Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging (original) (raw)

• Moerner, W. E. & Kador, L. Optical detection and spectroscopy of single molecules in a solid. Phys. Rev. Lett. 62, 2535–2538 (1989).
  Article CAS PubMed Google Scholar
• Orrit, M. & Bernard, J. Single pentacene molecules detected by fluorescence excitation in a _p_-terphenyl crystal. Phys. Rev. Lett. 65, 2716–2719 (1990).
  Article CAS PubMed Google Scholar
• Ambrose, W. P. & Moerner, W. E. Fluorescence spectroscopy and spectral diffusion of single impurity molecules in a crystal. Nature 349, 225–227 (1991).
  Article CAS Google Scholar
• Dickson, R. M., Cubitt, A. B., Tsien, R. Y. & Moerner, W. E. On/off blinking and switching behavior of single molecules of green fluorescent protein. Nature 388, 355–358 (1997).
  Article CAS PubMed Google Scholar
• Deich, J., Judd, E. M., McAdams, H. H. & Moerner, W. E. Visualization of the movement of single histidine kinase molecules in live Caulobacter cells. Proc. Natl Acad. Sci. USA 101, 15921–15926 (2004). This paper provides the first evidence that single copies of fluorescent protein fusions can be imaged and analysed in bacteria.
  Article CAS PubMed PubMed Central Google Scholar
• Shapiro, L., McAdams, H. & Losick, R. Generating and exploiting polarity in bacteria. Science 298, 1942–1946 (2002).
  Article CAS PubMed Google Scholar
• Shapiro, L., McAdams, H. H. & Losick, R. Why and how bacteria localize proteins. Science 326, 1225–1228 (2009). This review describes the central role that protein localization patterns have in bacterial cell biology, which should be investigated using advanced imaging methods.
  Article CAS PubMed PubMed Central Google Scholar
• Niu, L. & Yu, P. Investigating intracellular dynamics of FtsZ cytoskeleton with photoactivation single-molecule tracking. Biophys. J. 95, 2009–2016 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Manley, S. et al. High-density mapping of single-molecule trajectories with photoactivated localization microscopy. Nature Methods 5, 155–157 (2008).
  Article CAS PubMed Google Scholar
• Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642–1645 (2006).
  Article CAS PubMed Google Scholar
• Hess, S. T., Girirajan, T. P. K. & Mason, M. D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91, 4258–4272 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Rust, M. J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nature Methods 3, 793–796 (2006). References 10, 11, and 12 are the first reports of super-resolution imaging by single-molecule localization and active control of emitter concentrations.
  Article CAS PubMed PubMed Central Google Scholar
• Xie, X. S., Choi, P. J., Li, G. W., Lee, N. K. & Lia, G. Single-molecule approach to molecular biology in living bacterial cells. Annu. Rev. Biophys. 37, 417–444 (2008). This review covers bacterial single-molecule studies up to 2008.
  Article CAS PubMed Google Scholar
• Reyes-Lamothe, R., Sherratt, D. J. & Leake, M. C. Stoichiometry and architecture of active, DNA replication machinery in Escherichia coli. Science 328, 498–501 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Lia, G., Michel, B. & Allemand, J. Polymerase exchange during Okazaki fragment synthesis observed in living cells. Science 335, 328–331 (2012).
  Article CAS PubMed Google Scholar
• Robinson, A. & van Oijen, A. M. Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies. Nature Rev. Microbiol. 11, 303–315 (2013).
  Article CAS Google Scholar
• Typas, A., Banzhaf, M., Gross, C. A. & Vollmer, W. From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nature Rev. Microbiol. 10, 123–136 (2012). This review describes the dynamics of MreB and FtsZ and their role in cell wall synthesis.
  Article CAS Google Scholar
• Adams, D. W. & Errington, J. Bacterial cell division: assembly, maintenance and disassembly of the Z ring. Nature Rev. Microbiol. 7, 642–653 (2009).
  Article CAS Google Scholar
• Gerdes, K., Howard, M. & Szardenings, F. Pushing and pulling in prokaryotic DNA segregation. Cell 141, 927–942 (2010).
