Marine Biotechnology

, Volume 10, Issue 3, pp 328–342 | Cite as

Spectral Diversity of Fluorescent Proteins from the Anthozoan Corynactis californica

  • Christine E. Schnitzler
  • Robert J. Keenan
  • Robert McCord
  • Artur Matysik
  • Lynne M. Christianson
  • Steven H. D. Haddock
Original Article


Color morphs of the temperate, nonsymbiotic corallimorpharian Corynactis californica show variation in pigment pattern and coloring. We collected seven distinct color morphs of C. californica from subtidal locations in Monterey Bay, California, and found that tissue– and color–morph-specific expression of at least six different genes is responsible for this variation. Each morph contains at least three to four distinct genetic loci that code for these colors, and one morph contains at least five loci. These genes encode a subfamily of new GFP-like proteins, which fluoresce across the visible spectrum from green to red, while sharing between 75% to 89% pairwise amino-acid identity. Biophysical characterization reveals interesting spectral properties, including a bright yellow protein, an orange protein, and a red protein exhibiting a “fluorescent timer” phenotype. Phylogenetic analysis indicates that the FP genes from this species evolved together but that diversification of anthozoan fluorescent proteins has taken place outside of phylogenetic constraints, especially within the Corallimorpharia. The discovery of more examples of fluorescent proteins in a non-bioluminescent, nonsymbiotic anthozoan highlights possibilities of adaptive ecological significance unrelated to light regulation for algal symbionts. The patterns and colors of fluorescent proteins in C. californica and similar species may hold meaning for organisms that possess the visual pigments to distinguish them.


GFP-like Fluorescent protein Corallimorpharian Phenotypic plasticity Pigment 



The authors thank Laura Figoski (MBARI) and Maureen Downing (University of Chicago) for help with expression and purification of the FPs; Denis Klimov, Zbigniew Kolber, and Ken Johnson from MBARI and Keith Moffatt from University of Chicago provided equipment used in spectroscopic quantification; the authors also thank Kenneth Coale and Jon Geller of MLML for academic support and Jason Felton for assistance in the field; Mike Lassner, Claus Krebber, and Steve Bass from Maxygen for their enthusiastic support during the initial stages of this project; and two anonymous reviewers for insightful comments that improved the manuscript. Supported in part by the David and Lucile Packard Foundation.


  1. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Autom Contr 19:716–723CrossRefGoogle Scholar
  2. Arbeloa FL, Ojeda PR, Arbeloa IL (1989) Fluorescence self-quenching of the molecular forms of rhodamine B in aqueous and ethanolic solutions. J Luminescence 44:105–112CrossRefGoogle Scholar
  3. Baird GS, Zacharias DA, Tsien RY (2000) Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral. Proc Natl Acad Sci USA 97:11984–11989PubMedCrossRefGoogle Scholar
  4. Berntson EA, France SC, Mullineaux LS (1999) Phylogenetic relationships within the Class Anthozoa (Phylum Cnidaria) based on nuclear 18S rDNA sequences. Mol Phylogenet Evol 13:417–433PubMedCrossRefGoogle Scholar
  5. Bessette PH, Daugherty PS (2004) Flow cytometric screening of cDNA expression libraries for fluorescent proteins. Biotechnol Prog 20:963–967PubMedCrossRefGoogle Scholar
