Skip to main content

Fluorescent Reporters and Methods to Analyze Fluorescent Signals

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 983))

Abstract

The use of fluorescent reporters and the development of new imaging technologies have revolutionized studies in cell biology. During recent years the number of fluorescent proteins offering the ability to visualize the distribution of proteins, organelles, and cells has increased tremendously. In parallel, the imaging tools available were refined rapidly enabling now the use of a huge spectrum of specialized methods to explore the cellular and subcellular localization and dynamics of fluorescently tagged markers. This chapter presents an overview of fluorescent reporters and methods available, and describes a selection of those that are routinely applicable in imaging studies using Dictyostelium discoideum.

This is a preview of subscription content, log in via an institution.

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA (2010) Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev 90:1103–1163

    Article  CAS  PubMed  Google Scholar 

  2. Kremers GJ, Gilbert SG, Cranfill PJ, Davidson MW, Piston DW (2011) Fluorescent proteins at a glance. J Cell Sci 124:157–160

    Article  CAS  PubMed  Google Scholar 

  3. Veltman DM, Akar G, Bosgraaf L, van Haastert PJ (2009) A new set of small, extrachromosomal expression vectors for Dictyostelium discoideum. Plasmid 61:110–118

    Article  CAS  PubMed  Google Scholar 

  4. Müller-Taubenberger A (2006) Application of Fluorescent protein tags as reporters in live-cell imaging studies. Methods Mol Biol 346:229–246

    PubMed  Google Scholar 

  5. Dubin M, Nellen W (2010) A versatile set of tagged expression vectors to monitor protein localisation and function in Dictyostelium. Gene 465:1–8

    Article  CAS  PubMed  Google Scholar 

  6. Bukharova T, Weijer G, Bosgraaf L, Dormann D, van Haastert PJ, Weijer CJ (2005) Paxillin is required for cell-substrate adhesion, cell sorting and slug migration during Dictyostelium development. J Cell Sci 118:4295–4310

    Article  PubMed  Google Scholar 

  7. Moores SL, Sabry JH, Spudich JA (1996) Myosin dynamics in live Dictyostelium cells. Proc Natl Acad Sci U S A 93:443–446

    Article  CAS  PubMed  Google Scholar 

  8. Maniak M, Rauchenberger R, Albrecht R, Murphy J, Gerisch G (1995) Coronin involved in phagocytosis: dynamics of particle-induced relocalization visualized by a green fluorescent protein Tag. Cell 83:915–924

    Article  CAS  PubMed  Google Scholar 

  9. Heim R, Tsien RY (1996) Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Curr Biol 6:178–182

    Article  CAS  PubMed  Google Scholar 

  10. Xu X, Brzostowski JA, Jin T (2006) Using quantitative fluorescence microscopy and FRET imaging to measure spatiotemporal signaling events in single living cells. Methods Mol Biol 346:281–296

    CAS  PubMed  Google Scholar 

  11. Janetopoulos C, Jin T, Devreotes P (2001) Receptor-mediated activation of heterotrimeric G-proteins in living cells. Science 291:2408–2411

    Article  CAS  PubMed  Google Scholar 

  12. Fischer M, Haase I, Simmeth E, Gerisch G, Müller-Taubenberger A (2004) A brilliant monomeric red fluorescent protein to visualize cytoskeleton dynamics in Dictyostelium. FEBS Lett 577:227–232

    Article  CAS  PubMed  Google Scholar 

  13. Shaner NC, Campbell RE, Steinbach PA, Giepmans BN, Palmer AE, Tsien RY (2004) Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 22:1567–1572

    Article  CAS  PubMed  Google Scholar 

  14. Merzlyak EM, Goedhart J, Shcherbo D, Bulina ME, Shcheglov AS, Fradkov AF, Gaintzeva A, Lukyanov KA, Lukyanov S, Gadella TW, Chudakov DM (2007) Bright monomeric red fluorescent protein with an extended fluorescence lifetime. Nat Methods 4:555–557

    Article  CAS  PubMed  Google Scholar 

  15. Wang L, Jackson WC, Steinbach PA, Tsien RY (2004) Evolution of new nonantibody proteins via iterative somatic hypermutation. Proc Natl Acad Sci U S A 101:16745–16749

    Article  CAS  PubMed  Google Scholar 

  16. Pedelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS (2006) Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol 24:79–88

    Article  CAS  PubMed  Google Scholar 

  17. Diez S, Gerisch G, Anderson K, Müller-Taubenberger A, Bretschneider T (2005) Subsecond reorganization of the actin network in cell motility and chemotaxis. Proc Natl Acad Sci U S A 102:7601–7606