  Article CAS PubMed Google Scholar
• Bi, E. & Lutkenhaus, J. FtsZ ring structure associated with division in Escherichia Coli. Nature 354, 161–164 (1991).
  Article CAS PubMed Google Scholar
• Jones, L. J. F., Carballido-López, R. & Errington, J. Control of cell shape in bacteria: helical, actin-like filaments in Bacillus subtilis. Cell 104, 913–922 (2001).
  Article CAS PubMed Google Scholar
• van den Ent, E., Amos, L. A. & Loewe, J. Prokaryotic origin of the actin cytoskelecton. Nature 413, 39–44 (2001).
  Article CAS PubMed Google Scholar
• Celler, K., Koning, R. I., Koster, A. J. & van Wezel, G. P. Multidimensional view of the bacterial cytoskeleton. J. Bacteriol. 195, 1627–1636 (2013).
  Article PubMed PubMed Central Google Scholar
• Cabeen, M. T. & Jacobs-Wagner, C. The bacterial cytoskeleton. Annu. Rev. Genet. 44, 365–392 (2010).
  Article CAS PubMed Google Scholar
• Figge, R. M., Divakaruni, A. V. & Gober, J. W. MreB, the cell shape-determining bacterial actin homologue, co-ordinates cell wall morphogenesis in Caulobacter crescentus. Mol. Microbiol. 51, 1321–1332 (2004).
  Article CAS PubMed Google Scholar
• Gitai, Z., Dye, N. & Shapiro, L. An actin-like gene can determine cell polarity in bacteria. Proc. Natl Acad. Sci. USA 101, 8643–8648 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Gitai, Z., Dye, N. A., Reisenauer, A., Wachi, M. & Shapiro, L. MreB actin-mediated segregation of a specific region of a bacterial chromosome. Cell 120, 329–341 (2005).
  Article CAS PubMed Google Scholar
• Divakaruni, A. V., Loo, R. R. O., Xie, Y., Loo, J. A. & Gober, J. W. The cell-shape protein MreC interacts with extracytoplasmic proteins including cell wall assembly complexes in Caulobacter cresentus. Proc. Natl Acad. Sci. USA 102, 18602–18607 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Iwai, N. et al. Structure–activity relationship of _s_-benzylisothiourea derivatives to induce spherical cells in Escherichia coli. Biosci. Biotechnol. Biochem. 68, 2265–2269 (2004).
  Article CAS PubMed Google Scholar
• Bean, G. J. et al. A22 disrupts the bacterial actin cytoskeleton by directly binding and inducing a low-affinity state in MreB. Biochemistry 48, 4852–4857 (2009).
  Article CAS PubMed Google Scholar
• Carballido-Lopez, R. The bacterial actin-like cytoskeleton. Microbiol. Mol. Biol. Rev. 70, 888–909 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Shaevitz, J. W. & Gitai, Z. The structure and function of bacterial actin homologs. Cold Spring Harb. Perspect. Biol. 2, a000364 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Takacs, C. N. et al. MreB drives de novo rod morphogenesis in Caulobacter crescentus via remodeling of the cell wall. J. Bacteriol. 192, 1671–1684 (2010).
  Article CAS PubMed Google Scholar
• Dye, N. A., Pincus, Z., Theriot, J. A., Shapiro, L. & Gitai, Z. Two independent spiral structures control cell shape in Caulobacter. Proc. Natl Acad. Sci. USA 102, 18608–18613 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Divakaruni, A. V., Baida, C., White, C. L. & Gober, J. W. The cell shape proteins MreB and MreC control cell morphogenesis by positioning cell wall synthetic complexes. Mol. Microbiol. 66, 174–188 (2007).
  Article CAS PubMed Google Scholar
• den Blaauwen, T., de Pedro, M. A., Nguyen-Disteche, M. & Ayala, J. A. Morphogenesis of rod-shaped sacculi. FEMS Microbiol. Rev. 32, 321–344 (2008).
  Article CAS PubMed Google Scholar
• 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. Proc. Natl Acad. Sci. USA 103, 10929–10934 (2006). This study shows that single copies of MreB move in a slow, directed, circumferential fashion around the cell periphery in C. crescentus.
