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Progress and prospects for small-molecule probes of bacterial imaging

Nature Chemical Biology volume 12, pages 472–478 (2016)Cite this article

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Abstract

Fluorescence microscopy is an essential tool for the exploration of cell growth, division, transcription and translation in eukaryotes and prokaryotes alike. Despite the rapid development of techniques to study bacteria, the size of these organisms (1–10 μm) and their robust and largely impenetrable cell envelope present major challenges in imaging experiments. Fusion-based strategies, such as attachment of the protein of interest to a fluorescent protein or epitope tag, are by far the most common means for examining protein localization and expression in prokaryotes. While valuable, the use of genetically encoded tags can result in mislocalization or altered activity of the desired protein, does not provide a readout of the catalytic state of enzymes and cannot enable visualization of many other important cellular components, such as peptidoglycan, lipids, nucleic acids or glycans. Here, we highlight the use of biomolecule-specific small-molecule probes for imaging in bacteria.

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Figure 1: Genetically encoded tags for bacterial imaging.
Figure 2: Schematic representation of bacterial peptidoglycan (PG).
Figure 3: Antibiotic-inspired probes and images obtained with these compounds.
Figure 4: Peptidoglycan-inspired probes and images obtained with these compounds.
Figure 5: Carbohydrate-inspired and turnover-dependent probe designs.

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References

  1. Shapiro, L., McAdams, H.H. & Losick, R. Why and how bacteria localize proteins. Science 326, 1225–1228 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Rudner, D.Z. & Losick, R. Protein subcellular localization in bacteria. Cold Spring Harb. Perspect. Biol. 2, a000307 (2010).

    PubMed  PubMed Central  Google Scholar 

  3. Feilmeier, B.J., Iseminger, G., Schroeder, D., Webber, H. & Phillips, G.J. Green fluorescent protein functions as a reporter for protein localization in Escherichia coli. J. Bacteriol. 182, 4068–4076 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Jarvik, J.W. & Telmer, C.A. Epitope tagging. Annu. Rev. Genet. 32, 601–618 (1998).

    CAS  PubMed  Google Scholar 

  5. Brizzard, B. Epitope tagging. Biotechniques 44, 693–695 (2008).

    CAS  PubMed  Google Scholar 

  6. Dean, K.M. & Palmer, A.E. Advances in fluorescence labeling strategies for dynamic cellular imaging. Nat. Chem. Biol. 10, 512–523 (2014). An overview of the improvements made in fluorescence labeling approaches.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Griffin, B.A., Adams, S.R. & Tsien, R.Y. Specific covalent labeling of recombinant protein molecules inside live cells. Science 281, 269–272 (1998).

    CAS  PubMed  Google Scholar 

  8. Zhang, J., Campbell, R.E., Ting, A.Y. & Tsien, R.Y. Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 3, 906–918 (2002).

    CAS  PubMed  Google Scholar 

  9. Lang, K. & Chin, J.W. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem. Rev. 114, 4764–4806 (2014).

    CAS  PubMed  Google Scholar 

  10. Landgraf, D., Okumus, B., Chien, P., Baker, T.A. & Paulsson, J. Segregation of molecules at cell division reveals native protein localization. Nat. Methods 9, 480–482 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Margolin, W. The price of tags in protein localization studies. J. Bacteriol. 194, 6369–6371 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Domínguez-Escobar, J. et al. Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria. Science 333, 225–228 (2011).

    PubMed  Google Scholar 

  13. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Huang, B., Bates, M. & Zhuang, X. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78, 993–1016 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Koch, A.L. What size should a bacterium be? A question of scale. Annu. Rev. Microbiol. 50, 317–348 (1996).

    CAS  PubMed  Google Scholar 

  17. Erickson, H.P., Taylor, D.W., Taylor, K.A. & Bramhill, D. Bacterial cell division protein FtsZ assembles into protofilament sheets and minirings, structural homologs of tubulin polymers. Proc. Natl. Acad. Sci. USA 93, 519–523 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Fu, G. et al. In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM). PLoS One 5, e12682 (2010).

    PubMed  Google Scholar 

  19. Buss, J. et al. In vivo organization of the FtsZ-ring by ZapA and ZapB revealed by quantitative super-resolution microscopy. Mol. Microbiol. 89, 1099–1120 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Holden, S.J. et al. High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization. Proc. Natl. Acad. Sci. USA 111, 4566–4571 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Chang, P.V. & Bertozzi, C.R. Imaging beyond the proteome. Chem. Commun. (Camb.) 48, 8864–8879 (2012).