    Article  CAS  PubMed  Google Scholar 

  18. Schneider N, Weber I, Faix J, Prassler J, Müller-Taubenberger A, Köhler J, Burghardt E, Gerisch G, Marriott G (2003) A Lim protein involved in the progression of cytokinesis and regulation of the mitotic spindle. Cell Motil Cytoskeleton 56:130–139

    Article  CAS  PubMed  Google Scholar 

  19. Bretschneider T, Diez S, Anderson K, Heuser J, Clarke M, Müller-Taubenberger A, Köhler J, Gerisch G (2004) Dynamic actin patterns and Arp2/3 assembly at the substrate-attached surface of motile cells. Curr Biol 14:1–10

    Article  CAS  PubMed  Google Scholar 

  20. Riedl J, Crevenna AH, Kessenbrock K, Yu JH, Neukirchen D, Bista M, Bradke F, Jenne D, Holak TA, Werb Z, Sixt M, Wedlich-Söldner R (2008) Lifeact: a versatile marker to visualize F-actin. Nat Methods 5:605–607

    Article  CAS  PubMed  Google Scholar 

  21. Ando R, Hama H, Yamamoto-Hino M, Mizuno H, Miyawaki A (2002) An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc Natl Acad Sci U S A 99:12651–12656

    Article  CAS  PubMed  Google Scholar 

  22. Wiedenmann J, Ivanchenko S, Oswald F, Schmitt F, Röcker C, Salih A, Spindler KD, Nienhaus GU (2004) EosFP, a fluorescent marker protein with UV-inducible green-to-red fluorescence conversion. Proc Natl Acad Sci U S A 101:15905–15910

    Article  CAS  PubMed  Google Scholar 

  23. Müller-Taubenberger A, Anderson KI (2007) Recent advances using green and red fluorescent protein variants. Appl Microbiol Biotechnol 77:1–12

    Article  PubMed  Google Scholar 

  24. Gurskaya NG, Verkhusha VV, Shcheglov AS, Staroverov DB, Chepurnykh TV, Fradkov AF, Lukyanov S, Lukyanov KA (2006) Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light. Nat Biotechnol 24:461–465

    Article  CAS  PubMed  Google Scholar 

  25. Chudakov DM, Lukyanov S, Lukyanov KA (2007) Tracking intracellular protein movements using photoswitchable fluorescent proteins PS-CFP2 and Dendra2. Nat Protoc 2:2024–2032

    Article  CAS  PubMed  Google Scholar 

  26. Schnell U, Dijk F, Sjollema KA, Giepmans BN (2012) Immunolabeling artifacts and the need for live-cell imaging. Nat Methods 9:152–158

    Article  CAS  PubMed  Google Scholar 

  27. Trusolino L, Comoglio PM (2002) Scatter-factor and semaphorin receptors: cell signalling for invasive growth. Nat Rev Cancer 2:289–300

    Article  CAS  PubMed  Google Scholar 

  28. Charo IF, Taubman MB (2004) Chemokines in the pathogenesis of vascular disease. Circ Res 95:858–866

    Article  CAS  PubMed  Google Scholar 

  29. Eccles DM (2004) Hereditary cancer: guidelines in clinical practice. Breast and ovarian cancer genetics. Ann Oncol 15(Suppl 4):iv133–iv138

    Article  PubMed  Google Scholar 

  30. Schleicher M, Noegel AA (1992) Dynamics of the Dictyostelium cytoskeleton during chemotaxis. New Biol 4:461–472

    CAS  PubMed  Google Scholar 

  31. Gerisch G (2009) Imaging actin cytoskeleton dynamics in Dictyostelium chemotaxis. Methods Mol Biol 571:385–400

    Article  CAS  PubMed  Google Scholar 

  32. Skoge M, Adler M, Groisman A, Levine H, Loomis WF, Rappel WJ (2010) Gradient sensing in defined chemotactic fields. Integr Biol (Camb) 2:659–668

    Article  CAS  Google Scholar 

  33. Meier B, Zielinski A, Weber C, Arcizet D, Youssef S, Franosch T, Rädler JO, Heinrich D (2011) Chemotactic cell trapping in controlled alternating gradient fields. Proc Natl Acad Sci U S A 108:11417–11422

    Article  CAS  PubMed  Google Scholar 

  34. Beta C, Wyatt D, Rappel WJ, Bodenschatz E (2007) Flow photolysis for spatiotemporal stimulation of single cells. Anal Chem 79:3940–3944

    Article  CAS  PubMed  Google Scholar 

  35. Berenstein I, Beta C (2011) Flow-induced control of chemical turbulence. J Chem Phys 135:164901

    Article  PubMed  Google Scholar 

  36. Breslauer DN, Lee PJ, Lee LP (2006) Microfluidics-based systems biology. Mol Biosyst 2:97–112

    Article  CAS  PubMed  Google Scholar 

  37. Whitesides GM, Ostuni E, Takayama S, Jiang X, Ingber DE (2001) Soft lithography in biology and biochemistry. Annu Rev Biomed Eng 3:335–373