  Article CAS PubMed PubMed Central Google Scholar
• Biteen, J. S. et al. Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP. Nature Methods 5, 947–949 (2008). This study introduces eYFP protein fusion constructs as a suitable label for super-resolution imaging in live bacteria.
  Article CAS PubMed PubMed Central Google Scholar
• Garner, E. C. et al. Coupled, circumferential motions of the cell wall synthesis machinery and MreB filaments in B. subtilis. Science 333, 222–225 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Dominguez-Escobar, J. et al. Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria. Science 333, 225–228 (2011).
  Article CAS PubMed Google Scholar
• van Teeffelen, S. et al. The bacterial actin MreB rotates, and rotation depends on cell-wall assembly. Proc. Natl Acad. Sci. USA 108, 15822–15827 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Swulius, M. T. et al. Long helical filaments are not seen encircling cells in electron cryotomograms of rod-shaped bacteria. Biochem. Biophys. Res. Commun. 407, 650–655 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Swulius, M. T. & Jensen, G. J. The helical MreB cytoskeleton in Escherichia coli MC1000/pLE7 is an artifact of the N-terminal yellow fluorescent protein tag. J. Bacteriol. 194, 6382–6386 (2012). This study shows that the helical shape of MreB superstructure is an artefact of the fluorescent protein fusion construct that was used.
  Article CAS PubMed PubMed Central Google Scholar
• Bendezu, F. O., Hale, C. A., Bernhardt, T. G. & de Boer, P. A. J. RodZ (YfgA) is required for proper assembly of the MreB actin cytoskeleton and cell shape in E. coli. EMBO J. 28, 193–204 (2009).
  Article CAS PubMed Google Scholar
• Salje, J., van den Ent, F., de Boer, P. & Loewe, J. Direct membrane binding by bacterial actin MreB. Mol. Cell 43, 478–487 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• White, C. L., Kitich, A. & Gober, J. W. Positioning cell wall synthetic complexes by the bacterial morphogenetic proteins MreB and MreD. Mol. Microbiol. 76, 616–633 (2010).
  Article CAS PubMed Google Scholar
• Erickson, H. P., Anderson, D. E. & Osawa, M. FtsZ in bacterial cytokinesis: cytoskeleton and force generator all in one. Microbiol. Mol. Biol. Rev. 74, 504–528 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Huang, K., Durand-Heredia, J. & Janakiraman, A. FtsZ ring stability: of bundles, tubules, crosslinks, and curves. J. Bacteriol. 195, 1859–1868 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Osawa, M., Anderson, D. E. & Erickson, H. P. Reconstitution of contractile FtsZ rings in liposomes. Science 320, 792–794 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Li, Z., Trimble, M. J., Brun, Y. V. & Jensen, G. J. The structure of FtsZ filaments in vivo suggests a force-generating role in cell division. EMBO J. 26, 4694–4708 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Fu, G. et al. In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM). PLoS ONE 5, e12680 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Ben-Yehuda, S. & Losick, R. Asymmetric cell division in B. subtilis involves a spiral-like intermediate of the cytokinetic protein FtsZ. Cell 109, 257–266 (2002).
  Article CAS PubMed Google Scholar
• Thanedar, S. & Margolin, W. FtsZ exhibits rapid movement and oscillation waves in helix-like patterns in Escherichia coli. Curr. Biol. 14, 1167–1173 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Thanbichler, M. & Shapiro, L. MipZ, a spatial regulator coordinating chromosome segregation with cell division in Caulobacter. Cell 126, 1–16 (2006).
  Article CAS Google Scholar
• Peters, P. C., Migocki, M. D., Thoni, C. & Harry, E. J. A new assembly pathway for the cytokinetic Z ring from a dynamic helical structure in vegetatively growing cells of Bacillus subtilis. Mol. Microbiol. 64, 487–499 (2007).