    CAS  Google Scholar 

  23. Stracy, M., Uphoff, S., Garza de Leon, F. & Kapanidis, A.N. In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair. FEBS Lett. 588, 3585–3594 (2014).

    CAS  PubMed  Google Scholar 

  24. Song, W., Strack, R.L. & Jaffrey, S.R. Imaging bacterial protein expression using genetically encoded RNA sensors. Nat. Methods 10, 873–875 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Schimak, M.P. et al. MiL-FISH: Multilabeled oligonucleotides for fluorescence in situ hybridization improve visualization of bacterial cells. Appl. Environ. Microbiol. 82, 62–70 (2016).

    CAS  PubMed  Google Scholar 

  26. Spahn, C., Endesfelder, U. & Heilemann, M. Super-resolution imaging of Escherichia coli nucleoids reveals highly structured and asymmetric segregation during fast growth. J. Struct. Biol. 185, 243–249 (2014).

    CAS  PubMed  Google Scholar 

  27. Schoen, I., Ries, J., Klotzsch, E., Ewers, H. & Vogel, V. Binding-activated localization microscopy of DNA structures. Nano Lett. 11, 4008–4011 (2011).

    CAS  PubMed  Google Scholar 

  28. Chan, J., Dodani, S.C. & Chang, C.J. Reaction-based small-molecule fluorescent probes for chemoselective bioimaging. Nat. Chem. 4, 973–984 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Vollmer, W., Blanot, D. & de Pedro, M.A. Peptidoglycan structure and architecture. FEMS Microbiol. Rev. 32, 149–167 (2008).

    CAS  PubMed  Google Scholar 

  30. Vollmer, W. & Seligman, S.J. Architecture of peptidoglycan: more data and more models. Trends Microbiol. 18, 59–66 (2010).

    CAS  PubMed  Google Scholar 

  31. Matias, V.R. & Beveridge, T.J. Cryo-electron microscopy reveals native polymeric cell wall structure in Bacillus subtilis 168 and the existence of a periplasmic space. Mol. Microbiol. 56, 240–251 (2005).

    CAS  PubMed  Google Scholar 

  32. Bugg, T.D., Braddick, D., Dowson, C.G. & Roper, D.I. Bacterial cell wall assembly: still an attractive antibacterial target. Trends Biotechnol. 29, 167–173 (2011).

    CAS  PubMed  Google Scholar 

  33. Typas, A., Banzhaf, M., Gross, C.A. & Vollmer, W. From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat. Rev. Microbiol. 10, 123–136 (2012).

    CAS  Google Scholar 

  34. Lovering, A.L., Safadi, S.S. & Strynadka, N.C. Structural perspective of peptidoglycan biosynthesis and assembly. Annu. Rev. Biochem. 81, 451–478 (2012).

    CAS  PubMed  Google Scholar 

  35. Tipper, D.J. & Strominger, J.L. Mechanism of action of penicillins: a proposal based on their structural similarity to acyl-D-alanyl-D-alanine. Proc. Natl. Acad. Sci. USA 54, 1133–1141 (1965).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Blumberg, P.M., Yocum, R.R., Willoughby, E. & Strominger, J.L. Binding of [14C]penicillin G to the membrane-bound and the purified D-alanine carboxypeptidases from Bacillus stearothermophilus and Bacillus subtilis and its release. J. Biol. Chem. 249, 6828–6835 (1974).

    CAS  PubMed  Google Scholar 

  37. Zhao, G., Meier, T.I., Kahl, S.D., Gee, K.R. & Blaszczak, L.C. BOCILLIN FL, a sensitive and commercially available reagent for detection of penicillin-binding proteins. Antimicrob. Agents Chemother. 43, 1124–1128 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Gee, K.R., Kang, H.C., Meier, T.I., Zhao, G. & Blaszcak, L.C. Fluorescent bocillins: synthesis and application in the detection of penicillin-binding proteins. Electrophoresis 22, 960–965 (2001).

    CAS  PubMed  Google Scholar 

  39. Heal, W.P. & Tate, E.W. Application of activity-based protein profiling to the study of microbial pathogenesis. Top. Curr. Chem. 324, 115–135 (2012).

    CAS  PubMed  Google Scholar 

  40. Puri, A.W. & Bogyo, M. Applications of small molecule probes in dissecting mechanisms of bacterial virulence and host responses. Biochemistry 52, 5985–5996 (2013).