    Article  CAS  PubMed  Google Scholar 

  38. Beta C (2009) Spatiotemporal stimulation of single cells using flow photolysis. Methods Mol Biol 571:321–332

    Article  CAS  PubMed  Google Scholar 

  39. Song L, Nadkarni SM, Bodeker HU, Beta C, Bae A, Franck C, Rappel WJ, Loomis WF, Bodenschatz E (2006) Dictyostelium discoideum chemotaxis: threshold for directed motion. Eur J Cell Biol 85:981–989

    Article  CAS  PubMed  Google Scholar 

  40. Jeon NL, Chiu DT, Choi IS, Stroock AD, Whitesides GM (2000) Generation of solution and surface gradients using microfluidic systems. Langmuir 16:8311–8316

    Article  CAS  Google Scholar 

  41. Beta C, Bodenschatz E (2011) Microfluidic tools for quantitative studies of eukaryotic chemotaxis. Eur J Cell Biol 90:811–816

    Article  CAS  PubMed  Google Scholar 

  42. Rhoads DS, Nadkarni SM, Song L, Voeltz C, Bodenschatz E, Guan JL (2005) Using microfluidic channel networks to generate gradients for studying cell migration. Methods Mol Biol 294:347–357

    PubMed  Google Scholar 

  43. Shina MC, Müller R, Blau-Wasser R, Glöckner G, Schleicher M, Eichinger L, Noegel AA, Kolanus W (2012) A cytohesin homolog in Dictyostelium amoebae. PLoS One 5:e9378

    Article  Google Scholar 

  44. Shina MC, Ünal C, Eichinger L, Müller-Taubenberger A, Schleicher M, Steinert M, Noegel AA (2010) A Coronin7 homolog with functions in actin-driven processes. J Biol Chem 285:9249–9261

    Article  CAS  PubMed  Google Scholar 

  45. Ishikawa-Ankerhold HC, Ankerhold R, Drummen GPC (2012) Advanced fluorescence microscopy techniques-FRAP, FLIP, FLAP, FRET and FLIM. Molecules 17:4047–4132

    Article  CAS  PubMed  Google Scholar 

  46. Paddock SW (2000) Principles and practices of laser scanning confocal microscopy. Mol Biotechnol 16:127–149

    Article  CAS  PubMed  Google Scholar 

  47. Pawley JB (2006) Fundamental limits in confocal microscopy. In: Pawley JB (ed) Handbook of biological confocal microscopy, 3rd edn. Springer, New York, pp 20–42, Chapter 2

    Chapter  Google Scholar 

  48. Wright SJ, Wright DJ (2002) Introduction to confocal microscopy. Methods Cell Biol 70:1–85

    Article  PubMed  Google Scholar 

  49. Sheppard CJR, Shotton DM (1997) Introduction. In: Sheppard CJR, Shotton DM (eds) Confocal laser scanning microscopy. Springer, New York, pp 1–13

    Google Scholar 

  50. Hanakam F, Albrecht R, Eckerskorn C, Matzner M, Gerisch G (1996) Myristoylated and non-myristoylated forms of the pH sensor protein hisactophilin II: intracellular shuttling to plasma membrane and nucleus monitored in real time by a fusion with green fluorescent protein. EMBO J 15:2935–2943

    CAS  PubMed  Google Scholar 

  51. Patterson G, Day RN, Piston D (2001) Fluorescent protein spectra. J Cell Sci 114:837–838

    CAS  PubMed  Google Scholar 

  52. Filic V, Marinovic M, Faix J, Weber I (2012) A dual role for Rac1 GTPases in the regulation of cell motility. J Cell Sci 125:387–398

    Article  CAS  PubMed  Google Scholar 

  53. Campbell RE, Tour O, Palmer AE, Steinbach PA, Baird GS, Zacharias DA, Tsien RY (2002) A monomeric red fluorescent protein. Proc Natl Acad Sci U S A 99:7877–7882

    Article  CAS  PubMed  Google Scholar 

  54. Patterson GH, Lippincott-Schwartz J (2002) A photoactivatable GFP for selective photolabeling of proteins and cells. Science 297:1873–1877

    Article  CAS  PubMed  Google Scholar 

  55. Bretschneider T, Jonkman J, Köhler J, Medalia O, Barisic K, Weber I, Stelzer EH, Baumeister W, Gerisch G (2002) Dynamic organization of the actin system in the motile cells of Dictyostelium. J Muscle Res Cell Motil 23:639–649