  Article CAS PubMed Google Scholar
• Anderson, D. E., Guieros-Filho, F. J. & Erickson, H. P. Assembly dynamics of FtsZ rings in Bacillus subtilis and Escherichia coli and effects of FtsZ-regulating proteins. J. Bacteriol. 186, 5775–5781 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Biteen, J. S., Goley, E. D., Shapiro, L. & Moerner, W. E. Three-dimensional super-resolution imaging of the midplane protein FtsZ in live Caulobacter crescentus cells using astigmatism. ChemPhysChem 13, 1007–1012 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Eswaramoorthy, P. et al. Cellular architecture mediates DivIVA ultrastructure and regulates Min activity in Bacillus subtilis. mBio 2, e00257-11 (2011).
  Article PubMed PubMed Central CAS Google Scholar
• Strauss, M. P. et al. 3D-SIM super resolution microscopy reveals a bead-like arrangement for FtsZ and the division machinery: implications for triggering cytokinesis. PLoS Biol. 10, e1001389 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Jennings, P. C., Cox, G. C., Monahan, L. G. & Harry, E. J. Super-resolution imaging of the bacterial cytokinetic protein FtsZ. Micron 42, 336–341 (2011).
  Article CAS PubMed Google Scholar
• Bowman, G. R. et al. A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole. Cell 134, 945–955 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Bowman, G. R. et al. Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function. Mol. Microbiol. 76, 173–189 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Ebersbach, G., Briegel, A., Jensen, G. J. & Jacobs-Wagner, C. A self-associating protein critical for chromosome attachment, division, and polar organization in Caulobacter. Cell 134, 956–968 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Gahlmann, A. et al. Quantitative multicolor subdiffraction imaging of bacterial protein ultrastructures in 3D. Nano Lett. 13, 987–993 (2013). This paper introduces a method of two-colour, super-resolution imaging to accurately colocalize single molecules that are labelled with different fluorophores.
  Article CAS PubMed PubMed Central Google Scholar
• Wery, M., Woldringh, C. L. & Rouvière-Yaniv, J. HU-GFP and DAPI co-localize on the Escherichia coli nucleoid. Biochimie 83, 193–200 (2001).
  Article CAS PubMed Google Scholar
• Llopis, P. M. et al. Spatial organization of the flow of genetic information in bacteria. Nature 466, 77–81 (2010).
  Article CAS PubMed Central Google Scholar
• Dillon, S. C. & Dorman, C. J. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nature Rev. Microbiol. 8, 185–195 (2010).
  Article CAS Google Scholar
• Sarkar, T., Vitoc, I., Mukerji, I. & Hud, N. V. Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines. Nucleic Acids Res. 35, 951–961 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• 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. 100, L31–L33 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Illian, J., Penttinen, A., Stoyan, H. & Stoyan, D. Statistical Analysis and Modelling of Spatial Point Patterns. (John Wiley & Sons, 2008).
  Google Scholar
• Wang, W., Li, G., Chen, C., Xie, X. S. & Zhuang, X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 333, 1445–1449 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306–1311 (2002).
  Article CAS PubMed Google Scholar
• Badrinarayanan, A., Reyes-Lamothe, R., Uphoff, S., Leake, M. C. & Sherratt, D. J. In vivo architecture and action of bacterial structural maintenance of chromosome proteins. Science 338, 528–531 (2012). This paper determines the minimal functional complex of MukBEF in living cells using single-molecule imaging and stoichimetry analysis.
  Article CAS PubMed Google Scholar
• Kleine Borgmann, L. A., Ries, J., Ewers, H., Ulbrich, M. H. & Graumann, P. L. The bacterial SMC complex displays two distinct modes of interaction with the chromosome. Cell Rep. 3, 1483–1492 (2013).
  Article CAS PubMed Google Scholar
• Niki, H. et al. Escherichia coli MukB protein involved in chromosome partition forms a homodimer with a rod-and-hinge structure having DNA-binding and ATP/GTP binding activities. EMBO J. 11, 5101–5109 (1992).
  Article CAS PubMed PubMed Central Google Scholar
• Yamanaka, K., Ogura, T., Niki, H. & Hiraga, S. Identification of two new genes, mukE and mukF, involved in chromosome partitioning in Escherichia coli. Mol. Gen. Genet. 250, 241–251 (1996).
