Journal of Molecular Evolution

, Volume 62, Issue 3, pp 332–339 | Cite as

Adaptive Evolution of Multicolored Fluorescent Proteins in Reef-Building Corals

  • Steven F. Field
  • Maria Y. Bulina
  • Ilya V. Kelmanson
  • Joseph P. Bielawski
  • Mikhail V. Matz


Here we investigate the evolutionary scenarios that led to the appearance of fluorescent color diversity in reef-building corals. We show that the mutations that have been responsible for the generation of new cyan and red phenotypes from the ancestral green were fixed with the help of positive natural selection. This fact strongly suggests that the color diversity is a product of adaptive evolution. An unexpected finding was a set of residues arranged as an intermolecular binding interface, which was also identified as a target of positive selection but is nevertheless not related to color diversification. We hypothesize that multicolored fluorescent proteins evolved as part of a mechanism regulating the relationships between the coral and its algal endosymbionts (zooxanthellae). We envision that the effect of the proteins’ fluorescence on algal physiology may be achieved not only through photosynthesis modulation, but also through regulatory photosensors analogous to phytochromes and cryptochromes of higher plants. Such a regulation would require relatively subtle, but spectrally precise, modifications of the light field. Evolution of such a mechanism would explain both the adaptive diversification of colors and the coevolutionary chase at the putative algae-protein binding interface in coral fluorescent proteins.


Green fluorescent protein Fluorescence Color evolution Positive selection Symbiosis 



This work was supported by grants from the National Institute of Health and U.S. Department of Defense (M.V.M.) and grants from the Natural Sciences and Engineering Research Council of Canada and the Genome Atlantic Centre of Genome Canada (J.P.B.). We thank Dr. Nick V. Grishin for providing access to computer resources.