    CAS  PubMed  Google Scholar 

  41. Staub, I. & Sieber, S.A. Beta-lactams as selective chemical probes for the in vivo labeling of bacterial enzymes involved in cell wall biosynthesis, antibiotic resistance, and virulence. J. Am. Chem. Soc. 130, 13400–13409 (2008).

    CAS  PubMed  Google Scholar 

  42. Böttcher, T. & Sieber, S.A. Beta-lactones as specific inhibitors of ClpP attenuate the production of extracellular virulence factors of Staphylococcus aureus. J. Am. Chem. Soc. 130, 14400–14401 (2008).

    PubMed  Google Scholar 

  43. Böttcher, T. & Sieber, S.A. Structurally refined beta-lactones as potent inhibitors of devastating bacterial virulence factors. ChemBioChem 10, 663–666 (2009).

    PubMed  Google Scholar 

  44. Zeiler, E., Korotkov, V.S., Lorenz-Baath, K., Böttcher, T. & Sieber, S.A. Development and characterization of improved β-lactone-based anti-virulence drugs targeting ClpP. Bioorg. Med. Chem. 20, 583–591 (2012).

    CAS  PubMed  Google Scholar 

  45. Kocaoglu, O. et al. Selective penicillin-binding protein imaging probes reveal substructure in bacterial cell division. ACS Chem. Biol. 7, 1746–1753 (2012). First example of selective PBP imaging using an activity-based probe. This study provides precedent for the use of β-lactam antibiotics to facilitate microscopy-based study of the PBPs.

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Kocaoglu, O. & Carlson, E.E. Penicillin-binding protein imaging probes. Curr. Protoc. Chem. Biol. 5, 239–250 (2013).

    PubMed  PubMed Central  Google Scholar 

  47. Kocaoglu, O. & Carlson, E.E. Profiling of β-lactam selectivity for penicillin-binding proteins in Escherichia coli strain DC2. Antimicrob. Agents Chemother. 59, 2785–2790 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Kocaoglu, O., Tsui, H.-C.T., Winkler, M.E. & Carlson, E.E. Profiling of β-lactam selectivity for penicillin-binding proteins in Streptococcus pneumoniae D39. Antimicrob. Agents Chemother. 59, 3548–3555 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Daniel, R.A. & Errington, J. Control of cell morphogenesis in bacteria: two distinct ways to make a rod-shaped cell. Cell 113, 767–776 (2003). Beautiful demonstration of the utility of vancomycin as an imaging agent to visualize nascent peptidoglycan.

    CAS  PubMed  Google Scholar 

  50. Tiyanont, K. et al. Imaging peptidoglycan biosynthesis in Bacillus subtilis with fluorescent antibiotics. Proc. Natl. Acad. Sci. USA 103, 11033–11038 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Gautam, S. et al. An activity-based probe for studying crosslinking in live bacteria. Angew. Chem. Int. Edn Engl. 54, 10492–10496 (2015).

    CAS  Google Scholar 

  52. Liu, H., Sadamoto, R., Sears, P.S. & Wong, C.H. An efficient chemoenzymatic strategy for the synthesis of wild-type and vancomycin-resistant bacterial cell-wall precursors: UDP-N-acetylmuramyl-peptides. J. Am. Chem. Soc. 123, 9916–9917 (2001).

    CAS  PubMed  Google Scholar 

  53. Sadamoto, R. et al. Cell-wall engineering of living bacteria. J. Am. Chem. Soc. 124, 9018–9019 (2002).

    CAS  PubMed  Google Scholar 

  54. Olrichs, N.K. et al. A novel in vivo cell-wall labeling approach sheds new light on peptidoglycan synthesis in Escherichia coli. ChemBioChem 12, 1124–1133 (2011).

    CAS  PubMed  Google Scholar 

  55. 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).

    CAS  Google Scholar 

  56. Siegrist, M.S. et al. D-Amino acid chemical reporters reveal peptidoglycan dynamics of an intracellular pathogen. ACS Chem. Biol. 8, 500–505 (2013).

    CAS  PubMed  Google Scholar 

  57. Shieh, P., Siegrist, M.S., Cullen, A.J. & Bertozzi, C.R. Imaging bacterial peptidoglycan with near-infrared fluorogenic azide probes. Proc. Natl. Acad. Sci. USA 111, 5456–5461 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Lebar, M.D. et al. Reconstitution of peptidoglycan cross-linking leads to improved fluorescent probes of cell wall synthesis. J. Am. Chem. Soc. 136, 10874–10877 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Pidgeon, S.E. et al. Metabolic profiling of bacteria by unnatural C-terminated D-amino acids. Angew. Chem. Int. Edn Engl. 54, 6158–6162 (2015).