  CAS PubMed Google Scholar
• Wang, X., Llopis, P. M. & Rudner, D. Z. Organization and segregation of bacterial chromosomes. Nature Rev. Genet. 14, 191–203 (2013).
  Article CAS PubMed Google Scholar
• den Blaauwen, T., Lindqvist, A., Lowe, J. & Nanninga, N. Distribution of the Escherichia coli structural maintenance of chromosomes (SMC)-like protein MukB in the cell. Mol. Microbiol. 42, 1179–1188 (2001).
  Article CAS PubMed Google Scholar
• Lindow, J., Kuwano, M., Moriya, S. & Grossman, A. Subcellular localization of the Bacillus subtilis structural maintenance of chromosomes (SMC) protein. Mol. Microbiol. 46, 997–1009 (2002).
  Article CAS PubMed Google Scholar
• Mascarenhas, J., Soppa, J., Strunnikov, A. & Graumann, P. Cell cycle-dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein. EMBO J. 21, 3108–3118 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Leake, M. C. et al. Stoichiometry and turnover in single, functioning membrane protein complexes. Nature 443, 355–358 (2006).
  Article CAS PubMed Google Scholar
• Uphoff, S., Reyes-Lamothe, R., Garza de Leon, F., Sherratt, D. J. & Kapanidis, A. N. Single-molecule DNA repair in live bacteria. Proc. Natl Acad. Sci. USA 110, 8063–8068 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Ptacin, J. L. et al. A spindle-like apparatus guides bacterial chromosome segregation. Nature Cell Biol. 12, 791–798 (2010). This study shows that the chromosome-partitioning protein ParB in C. crescentus moves along a receding ParA structure during chromosome segregation.
  Article CAS PubMed Google Scholar
• Miller, O. L., Hamkalo, B. A. & Thomas, C. A. Visualization of bacterial genes in action. Science 169, 392–395 (1970).
  Article PubMed Google Scholar
• Robinow, C. & Kellenberger, E. The bacterial nucleoid revisited. Microbiol. Rev. 58, 211–232 (1994).
  Article CAS PubMed PubMed Central Google Scholar
• Woldringh, C. L. The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation. Mol. Microbiol. 45, 17–29 (2002).
  Article CAS PubMed Google Scholar
• Norris, V. & Madsen, M. Autocatalytic gene expression occurs via transertion and membrane domain formation and underlies differentiation in bacteria: a model. J. Mol. Biol. 253, 739–748 (1995).
  Article CAS PubMed Google Scholar
• Bakshi, S., Siryaporn, A., Goulian, M. & Weisshaar, J. C. Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells. Mol. Microbiol. 85, 21–38 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Nevo-Dinur, K., Nussbaum-Shochat, A., Ben-Yehuda, S. & Amster-Choder, O. Translation-independent localization of mRNA in E. coli. Science 331, 1081–1084 (2011).
  Article CAS PubMed Google Scholar
• Yu, J., Xiao, J., Ren, X., Lao, K. & Xie, X. S. Probing gene expression in live cells, one protein molecule at a time. Science 311, 1600–1603 (2006). This paper uses single-molecule imaging to directly observe gene expression dynamics in live cells.
  Article CAS PubMed Google Scholar
• Choi, P. J., Cai, L., Frieda, K. & Xie, X. S. A. Stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322, 442–446 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Taniguchi, Y. et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329, 533–538 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Elf, J., Li, G. W. & Xie, X. S. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191–1194 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• von Hippel, P. H. & Berg, O. G. Facilitated target location in biological systems. J. Biol. Chem. 264, 675–678 (1989).
  Article CAS PubMed Google Scholar
• Sletten, E. M. & Bertozzi, C. R. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew. Chem. Int. Edn Engl. 48, 6974–6998 (2009).
  Article CAS Google Scholar
• Sauer, M. Localization microscopy coming of age: from concepts to biological impact. J. Cell. Sci. 126, 3505–3513 (2013). This paper provides a comprehensive review of single-molecule localization microscopy, with a thorough discussion of current challenges.