  6. Bevis BJ, Glick BS (2002) Rapidly maturing variants of the Discosoma red fluorescent protein (DsRed). Nat Biotechnol 20:83–87PubMedCrossRefGoogle Scholar
  7. Brakefield PM, French V (1999) Butterfly wings: the evolution of development of colour patterns. BioEssays 21:391–401CrossRefGoogle Scholar
  8. Campbell RE, Tour O, Palmer AE, Steinbach PA, Baird GS, Zacharias DA, Tsien RY (2002) A monomeric red fluorescent protein. Proc Natl Acad Sci USA 99:7877–7882PubMedCrossRefGoogle Scholar
  9. Carlgren O (1949) A survey of the Ptychodactiaria, Corallimorpharia and Actinaria. Kungliga Svenska Vetenskapsakademiens Handlingar 1:1–129Google Scholar
  10. Chadwick NE (1987) Interspecific aggressive behavior of the corallimorpharian Corynactis californica (Cnidaria: Anthozoa): effects on sympatric corals and sea anemones. Biol Bull 173:110–125CrossRefGoogle Scholar
  11. Chadwick NE, Adams C (1991) Locomotion, asexual reproduction, and killing of corals by the corallimorpharian Corynactis californica. Hydrobiologia 216/217:263–269CrossRefGoogle Scholar
  12. Cott HB (1957) Adaptive coloration in animals. Methuen, LondonGoogle Scholar
  13. Dove SG, Hoegh-Guldberg O, Ranganathan S (2001) Major colour patterns of reef-building corals are due to a family of GFP-like proteins. Coral Reefs 19:197–204CrossRefGoogle Scholar
  14. Dunn DF (1982) Cnidaria. In: Parker SP (ed) Synopsis and classification of living organisms. McGraw-Hill, New YorkGoogle Scholar
  15. Edgar R (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797PubMedCrossRefGoogle Scholar
  16. Elowitz MB, Surette MG, Wolf PE, Stock J, Leibler S (1997) Photoactivation turns green fluorescent protein red. Current Biol 7:809–812CrossRefGoogle Scholar
  17. France SC, Rosel PE, Agenbroad JE, Mullineaux LS, Kocher TD (1996) DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two subclass organization of the Anthozoa (Cnidaria). Mol Mar Biol Biotechnol 5:15–28PubMedGoogle Scholar
  18. Gilmore AM, Larkum AWD, Salih A, Itoh S, Shibata Y, Bena C, Yamasaki H, Papina M, Woesik RV (2003) Simultaneous time-resolution of the emission spectra of fluorescent proteins and zooxanthellae chlorophyll in reef-building corals. Photochem Photobiol 77:515–523PubMedCrossRefGoogle Scholar
  19. Gross LA, Baird GS, Hoffman RC, Baldridge KK, Tsien RY (2000) The structure of the chromophore within DsRed, a red fluorescent protein from coral. Proc Natl Acad Sci USA 97:11990—11995PubMedCrossRefGoogle Scholar
  20. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696—704PubMedCrossRefGoogle Scholar
  21. Haddock SHD, Dunn CW, Pugh PR, Schnitzler CE (2005) Bioluminescent and red fluorescent lures in a deep-sea siphonophore. Science 309:263PubMedCrossRefGoogle Scholar
  22. Haderlie EC, Hand C, Gladfelter WB (1980) Cnidaria (Coelenterata): the sea anemones and allies. In: Morris RH, Abbott DP, Haderlie EC (eds) Intertidal invertebrates of California. Stanford University Press, StanfordGoogle Scholar
  23. Hand C (1954) The sea anemones of central California. Part I. The corallimorpharian and athenarian anemones. Wasmann J Biol 12:345–375Google Scholar
  24. Hansson L-A (2004) Plasticity in pigmentation induced by conflicting threats from predation and UV radiation. Ecology 85:1005–1016CrossRefGoogle Scholar
  25. Holts LJ, Beauchamp KA (1993) Sexual reproduction in the corallimorpharian sea anemone Corynactis californica in a central California kelp forest. Mar Biology 116:129–136CrossRefGoogle Scholar
