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MBE Advance Access originally published online on February 12, 2004
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Mol. Biol. Evol. 21(5):841-850. 2004
DOI: 10.1093/molbev/msh079
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

GFP-like Proteins as Ubiquitous Metazoan Superfamily: Evolution of Functional Features and Structural Complexity

Dmitry A. Shagin*,1, Ekaterina V. Barsova*,1, Yurii G. Yanushevich*, Arkady F. Fradkov*, Konstantin A. Lukyanov*, Yulii A. Labas{dagger}, Tatiana N. Semenova{ddagger}, Juan A. Ugalde§,||, Ann Meyers§, Jose M. Nunez§, Edith A. Widder, Sergey A. Lukyanov* and Mikhail V. Matz§,#

* Institute of Bioorganic Chemistry RAS, Moscow, Russia
{dagger} Institute of Biochemistry RAS, Moscow, Russia
{ddagger} Shirshov Institute of Oceanology RAS, Moscow, Russia
§ Whitney laboratory, University of Florida, St. Augustine
|| Laboratory of Bioinformatics and Gene Expression, INTA–University of Chile, Santiago, Chile
Harbor Branch Oceanographic Institution, Fort Pierce, Florida
# Department of Molecular Genetics and Microbiology, University of Florida, Gainesville

E-mail address: matz{at}whitney.ufl.edu.

Homologs of the green fluorescent protein (GFP), including the recently described GFP-like domains of certain extracellular matrix proteins in Bilaterian organisms, are remarkably similar at the protein structure level, yet they often perform totally unrelated functions, thereby warranting recognition as a superfamily. Here we describe diverse GFP-like proteins from previously undersampled and completely new sources, including hydromedusae and planktonic Copepoda. In hydromedusae, yellow and nonfluorescent purple proteins were found in addition to greens. Notably, the new yellow protein seems to follow exactly the same structural solution to achieving the yellow color of fluorescence as YFP, an engineered yellow-emitting mutant variant of GFP. The addition of these new sequences made it possible to resolve deep-level phylogenetic relationships within the superfamily. Fluorescence (most likely green) must have already existed in the common ancestor of Cnidaria and Bilateria, and therefore GFP-like proteins may be responsible for fluorescence and/or coloration in virtually any animal. At least 15 color diversification events can be inferred following the maximum parsimony principle in Cnidaria. Origination of red fluorescence and nonfluorescent purple-blue colors on several independent occasions provides a remarkable example of convergent evolution of complex features at the molecular level.

Key Words: DsRed • chromophore • coral • color • nidogen • convergent evolution


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