Liu B., Lu J., Liu Y., et al. Rational design of true monomeric and bright photoactivatable fluorescent proteins. Nat Methods 2012, 9:727-729.
47. Lee H.L., Lord S.J., Iwanaga S., Zhan K., Xie H., Williams J.C., Wang H., Bowman G.R., Goley E.D., Shapiro L., et al. Superresolution imaging of targeted proteins in fixed and living cells using photoactivatable organic fluorophores. J Am Chem Soc 2010, 132:15099-15101.
48. Ries J., Kaplan C., Platonova E., Eghlidi H., Ewers H. A simple, versatile method for GFP-based super-resolution microscopy via nanobodies. Nat Methods 2012, 9:582-584.
49. Cox S., Rosten E., Monypenny J., Jovanovic-Talisman T., Burnette D.T., Lippincott-Schwartz J., Jones G.E., Heintzmann R. Bayesian localization microscopy reveals nanoscale podosome dynamics. Nat Methods 2012, 9:195-200.
50. Burnette D.T., Sengupta P., Dai Y., Lippincott-Schwartz J., Kachar B. Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules. Proc Natl Acad Sci USA 2011, 108:21081-21086.
51. Sliusarenko O., Heinritz J., Emonet T., Jacobs-Wagner C. High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics. Mol Microbiol 2011, 80:612-627.
52. Conrad C., Wunsche A., Tan T.H., Bulkescher J., Sieckmann F., Verissimo F., Edelstein A., Walter T., Liebel U., Pepperkok R., et al. Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Nat Methods 2011, 8:246-249.
53. McEvoy A.L., Greenfield D., Bates M., Liphardt J. Q&A: single-molecule localization microscopy for biological imaging. BMC Biol 2010, 8:106.