  Article CAS PubMed Google Scholar
• Plass, T. et al. Amino acids for Diels–Alder reactions in living cells. Angew. Chem. Int. Edn Engl. 51, 4166–4170 (2012).
  Article CAS Google Scholar
• Plass, T., Milles, S., Koehler, C., Schultz, C. & Lemke, E. A. Genetically encoded copper-free click chemistry. Angew. Chem. Int. Edn Engl. 50, 3878–3881 (2011).
  Article CAS Google Scholar
• Lang, K. et al. Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction. Nature Chem. 4, 298–304 (2012).
  Article CAS Google Scholar
• Lang, K. et al. Genetic encoding of bicyclononynes and _trans_-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels–Alder reactions. J. Am. Chem. Soc. 134, 10317–10320 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Charbon, G. et al. Subcellular protein localization by using a genetically encoded fluorescent amino acid. ChemBioChem 12, 1818–1821 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Lukinavicius, G. et al. A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nature Chem. 5, 132–139 (2013).
  Article CAS Google Scholar
• Puthenveetil, S., Liu, D. S., White, K. A., Thompson, S. & Ting, A. Y. Yeast display evolution of a kinetically efficient 13-amino acid substrate for lipoic acid ligase. J. Am. Chem. Soc. 131, 16430–16438 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Fernandez-Suarez, M. & Ting, A. Y. Fluorescent probes for super-resolution imaging in living cells. Nature Rev. Mol. Cell Biol. 9, 929–943 (2008). This paper reviews fluorescent probes for super-resolution imaging.
  Article CAS Google Scholar
• Uttamapinant, C. et al. A fluorophore ligase for site-specific protein labeling inside living cells. Proc. Natl Acad. Sci. USA 107, 10914–10919 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Liu, D. S. et al. Diels–Alder cycloaddition for fluorophore targeting to specific proteins inside living cells. J. Am. Chem. Soc. 134, 792–795 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Siegrist, M. S. et al. D-amino acid chemical reporters reveal peptidoglycan dynamics of an intracellular pathogen. ACS Chem. Biol. 8, 500–505 (2013).
  Article CAS PubMed Google Scholar
• Kuru, E. et al. In situ probing of newly synthesized peptidoglycan in live bacteria with fluorescent d-amino acids. Angew. Chem. Int. Edn Engl. 51, 12519–12523 (2012).
  Article CAS Google Scholar
• Szent-Gyorgyi, C. et al. Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nature Biotech. 26, 235–240 (2008).
  Article CAS Google Scholar
• Yushchenko, D. A., Zhang, M., Yan, Q., Waggoner, A. S. & Bruchez, M. P. Genetically targetable and color-switching fluorescent probe. ChemBioChem 13, 1564–1568 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Benke, A., Olivier, N., Gunzenhaeuser, J. & Manley, S. Multicolor single molecule tracking of stochastically active synthetic dyes. Nano Lett. 12, 2619–2624 (2012).
  Article CAS PubMed Google Scholar
• Lee, H. D. et al. Superresolution imaging of targeted proteins in fixed and living cells using photoactivatable organic fluorophores. J. Am. Chem. Soc. 132, 15099–15101 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Hell, S. W. & Wichmann, J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19, 780–782 (1994).
  Article CAS PubMed Google Scholar
• 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. Proc. Natl Acad. Sci. USA 102, 17565–17569 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Gustafsson, M. G. L. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198, 82–87 (2000).
  Article CAS PubMed Google Scholar
• Gustafsson, M. G. L. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl Acad. Sci. USA 102, 13081–13086 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Moerner, W. E. New directions in single-molecule imaging and analysis. Proc. Natl Acad. Sci. USA 104, 12596–12602 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Hell, S. W. Microscopy and its focal switch. Nature Methods 6, 24–32 (2009).