  26. Huelsenbeck JP, Ronquist FR (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  27. Ip D, Chan S-H, Allen M, Bycroft M, Wan D, Wong K-B (2004) Crystallization and preliminary crystallographic analysis of a novel orange fluorescent protein from the Cnidaria tube anemone Cerianthus sp. Acta Crystallographica Section D Biol Crystallography 60:340–341CrossRefGoogle Scholar
  28. Ip DT, Wong KB, Wan DC (2007) Characterization of novel orange fluorescent protein cloned from Cnidarian tube anemone Cerianthus sp. Mar Biotechnol 9:469–478PubMedCrossRefGoogle Scholar
  29. Jones DT, Taylor WR, Thornton JM (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33:3038–3049PubMedCrossRefGoogle Scholar
  30. Karasawa S, Araki T, Nagai T, Mizuno H, Miyawaki A (2004) Cyan-emitting and orange-emitting fluorescent proteins as a donor/acceptor pair for fluorescence resonance energy transfer. Biochem J 381:307–312PubMedCrossRefGoogle Scholar
  31. Kawaguti S (1944) On the physiology of reef corals. VI. Study on the pigments. Palau Trop Biol Stn Stud 2:617–673Google Scholar
  32. Kawaguti S (1969) The effect of green fluorescent pigment on the productivity of the reef corals. Micronesica 5:313Google Scholar
  33. Keane T, Creevey C, Pentony M, Naughton T, Mcinerney J (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evolutionary Biol 6:29CrossRefGoogle Scholar
  34. Kelmanson IV, Matz MV (2003) Molecular basis and evolutionary origins of color diversity in great star coral Montastraea cavernosa (Scleractinia: Faviida). Mol Biol Evol 20:1125–1133PubMedCrossRefGoogle Scholar
  35. Labas YA, Gurskaya NG, Yanushevich YG, Fradkov AF, Lukyanov KA, Lukyanov SA, Matz MV (2002) Diversity and evolution of the green fluorescent protein family. Proc Natl Acad Sci USA 99:4256–4261PubMedCrossRefGoogle Scholar
  36. Lakowicz JR (1999) Principles of fluorescence spectroscopy. Kluwer/Plenum, New YorkGoogle Scholar
  37. Limbaugh C, North W (1956) Fluorescent, Benthic, Pacific Coast invertebrates. Nature 178:497–498CrossRefGoogle Scholar
  38. Losey GS, Mcfarland WN, Loew ER, Zamzow JP, Nelson PA, Marshall NJ (2003) Visual biology of Hawaiian coral reef fishes. I. Ocular transmission and visual pigments. Copeia 3:433–454CrossRefGoogle Scholar
  39. Maddison DR, Maddison WP (2000) MacClade 4: analysis of phylogeny and character evolution. Sinauer Associates, SunderlandGoogle Scholar
  40. Magde D, Wong R, Seybold PG (2002) Fluorescence quantum yields and their relation to lifetimes of rhodamine 6G and fluorescein in nine solvents: improved absolute standards for quantum yields. Photochem Photobiol 75:327–334PubMedCrossRefGoogle Scholar
  41. Marshall NJ (2000) Communication and camouflage with the same "bright" colours in reef fish. Philos Trans Royal Soc London B 355:1243–1248CrossRefGoogle Scholar
  42. Marshall NJ, Jennings K, Mcfarland WN, Loew ER, Losey GS (2003a) Visual biology of Hawaiian coral reef fishes. II. Colors of Hawaiian coral reef fish. Copeia 3:455–466CrossRefGoogle Scholar
  43. Marshall NJ, Jennings K, Mcfarland WN, Loew ER, Losey GS (2003b) Visual biology of Hawaiian coral reef fishes. III. Environmental light and an integrated approach to the ecology of reef fish vision. Copeia 3:467–480CrossRefGoogle Scholar
  44. Matz MV, Fradkov AF, Labas YA, Savitsky AP, Zaraisky AG, Markelov ML, Lukyanov SA (1999) Fluorescent proteins from nonbioluminescent Anthozoa species. Nat Biotechnol 17:969–973PubMedCrossRefGoogle Scholar
