Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment.

David F Gruber,Jelena Platisa,Vincent A Pieribone,John S Sparks,Rob Desalle,Shaadi Mehr,Jean P Gaffney

doi:10.1371/journal.pone.0140972

Abstract

We report the identification and characterization of two new members of a family of bilirubin-inducible fluorescent proteins (FPs) from marine chlopsid eels and demonstrate a key region of the sequence that serves as an evolutionary switch from non-fluorescent to fluorescent fatty acid-binding proteins (FABPs). Using transcriptomic analysis of two species of brightly fluorescent Kaupichthys eels (Kaupichthys hyoproroides and Kaupichthys n. sp.), two new FPs were identified, cloned and characterized (Chlopsid FP I and Chlopsid FP II). We then performed phylogenetic analysis on 210 FABPs, spanning 16 vertebrate orders, and including 163 vertebrate taxa. We show that the fluorescent FPs diverged as a protein family and are the sister group to brain FABPs. Our results indicate that the evolution of this family involved at least three gene duplication events. We show that fluorescent FABPs possess a unique, conserved tripeptide Gly-Pro-Pro sequence motif, which is not found in non-fluorescent fatty acid binding proteins. This motif arose from a duplication event of the FABP brain isoforms and was under strong purifying selection, leading to the classification of this new FP family. Residues adjacent to the motif are under strong positive selection, suggesting a further refinement of the eel protein’s fluorescent properties. We present a phylogenetic reconstruction of this emerging FP family and describe additional fluorescent FABP members from groups of distantly related eels. The elucidation of this class of fish FPs with diverse properties provides new templates for the development of protein-based fluorescent tools. The evolutionary adaptation from fatty acid-binding proteins to fluorescent fatty acid-binding proteins raises intrigue as to the functional role of bright green fluorescence in this cryptic genus of reclusive eels that inhabit a blue, nearly monochromatic, marine environment.

Highlights

The photic marine environment is proving to be a crucible of evolution for novel biofluorescent molecules
Phylogenetic trees were generated and we found that eel fluorescent proteins (FPs) from the families Anguillidae and Chlopsidae are either sister to the FABP7 brain clade, which diverged from primitive fishes, or nested within it
The two major families of fluorescent molecules with sufficient molar brightness and expression to produce a fluorescent signal that is visually evident to humans, green fluorescent protein (GFP) and the current bilirubin binding proteins discussed here, have evolved exclusively in marine organisms

Summary

Introduction

The photic marine environment is proving to be a crucible of evolution for novel biofluorescent molecules. With increasing depth in the ocean, the intensity of sunlight decreases in an approximately exponential manner and the spectral quality of light changes, becoming increasingly restricted to a narrow range of wavelengths of blue light (470–490nm)[1]. This was first qualitatively described by Beebe [2] whose firsthand account conveys how the red, orange, yellow, and green components of sunlight disappeared during his bathysphere descent into the mesopelagic zone, leaving a predominately blue environment. Marine organisms biofluoresce by absorbing the dominant blue light, and reemitting it at a longer, lower energy wavelength, visually resulting in green, orange, and red fluorescence. Many fishes have been shown to possess yellow intraocular (lenses or cornea) filters [18], which could potentially function as long-pass filters and could enable enhanced perception of biofluorescence

Methods

Results

Conclusion