    Article  CAS  PubMed  Google Scholar 

  56. Elzie CA, Janetopoulos C (2009) FRAP analysis of chemosensory components of Dictyostelium. Methods Mol Biol 571:349–369

    Article  CAS  PubMed  Google Scholar 

  57. Potma EO, de Boeij WP, Bosgraaf L, Roelofs J, van Haastert PJ, Wiersma DA (2001) Reduced protein diffusion rate by cytoskeleton in vegetative and polarized Dictyostelium cells. Biophys J 81:2010–2019

    Article  CAS  PubMed  Google Scholar 

  58. Yumura S, Yoshida M, Betapudi V, Licate LS, Iwadate Y, Nagasaki A, Uyeda TQ, Egelhoff TT (2005) Multiple myosin II heavy chain kinases: roles in filament assembly control and proper cytokinesis in Dictyostelium. Mol Biol Cell 16:4256–4266

    Article  CAS  PubMed  Google Scholar 

  59. Elzie CA, Colby J, Sammons MA, Janetopoulos C (2009) Dynamic localization of G proteins in Dictyostelium discoideum. J Cell Sci 122:2597–2603

    Article  CAS  PubMed  Google Scholar 

  60. Fukuzawa M, Abe T, Williams JG (2003) The Dictyostelium prestalk cell inducer DIF regulates nuclear accumulation of a STAT protein by controlling its rate of export from the nucleus. Development 130:797–804

    Article  CAS  PubMed  Google Scholar 

  61. Yumura S (2001) Myosin II dynamics and cortical flow during contractile ring formation in Dictyostelium cells. J Cell Biol 154:137–146

    Article  CAS  PubMed  Google Scholar 

  62. Galdeen SA, Stephens S, Thomas DD, Titus MA (2007) Talin influences the dynamics of the myosin VII-membrane interaction. Mol Biol Cell 18:4074–4084

    Article  CAS  PubMed  Google Scholar 

  63. Itoh G, Yumura S (2007) A novel mitosis-specific dynamic actin structure in Dictyostelium cells. J Cell Sci 120:4302–4309

    Article  CAS  PubMed  Google Scholar 

  64. Dundr M, Hoffmann-Rohrer U, Hu Q, Grummt I, Rothblum LI, Phair RD, Misteli T (2002) A kinetic framework for a mammalian RNA polymerase in vivo. Science 298:1623–1626

    Article  CAS  PubMed  Google Scholar 

  65. Ishihama Y, Tadakuma H, Tani T, Funatsu T (2008) The dynamics of pre-mRNAs and poly(A)+ RNA at speckles in living cells revealed by iFRAP studies. Exp Cell Res 314:748–762

    Article  CAS  PubMed  Google Scholar 

  66. Houtsmuller AB (2005) Fluorescence recovery after photobleaching: application to nuclear proteins. Adv Biochem Eng Biotechnol 95:177–199

    CAS  PubMed  Google Scholar 

  67. Ehrlicher AJ, Nakamura F, Hartwig JH, Weitz DA, Stossel TP (2011) Mechanical strain in actin networks regulates FilGAP and integrin binding to filamin A. Nature 478:260–263

    Article  CAS  PubMed  Google Scholar 

  68. Dunn GA, Dobbie IM, Monypenny J, Holt MR, Zicha D (2002) Fluorescence localization after photobleaching (FLAP): a new method for studying protein dynamics in living cells. J Microsc 205:109–112

    Article  CAS  PubMed  Google Scholar 

  69. Dunn GA, Holt MR, Soong DY, Gray C, Zicha D (2004) Fluorescence localization after photobleaching (FLAP). Curr Protoc Cell Biol. Chapter 21, Unit 21.2

    Google Scholar 

  70. König I, Schwarz JP, Anderson KI (2008) Fluorescence lifetime imaging: association of cortical actin with a PIP3-rich membrane compartment. Eur J Cell Biol 87:735–741

    Article  PubMed  Google Scholar 

  71. Müller-Taubenberger A, Bretschneider T, Faix J, Konzok A, Simmeth E, Weber I (2002) Differential localization of the Dictyostelium kinase DPAKa during cytokinesis and cell migration. J Muscle Res Cell Motil 23:751–763

    Article  PubMed  Google Scholar 

Download references

Acknowledgment

This work was supported by DFG grants SFB 863 and SFB 914.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Annette Müller-Taubenberger .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Müller-Taubenberger, A., Ishikawa-Ankerhold, H.C. (2013). Fluorescent Reporters and Methods to Analyze Fluorescent Signals. In: Eichinger, L., Rivero, F. (eds) Dictyostelium discoideum Protocols. Methods in Molecular Biology, vol 983. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-302-2_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-302-2_5

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-301-5

  • Online ISBN: 978-1-62703-302-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics