Phylogenetic analysis of the metazoan carotenoid oxygenase superfamily: a new ancestral gene assemblage of BCO-like (BCOL) proteins

Eugenia Poliakov,Joseph Soucy,Igor B Rogozin,Susan Gentleman,T Michael Redmond

doi:10.1038/s41598-017-13521-x

Abstract

Here we describe a new family of carotenoid cleavage oxygenases (CCOs) in metazoans, the BCO2-like (BCOL) clade, which contains lancelet, nematode, and molluscan carotenoid oxygenase sequences. Phylogenetic analysis of CCOs in all kingdoms of life confirmed that the BCOL enzymes are an independent clade of ancient origin. One of the predicted lancelet BCOL proteins, cloned and analyzed for carotenoid cleavage activity in a bacterial carotenoid expression system, had activity similar to lancelet BCO2 proteins, although with a preference for cis isomers. Our docking predictions correlated well with the cis-favored activity. The extensive expansions of the new animal BCOL family in some species (e.g., lancelet) suggests that the carotenoid cleavage oxygenase superfamily has evolved in the “extremely high turnover” fashion: numerous losses and duplications of this family are likely to reflect complex regulation processes during development, and interactions with the environment. These findings also serve to provide a rationale for the evolution of the BCO-related outlier RPE65 retinol isomerase, an enzyme that does not utilize carotenoids as substrate or perform double-bond cleavage.

Highlights

Carotenoids comprise a major class of molecules in organisms such as algae and plants, where they are employed in photosynthetic light harvesting and light protection
We serendipitously found a novel family of animal BCO-like (BCOL) proteins with members found in lancelet (8 proteins with 23–28% amino acid identity with lamprey BCO2 in protein database analysis) and representatives in several other non-chordate species
In all four phylogenetic trees obtained, based on the maximum likelihood (ML), neighbor-joining (NJ), maximum parsimony (MP) and minimum evolution (ME) methods, BCO2-like oxygenases (BCOLs) sequences form a separate clade with the reliable bootstrap support: 44% (ML), 66% (MP), 98% (ME) and 99% (NJ) and are likely to be monophyletic (Fig. 2, Supplemental Figure S1)

Summary

Introduction

Carotenoids comprise a major class of molecules in organisms such as algae and plants, where they are employed in photosynthetic light harvesting and light protection. Crystal structures of the cyanobacteria Synechocystis apocarotenoid oxygenase (ACO)[2], vertebrate RPE65 retinol isomerase from Bos taurus[3], plant viviparous[14] (VP14) from Zea mays[4], and bacterial resveratrol-cleaving dioxygenase NOV1 from Novosphingobium[5] confirm the conservation of overall fold and active site arrangement in all superfamily members. Genetic studies of “yellow fat” phenotype in cattle, sheep, and chicken BCO2 mutations show that BCO2 is implicated in carotenoid homeostasis of various tissues[18,19,20,21] Given such promiscuous substrate specificity of BCO2-like proteins, we believe they could adapt to the specific carotenoid environment of different animals. The functional significance of this clade in those organisms in which it is expressed is not yet clear; given the phylogenetic distribution and the characteristics of the BCOLs, a role in carotenoid management is indicated

Methods

Results

Conclusion