  45. Matz MV, Lukyanov KA, Lukyanov SA (2002) Family of the green fluorescent protein: journey to the end of the rainbow. BioEssays 24:953–959PubMedCrossRefGoogle Scholar
  46. Matz MV, Marshall NJ, Vorobyev M (2006) Are corals colorful? Photochem Photobiol 82:345–350PubMedCrossRefGoogle Scholar
  47. Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL (2006) Naked corals: skeleton loss in Scleractinia. Proc Natl Acad Sci USA 103:9096–9100PubMedCrossRefGoogle Scholar
  48. Meroz-Fine E, Brickner I, Loya Y, Ilan M (2003) The hydrozoan coral Millepora dichotoma: speciation or phenotypic plasticity? Mar Biol 143:1175–1183CrossRefGoogle Scholar
  49. Merzlyak EM, Goedhart J, Shcherbo D, Bulina ME, Shcheglov AS, Fradkov AF, Gaintzeva A, Lukyanov KA, Lukyanov S, Gadella TWJ (2007) Bright monomeric red fluorescent protein with an extended fluorescence lifetime. Nat Methods 4:555–557PubMedCrossRefGoogle Scholar
  50. Muntz L, Norton TA, Ebling FJ, Kitching JA (1972) The ecology of Lough Ine. XVIII. Factors controlling the distribution of Corynactis viridis Allman. J Anim Ecol 41:735–750CrossRefGoogle Scholar
  51. Notredame C, Higgins D, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205–217PubMedCrossRefGoogle Scholar
  52. Ormö M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ (1996) Crystal structure of the Aequorea victoria green fluorescent protein. Science 273:1392–1395PubMedCrossRefGoogle Scholar
  53. Oswald F, Schmitt F, Leutenegger A, Ivanchenko S, D’angelo C, Salih A, Maslakova S, Bulina M, Schirmbeck R, Nienhaus GU, Matz MV, Wiedenmann J (2007) Contributions of host and symbiont pigments to the coloration of reef corals. Eur J Biochem 274:1102–1122Google Scholar
  54. Patterson GH, Knobel SM, Sharif WD, Kain SR, Piston DW (1997) Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy. Biophys J 73:2782–2790PubMedCrossRefGoogle Scholar
  55. Patterson G, Day RN, Piston D (2001) Fluorescent protein spectra. J Cell Sci 114:837–838PubMedGoogle Scholar
  56. Rambaut A (2007) FigTree, a graphical viewer of phylogenetic trees. Available at:
  57. Relyea RA (2004) Fine-tuned phenotypes: tadpole plasticity under 16 combinations of predators and competitors. Ecology 85:172–179CrossRefGoogle Scholar
  58. Salih A, Larkum A, Cox G, Köhl M, Hoegh-Guldberg O (2000) Fluorescent pigments in corals are photoprotective. Nature 408:850–853PubMedCrossRefGoogle Scholar
  59. Schlichter D, Meier U, Fricke HW (1994) Improvement of photosynthesis in zooxanthellate corals by autofluorescent chromatophores. Oecologia 99:124–131CrossRefGoogle Scholar
  60. Schmieder RW (1991) Ecology of an underwater island. Cordell Expeditions, Walnut CreekGoogle Scholar
  61. Shagin DA, Barsova EV, Yanushevich YG, Fradkov AF, Lukyanov KA, Labas YA, Semenova TN, Ugalde JA, Meyers A, Nunez JM, Widder EA, Lukyanov SA, Matz MV (2004) GFP-like proteins as ubiquitous metazoan superfamily: evolution of functional features and structural complexity. Mol Biol Evol 21:841–850PubMedCrossRefGoogle Scholar
  62. 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 22:1567–1572PubMedCrossRefGoogle Scholar
  63. Shaner NC, Steinbach PA, Tsien RY (2005) A guide to choosing fluorescent proteins. Nat Methods 2:905–909PubMedCrossRefGoogle Scholar
  64. Shu X, Shaner NC, Yarbrough CA, Tsien RY, Remington SJ (2006) Novel chromophores and buried charges control color in mFruits. Biochemistry 45:9639–9647PubMedCrossRefGoogle Scholar
  65. Simms D, Cizdziel PE, Chomczynski P (1993) TRIzol: a new reagent for optimal single-step isolation of RNA. Focus (Life Technologies) 15:99–102Google Scholar