Supplementary material

supp.pdf (1 mb)
Supplementary material


  1. 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 USA 99:12651–12656CrossRefPubMedGoogle Scholar
  2. Anisimova M, Bielawski JP, Yang ZH (2002) Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol Biol Evol 19:950–958PubMedGoogle Scholar
  3. Baker AC, Starger CJ, McClanahan TR, Glynn PW (2004) Corals’ adaptive response to climate change. Nature 430:741–741CrossRefPubMedGoogle Scholar
  4. Bielawski JP, Dunn KA, Sabehi G, Beja O (2004) Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment. Proc Natl Acad Sci USA 101:14824–14829CrossRefPubMedGoogle Scholar
  5. Chang BSW, Ugalde JA, Matz MV (2005) Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins. Methods Enzymol 395:652–670PubMedGoogle Scholar
  6. Douglas AE (1998) Host benefit and the evolution of specialization in symbiosis. Heredity 81:599–603Google Scholar
  7. Frank SA (1996) Host-symbiont conflict over the mixing of symbiotic lineages. Proc Roy Soc Lond Ser B Biol Sci 263:339–344Google Scholar
  8. Gurskaya NG, Savitsky AP, Yanushevich YG, Lukyanov SA, Lukyanov KA (2001) Color transitions in coral’s fluorescent proteins by site-directed mutagenesis. BMC Biochem 2:6CrossRefPubMedGoogle Scholar
  9. Hopf M, Gohring W, Mann K, Timpl R (2001a) Mapping of binding sites for nidogens, fibulin-2, fibronectin and heparin to different IG modules of perlecan. J Mol Biol 311:529–541CrossRefGoogle Scholar
  10. Hopf M, Gohring W, Ries A, Timpl R, Hohenester E (2001b) Crystal structure and mutational analysis of a perlecan-binding fragment of nidogen-1. Nature Structural Biol 8:634–640Google Scholar
  11. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755CrossRefPubMedGoogle Scholar
  12. Iglesias-Prieto R, Beltran VH, LaJeunesse TC, Reyes-Bonilla H, Thome PE (2004) Different algal symbionts explain the vertical distribution of dominant reef corals in the eastern Pacific. Proc Roy Soc Lond Ser B Biol Sci 271:1757–1763Google Scholar
  13. Ivarsson Y, Mackey AJ, Edalat M, Pearson WR, Mannervik B (2003) Identification of residues in glutathione transferase capable of driving functional diversification in evolution—A novel approach to protein redesign. J Biol Chem 278:8733–8738CrossRefPubMedGoogle Scholar
  14. Kawaguti S (1944) On the physiology of reef corals. VI. Study of the pigments. Palao Trop Biol Stn Stud 2:617–674Google Scholar
  15. Kelmanson I, Matz M (2003) Mol basis and evolutionary origins of color diversity in great star coral Montastraea cavernosa (Scleractinia: Faviida). Mol Biol Evol 20:1125–1133PubMedGoogle Scholar
  16. 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 99:4256–4261CrossRefPubMedGoogle Scholar
  17. LaJeunesse TC, Bhagooli R, Hidaka M, DeVantier L, Done T, Schmidt GW, Fitt WK, Hoegh-Guldberg O (2004a) Closely related Symbiodinium spp. differ in relative dominance in coral reef host communities across environmental, latitudinal and biogeographic gradients. Mar Ecol Prog Ser 284:147–161Google Scholar
  18. LaJeunesse TC, Thornhill DJ, Cox EF, Stanton FG, Fitt WK, Schmidt GW (2004b) High diversity and host specificity observed among symbiotic dinoflagellates in reef coral communities from Hawaii. Coral Reefs 23:596–603Google Scholar
  19. Matz MV, Lukyanov KA, Lukyanov SA (2002) Family of the green fluorescent protein: journey to the end of the rainbow. Bioessays 24:953–959CrossRefPubMedGoogle Scholar
  20. Mazel CH, Lesser MP, Gorbunov MY, Barry TM, Farrell JH, Wyman KD, Falkowski PG (2003) Green-fluorescent proteins in Caribbean corals. Limnol Oceanogr 48:402–411Google Scholar
  21. Mizuno H, Mal TK, Tong KI, Ando R, Furuta T, Ikura M, Miyawaki A (2003) Photo-induced peptide cleavage in the green-to-red conversion of a fluorescent protein. Mol Cell 12:1051–1058CrossRefPubMedGoogle Scholar
  22. Prescott M, Ling M, Beddoe T, Oakley AJ, Dove S, Hoegh-Guldberg O, Devenish RJ, Rossjohn J (2003) The 2.2 A crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation. Structure 11:275–284CrossRefPubMedGoogle Scholar
  23. Rowan R (1998) Diversity and ecology of zooxanthellae on coral reefs. J Phycol 34:407–417CrossRefGoogle Scholar
  24. Rowan R, (2004) Coral bleaching—Thermal adaptation in reef coral symbionts. Nature 430:742–742CrossRefPubMedGoogle Scholar
  25. Salih A, Larkum A, Cox G, Kuhl M, Hoegh-Guldberg O (2000) Fluorescent pigments in corals are photoprotective. Nature 408:850–853CrossRefPubMedGoogle Scholar
  26. Sawyer SL, Wu LI, Emerman M, Malik HS (2005) Positive selection of primate TRIM5 alpha identifies a critical species-specific retroviral restriction domain. Proc Natl Acad Sci USA 102:2832–2837CrossRefPubMedGoogle Scholar
  27. Shagin DA, Barsova EV, Yanushevich YG, Fradkov AF, Lukyanov KA, Labas YA, Ugalde JA, Semenova TN, Meyer AS, 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 21:841–850PubMedGoogle Scholar
  28. Suzuki Y, Nei M (2002) Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol Biol Evol 19:1865–1869PubMedGoogle Scholar
  29. Swanson WJ, Nielsen R, Yang QF (2003) Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol 20:18–20PubMedGoogle Scholar
  30. Tavare L (1986) Some probabilistic and statistical problems of the analysis of DNA sequences. Lect Math Life Sci 17:57–86Google Scholar
  31. Thornton JW (2004) Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Rev Genet 5:366–375Google Scholar
  32. Ugalde JA, Chang BSW, Matz MV (2004) Evolution of coral pigments recreated. Science 305:1433CrossRefPubMedGoogle Scholar
  33. Wall MA, Socolich M, Ranganathan R (2000) The structural basis for red fluorescence in the tetrameric GFP homologue DsRed. Nature Struct Biol 7:1133–1138PubMedGoogle Scholar
  34. Woolhouse MEJ, Webster PJ, Domingo E, Charlesworth B, Levin BR (2002) Biol and biomedical implications of the coevolution of pathogens and their hosts. Nature Genet 32:569–577CrossRefPubMedGoogle Scholar
  35. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555–556PubMedGoogle Scholar
  36. Yang ZH (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15:568–573PubMedGoogle Scholar
  37. Yang ZH (2005) The power of phylogenetic comparison in revealing protein function. Proc Natl Acad Sci USA 102:3179–3180PubMedGoogle Scholar
  38. Yang ZH, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503CrossRefPubMedGoogle Scholar
  39. Yang ZH, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19:908–917PubMedGoogle Scholar
  40. Yang ZH, Nielsen R, Goldman N, Pedersen AMK (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431–449PubMedGoogle Scholar
  41. Yanushevich YG, Staroverov DB, Savitsky AP, Fradkov AF, Gurskaya NG, Bulina ME, Lukyanov KA, Lukyanov SA (2002) A strategy for the generation of non-aggregating mutants of Anthozoa fluorescent proteins. FEBS Lett 511:11–14CrossRefPubMedGoogle Scholar
  42. 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-A resolution. Proc Natl Acad Sci USA 98:462–467CrossRefPubMedGoogle Scholar
  43. Zhang JZ, Rosenberg HF (2002) Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates. Proc Natl Acad Sci USA 99:5486–5491PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Steven F. Field
    • 1
  • Maria Y. Bulina
    • 1
    • 2
  • Ilya V. Kelmanson
    • 1
    • 2
  • Joseph P. Bielawski
    • 3
  • Mikhail V. Matz
    • 1
    • 4
  1. 1.Whitney Laboratory for Marine BioscienceUniversity of FloridaSt. AugustineUSA
  2. 2.Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussia
  3. 3.Department of BiologyDalhousie UniversityHalifaxCanada
  4. 4.Department of Molecular Genetics and MicrobiologyUniversity of FloridaGainesvilleUSA

Personalised recommendations