    CAS  Google Scholar 

  60. Schirner, K. et al. Lipid-linked cell wall precursors regulate membrane association of bacterial actin MreB. Nat. Chem. Biol. 11, 38–45 (2015).

    CAS  PubMed  Google Scholar 

  61. Monteiro, J.M. et al. Cell shape dynamics during the staphylococcal cell cycle. Nat. Commun. 6, 8055 (2015).

    CAS  PubMed  Google Scholar 

  62. Garrett, A.J., Harrison, M.J. & Manire, G.P. A search for the bacterial mucopeptide component, muramic acid, in Chlamydia. J. Gen. Microbiol. 80, 315–318 (1974).

    CAS  PubMed  Google Scholar 

  63. Fox, A. et al. Muramic acid is not detectable in Chlamydia psittaci or Chlamydia trachomatis by gas chromatography-mass spectrometry. Infect. Immun. 58, 835–837 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Pilhofer, M. et al. Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ. Nat. Commun. 4, 2856 (2013).

    PubMed  Google Scholar 

  65. Liechti, G.W. et al. A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis. Nature 506, 507–510 (2014). Demonstration of the presence of peptidoglycan in Chlamydia trachomatis using fluorescent D -amino acids for the first time.

    CAS  PubMed  Google Scholar 

  66. Wheeler, R., Mesnage, S., Boneca, I.G., Hobbs, J.K. & Foster, S.J. Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria. Mol. Microbiol. 82, 1096–1109 (2011).

    CAS  PubMed  Google Scholar 

  67. Tsui, H.C. et al. Pbp2x localizes separately from Pbp2b and other peptidoglycan synthesis proteins during later stages of cell division of Streptococcus pneumoniae D39. Mol. Microbiol. 94, 21–40 (2014). Beautiful combination of FDAAs, Van-FL, β-lactams and fusion proteins to explore PBP localization during division.

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Weidenmaier, C. et al. Lack of wall teichoic acids in Staphylococcus aureus leads to reduced interactions with endothelial cells and to attenuated virulence in a rabbit model of endocarditis. J. Infect. Dis. 191, 1771–1777 (2005).

    CAS  PubMed  Google Scholar 

  69. Tra, V.N. & Dube, D.H. Glycans in pathogenic bacteria—potential for targeted covalent therapeutics and imaging agents. Chem. Commun. (Camb.) 50, 4659–4673 (2014).

    CAS  Google Scholar 

  70. Woodruff, P.J. et al. Trehalose is required for growth of Mycobacterium smegmatis. J. Biol. Chem. 279, 28835–28843 (2004).

    CAS  PubMed  Google Scholar 

  71. Backus, K.M. et al. Uptake of unnatural trehalose analogs as a reporter for Mycobacterium tuberculosis. Nat. Chem. Biol. 7, 228–235 (2011). Describes the use of fluorescent unnatural trehalose for sensitive detection of Mycobacterium tuberculosis in mammalian cells.

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Swarts, B.M. et al. Probing the mycobacterial trehalome with bioorthogonal chemistry. J. Am. Chem. Soc. 134, 16123–16126 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Urbanek, B.L. et al. Chemoenzymatic synthesis of trehalose analogues: rapid access to chemical probes for investigating mycobacteria. ChemBioChem 15, 2066–2070 (2014).

    CAS  PubMed  Google Scholar 

  74. Dumont, A., Malleron, A., Awwad, M., Dukan, S. & Vauzeilles, B. Click-mediated labeling of bacterial membranes through metabolic modification of the lipopolysaccharide inner core. Angew. Chem. Int. Edn Engl. 51, 3143–3146 (2012).

    CAS  Google Scholar 

  75. Lee, M.K., Rai, P., Williams, J., Twieg, R.J. & Moerner, W.E. Small-molecule labeling of live cell surfaces for three-dimensional super-resolution microscopy. J. Am. Chem. Soc. 136, 14003–14006 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Gunsolus, I.L. et al. Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy. Analyst 139, 3174–3178 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Conley, N.R., Biteen, J.S. & Moerner, W.E. Cy3-Cy5 covalent heterodimers for single-molecule photoswitching. J. Phys. Chem. B 112, 11878–11880 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Nelson, J.W. et al. A biosynthetic strategy for re-engineering the Staphylococcus aureus cell wall with non-native small molecules. ACS Chem. Biol. 5, 1147–1155 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Wang, L., Brock, A., Herberich, B. & Schultz, P.G. Expanding the genetic code of Escherichia coli. Science 292, 498–500 (2001).