  66. Smith S (2007) Available at:
  67. Swofford DL (2003) PAUP*. Phylogenetic analysis using parsimony (*and other methods).Version 4.0b10. Sinauer & Associates, SunderlandGoogle Scholar
  68. Terskikh A, Fradkov A, Ermakova G, Zaraisky A, Tan P, Kajava AV, Zhao X, Lukyanov S, Matz M, Kim S, Weissman I, Siebert P (2000) "Fluorescent timer": protein that changes color with time. Science 290:1585–1588PubMedCrossRefGoogle Scholar
  69. Tupen JW (1999) Shell form and color variability in Alia carinata (Neogastropoda: Columbellidae). Veliger 42:249–259Google Scholar
  70. Ugalde JA, Chang BSW, Matz MV (2004) Evolution of coral pigments recreated. Science 305:1433PubMedCrossRefGoogle Scholar
  71. Verkhusha VV, Lukyanov KA (2004) The molecular properties and applications of Anthozoa fluorescent proteins and chromoproteins. Nat Biotechnol 22:289–296PubMedCrossRefGoogle Scholar
  72. Wachter RM, Elsliger MA, Kallio K, Hanson GT, Remington SJ (1998) Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein. Structure 6:1267–1277PubMedCrossRefGoogle Scholar
  73. Ward WW (2002) Fluorescent proteins: who’s got ’em and why? In: Stanley PE, Kricka LJ (eds) Bioluminescence and chemiluminescence. World Scientific, SingaporeGoogle Scholar
  74. Ward WW (2005) Biochemical and physical properties of green fluorescent protein. In: Chalfie M, Kain S (eds) Green fluorescent protein: properties, applications and protocols, 2nd ed. Wiley-Liss, Hoboken, New JerseyGoogle Scholar
  75. West HH (1979) Pigmentation in the sea anemone Corynactis californica. Comp Biochem Physiol B 64:195–200CrossRefGoogle Scholar
  76. Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691–699PubMedGoogle Scholar
  77. Wicksten M (1989) Why are there bright colors in sessile marine invertebrates? Bull Mar Sci 45:519–530Google Scholar
  78. Wiedenmann J, Schenk A, Rocker C, Girod A, Spindler K-D, Nienhaus GU (2002) A far-red fluorescent protein with fast maturation and reduced oligomerization tendency from Entacmaea quadricolor (Anthozoa, Actinaria). PNAS 99:11646–11651PubMedCrossRefGoogle Scholar
  79. Wiedenmann J, Ivanchenko S, Oswald F, Nienhaus G (2004) Identification of GFP-like proteins in non-bioluminescent, azooxanthellate Anthozoa opens new perspectives for bioprospecting. Mar Biotech 6:270–277Google Scholar
  80. Wilgenbusch J, Warren D, Swofford DL (2004) AWTY: a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Available at:
  81. Yarbrough D, Wachter RM, Kallio K, Matz MV, Remington SJ (2001) Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-Å resolution. Proc Natl Acad Sci USA 98:462–467PubMedCrossRefGoogle Scholar
  82. Zhang J, Campbell RE, Ting AY, Tsien RY (2002) Creating new fluorescent probes for cell biology. Nat Rev Mol Cell Biol 3:906–918PubMedCrossRefGoogle Scholar
  83. Zmasek C, Eddy S (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17:383–384PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Christine E. Schnitzler
    • 1
    • 2
    • 5
  • Robert J. Keenan
    • 3
  • Robert McCord
    • 4
  • Artur Matysik
    • 3
  • Lynne M. Christianson
    • 1
  • Steven H. D. Haddock
    • 1
  1. 1.Monterey Bay Aquarium Research InstituteMoss LandingUSA
  2. 2.Moss Landing Marine LaboratoriesMoss LandingUSA
  3. 3.Department of Biochemistry & Molecular BiologyUniversity of ChicagoChicagoUSA
  4. 4.Maxygen Inc.Redwood CityUSA
  5. 5.Department of ZoologyOregon State UniversityCorvallisUSA

Personalised recommendations