  Article CAS PubMed Google Scholar
• Coltharp, C. & Xiao, J. Superresolution microscopy for microbiology. Cell. Microbiol. 14, 1808–1818 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Lippincott-Schwartz, J. & Patterson, G. H. Photoactivatable fluorescent proteins for diffraction-limited and super-resolution imaging. Trends Cell Biol. 19, 555–565 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Heilemann, M., Dedecker, P., Hofkens, J. & Sauer, M. Photoswitches: key molecules for subdiffraction-resolution fluorescence imaging and molecular quantification. Laser Photon. Rev. 3, 180–202 (2009).
  Article CAS Google Scholar
• Moerner, W. E. Microscopy beyond the diffraction limit using actively controlled single molecules. J. Microsc. 246, 213–220 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Cordes, T. et al. Resolving single-molecule assembled patterns with superresolution blink-microscopy. Nano Lett. 10, 645–651 (2010).
  Article CAS PubMed Google Scholar
• Schoen, I., Ries, J., Klotzsch, E., Ewers, H. & Vogel, V. Binding-activated localization microscopy of DNA structures. Nano Lett. 11, 4008–4011 (2011).
  Article CAS PubMed Google Scholar
• Lee, M. K., Williams, J., Twieg, R. J., Rao, J. & Moerner, W. E. Enzymatic activation of nitro-aryl fluorogens in live bacterial cells for enzymatic turnover-activated localization microscopy. Chem. Sci. 4, 220–225 (2013).
  Article CAS Google Scholar
• Sharonov, A. & Hochstrasser, R. M. Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Proc. Natl Acad. Sci. USA 103, 18911–18916 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Sahl, S. J. & Moerner, W. E. Super-resolution fluorescence imaging with single molecules. Curr. Opin. Struct. Biol. 23 778–787 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Huang, F. et al. Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms. Nature Methods 10, 653–658 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Ondrus, A. E. et al. Fluorescent saxitoxins for live cell imaging of single voltage-gated sodium ion channels beyond the optical diffraction limit. Chem. Biol. 19, 902–912 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Jones, S. A., Shim, S., He, J. & Zhuang, X. Fast, three-dimensional super-resolution imaging of live cells. Nature Methods 8, 499–505 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Lill, Y. et al. Single-molecule study of molecular mobility in the cytoplasm of Escherichia coli. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 86, 021907 (2012).
  Article PubMed CAS Google Scholar
• Shaner, N. C., Steinbach, P. A. & Tsien, R. Y. A guide to choosing fluorescent proteins. Nature Methods 2, 905–909 (2005).
  Article CAS PubMed Google Scholar
• Subach, F. V. et al. Photoactivatable mCherry for high-resolution two-color fluorescence microscopy. Nature Methods 6, 153–159 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Patterson, G. H. & Lippincott-Schwartz, J. A photoactivatable GFP for selective photolabeling of proteins and cells. Science 297, 1873–1877 (2002).
  Article CAS PubMed Google Scholar
• Gurskaya, N. G. et al. Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nature Biotech. 24, 461–465 (2006).
  Article CAS Google Scholar
• Chudakov, D. M., Lukyanov, S. & Lukyanov, K. A. Tracking intracellular protein movements using photoswitchable fluorescent proteins PS-CFP2 and Dendra2. Nature Protoc. 2, 2024–2032 (2007).
  Article CAS Google Scholar
• McKinney, S. A., Murphy, C. S., Hazelwood, K. L., Davidson, M. W. & Looger, L. L. A bright and photostable photoconvertible fluorescent protein. Nature Methods 6, 131–133 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Biteen, J. S., Thompson, M. A., Tselentis, N. K., Shapiro, L. & Moerner, W. E. Superresolution imaging in live Caulobacter crescentus cells using photoswitchable enhanced yellow fluorescent protein. Nature Methods 5, 947–949 (2009).
  Article CAS Google Scholar
• Gunewardene, M. et al. Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cells. Biophys. J. 101, 1522–1528 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Landgraf, D., Okumus, B., Chien, P., Baker, T. A. & Paulsson, J. Segregation of molecules at cell division reveals native protein localization. Nature Methods 9, 480–482 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Li, G. & Elf, J. Single molecule approaches to transcription factor kinetics in living cells. FEBS Lett. 583, 3979–3983 (2009).
  Article CAS PubMed Google Scholar