    CAS  PubMed  Google Scholar 

  80. Charbon, G. et al. Subcellular protein localization by using a genetically encoded fluorescent amino acid. ChemBioChem 12, 1818–1821 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Beatty, K.E., Xie, F., Wang, Q. & Tirrell, D.A. Selective dye-labeling of newly synthesized proteins in bacterial cells. J. Am. Chem. Soc. 127, 14150–14151 (2005).

    CAS  PubMed  Google Scholar 

  82. Hatzenpichler, R. et al. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ. Microbiol. 16, 2568–2590 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Mahdavi, A. et al. Identification of secreted bacterial proteins by noncanonical amino acid tagging. Proc. Natl. Acad. Sci. USA 111, 433–438 (2014).

    CAS  PubMed  Google Scholar 

  84. Raulf, A. et al. Click chemistry facilitates direct labeling and super-resolution imaging of nucleic acids and proteins. RCS Adv. 4, 30462–30466 (2014).

    CAS  Google Scholar 

  85. Beatty, K.E. et al. Sulfatase-activated fluorophores for rapid discrimination of mycobacterial species and strains. Proc. Natl. Acad. Sci. USA 110, 12911–12916 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Smith, E.L., Bertozzi, C.R. & Beatty, K.E. An expanded set of fluorogenic sulfatase activity probes. ChemBioChem 15, 1101–1105 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Gloeckl, S. et al. Identification of a serine protease inhibitor which causes inclusion vacuole reduction and is lethal to Chlamydia trachomatis. Mol. Microbiol. 89, 676–689 (2013).

    CAS  PubMed  Google Scholar 

  88. Böttcher, T. & Sieber, S.A. Showdomycin as a versatile chemical tool for the detection of pathogenesis-associated enzymes in bacteria. J. Am. Chem. Soc. 132, 6964–6972 (2010).

    PubMed  Google Scholar 

  89. Chauvigné-Hines, L.M. et al. Suite of activity-based probes for cellulose-degrading enzymes. J. Am. Chem. Soc. 134, 20521–20532 (2012).

    PubMed  PubMed Central  Google Scholar 

  90. Sadler, N.C. et al. Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium. ACS Chem. Biol. 9, 291–300 (2014).

    CAS  PubMed  Google Scholar 

  91. Deng, X. et al. Proteome-wide quantification and characterization of oxidation-sensitive cysteines in pathogenic bacteria. Cell Host Microbe 13, 358–370 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Wilke, K.E., Francis, S. & Carlson, E.E. Activity-based probe for histidine kinase signaling. J. Am. Chem. Soc. 134, 9150–9153 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. Lee, M.K., Williams, J.C., 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. (Camb.) 4, 220–225 (2013).

    CAS  Google Scholar 

  94. Gustafsson, M.G. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198, 82–87 (2000).

    CAS  PubMed  Google Scholar 

  95. Hell, S.W. & Wichmann, J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19, 780–782 (1994).

    CAS  PubMed  Google Scholar 

  96. Schermelleh, L., Heintzmann, R. & Leonhardt, H. A guide to super-resolution fluorescence microscopy. J. Cell Biol. 190, 165–175 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Coltharp, C. & Xiao, J. Superresolution microscopy for microbiology. Cell. Microbiol. 14, 1808–1818 (2012). An excellent review comparing super-resolution microscopy techniques for bacterial cell imaging.

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642–1645 (2006).

    CAS  PubMed  Google Scholar 

  99. Rust, M.J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793–795 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Tuson, H.H. & Biteen, J.S. Unveiling the inner workings of live bacteria using super-resolution microscopy. Anal. Chem. 87, 42–63 (2015). Comprehensive review of cutting-edge strategies to examine bacteria using super-resolution microscopy techniques.

    CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by NIH DP2OD008592 (E.E.C.), a Pew Biomedical Scholar Award (E.E.C.), Sloan Research Fellow Award (E.E.C.) and Indiana University–Bloomington Department of Chemistry Start-Up Funds and a Marvin Carmack Fellowship (O.K.).

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  1. Erin E Carlson

    Present address: Current address: Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA.,

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  1. Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA

    Ozden Kocaoglu & Erin E Carlson

  2. Department of Chemistry, Indiana University, Bloomington, Indiana, USA

    Erin E Carlson

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Kocaoglu, O., Carlson, E. Progress and prospects for small-molecule probes of bacterial imaging. Nat Chem Biol 12, 472–478 (2016). https://doi.org/10.1038/nchembio.2109

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