Neofunctionalization in Vertebrates: The Example of Retinoic Acid Receptors

Hector Escriva,Jérôme Cartry,Stéphanie Bertrand,Marilyne Duffraisse,Muriel Umbhauer,Vincent Laudet,Hinrich Gronemeyer,Marc Robinson-Rechavi,Pierre Germain,Linda Holland

doi:10.1371/journal.pgen.0020102

Abstract

Understanding the role of gene duplications in establishing vertebrate innovations is one of the main challenges of Evo-Devo (evolution of development) studies. Data on evolutionary changes in gene expression (i.e., evolution of transcription factor-cis-regulatory elements relationships) tell only part of the story; protein function, best studied by biochemical and functional assays, can also change. In this study, we have investigated how gene duplication has affected both the expression and the ligand-binding specificity of retinoic acid receptors (RARs), which play a major role in chordate embryonic development. Mammals have three paralogous RAR genes—RARα, β, and γ—which resulted from genome duplications at the origin of vertebrates. By using pharmacological ligands selective for specific paralogues, we have studied the ligand-binding capacities of RARs from diverse chordates species. We have found that RARβ-like binding selectivity is a synapomorphy of all chordate RARs, including a reconstructed synthetic RAR representing the receptor present in the ancestor of chordates. Moreover, comparison of expression patterns of the cephalochordate amphioxus and the vertebrates suggests that, of all the RARs, RARβ expression has remained most similar to that of the ancestral RAR. On the basis of these results together, we suggest that while RARβ kept the ancestral RAR role, RARα and RARγ diverged both in ligand-binding capacity and in expression patterns. We thus suggest that neofunctionalization occurred at both the expression and the functional levels to shape RAR roles during development in vertebrates.

Highlights

The origin of organismal complexity is generally thought to be tightly linked to the evolution of new gene functions
Our results show that all the chordate retinoic acid receptor (RAR), including the reconstructed ancestral RAR (AncRAR), are able to transactivate in a dosedependent manner with all-trans retinoic acid (ATRA)
Despite their different transactivation patterns, all the chordate RARs bind the b-specific retinoid BMS641. This suggests that the ligand-binding pocket (LBP) of all the chordate RARs share common features

Summary

Introduction

The origin of organismal complexity is generally thought to be tightly linked to the evolution of new gene functions. Susumu Ohno proposed in 1970 that, in contrast to mutations, gene duplications can create evolutionary novelties [1]. He proposed, based on the genome weight of different deuterostomes, that two periods of genome duplication occurred during evolution of the vertebrate lineage [1]. This hypothesis has been revisited and discussed by different authors, and even if the precise timing and mechanisms of these gene duplications are still under discussion, their general importance during vertebrate evolution is widely accepted [2,3,4]. Many data suggest that the duplications took place at two distinct periods during evolution, one before the split of agnathans (hagfish and lampreys) and one before the split of cartilaginous fishes [9–

Methods

Results

Conclusion