Green fluorescent proteins (GFPs) are well known for their intensive use in cellular and molecular biology in applications that take advantage of the GFPs self-folding and built-in fluorophore characteristics as biomarker. Occurrence and function of GFPs in nature is less known. For a long time GFPs were described only from some cnidarians, and it is only recently that they were also found in copepod crustaceans. Here we describe the occurrence of a GFP from three species of amphioxus, namely Branchiostoma floridae, B. lanceolatum, and B. belcheri (Chordata: Cephalochordata). This is the first time an endogenous GFP has been found in any representative of the deuterostome branch of the Animal Kingdom. We have isolated and characterized a gene (AmphiGFP) from B. floridae that encodes a GFP protein related to those of cnidarians and copepods in both its amino acid sequence and its predicted higher order structure (an 11-stranded ß-barrel enclosing a fluorophore). Bayesian and maximum parsimony phylogenetic analyses demonstrate that the AmphiGFP protein is markedly more closely related to copepod than to cnidarian GFPs. In adults of all three amphioxus species, the green fluorescence is strikingly concentrated anteriorly. The anterior end is the only body part exposed to light in these shallow-water dwellers, suggesting possible photoreceptive or photoprotective functions for the endogenous GFP.
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