Evolution of retinoid and steroid signaling: vertebrate diversification from an amphioxus perspective

Abstract

Although the physiological relevance of retinoids and steroids in vertebrates is very well established, the origin and evolution of the genetic machineries implicated in their metabolic pathways is still very poorly understood. We investigated the evolution of these genetic networks by conducting an exhaustive survey of components of the retinoid and steroid pathways in the genome of the invertebrate chordate amphioxus (Branchiostoma floridae). Due to its phylogenetic position at the base of chordates, amphioxus is a very useful model to identify and study chordate versus vertebrate innovations, both on a morphological and a genomic level. We have characterized more than 220 amphioxus genes evolutionarily related to vertebrate components of the retinoid and steroid pathways and found that, globally, amphioxus has orthologs of most of the vertebrate components of these two pathways, with some very important exceptions. For example, we failed to identify a vertebrate-like machinery for retinoid storage, transport, and delivery in amphioxus and were also unable to characterize components of the adrenal steroid pathway in this invertebrate chordate. The absence of these genes from the amphioxus genome suggests that both an elaboration and a refinement of the retinoid and steroid pathways took place at the base of the vertebrate lineage. In stark contrast, we also identified massive amplifications in some amphioxus gene families, most extensively in the short-chain dehydrogenase/reductase superfamily, which, based on phylogenetic and genomic linkage analyses, were likely the result of duplications specific to the amphioxus lineage. In sum, this detailed characterization of genes implicated in retinoid and steroid signaling in amphioxus allows us not only to reconstruct an outline of these pathways in the ancestral chordate but also to discuss functional innovations in retinoid homeostasis and steroid-dependent regulation in both cephalochordate and vertebrate evolution.

FIG. 1.—

Vertebrate retinoid (A) and steroid (B) metabolism. (A) The main components of retinoid metabolism, storage, and transport in vertebrates are shown. Proteins are boxed, and retinoids are in black. Proteins of the same family are shown in identical colors. Enzymatic reactions are shown with arrows. The dotted arrow indicates retinoid transport and dotted lines highlight retinoid binding to proteins. (B) The main enzymatic reactions of steroidogenesis in vertebrates are indicated. Enzymatic reactions are shown with arrows. Proteins are boxed, and steroids are in black. Proteins of the same family are shown in identical colors.

FIG. 2.—

Schematic phylogeny of members of the SDR superfamily with activity against retinoids and/or steroids. The nomenclature of the three major SDR clusters (C1, C2, and C3) as well as of the individual SDR families is based on the recent reclassification of the SDR superfamily (Bray et al. 2009; Kallberg et al. 2010). Bootstrap values (NJ/ML) supporting the three major SDR clusters (C1, C2, and C3) and each of the 14 SDR families are indicated. Retinoid (blue) and steroid (orange) activities of the vertebrate enzymes are indicated, illustrating that both enzymatic activities are commonly found within the SDR superfamily, sometimes even within a single SDR family. Vertebrate branches are in green, whereas amphioxus branches are in red. The number of amphioxus sequences in each branch is indicated.

FIG. 3.—

Diagrammatic tree topologies of the (A) Adh, (B) Akr1, (C) Bco, (D) Aldh, (E) iLbp, (F) NlpC/P60, (G) Dgat, (H) Lipocalin, (I) Ttr/Urah, (J) Stra6, (K) Star, (L) Cyp, (M) Hsd3β, and (N) Srd5α families. Simplified phylogenies of the main components of retinoid and steroid metabolism are shown. Vertebrate branches are in green, amphioxus branches are in red, and branches containing sequences from the cnidarian Nematostella vectensis are in yellow.

FIG. 4.—

The evolutionary diversification of the retinoid and steroid genetic machineries in chordates. Gene duplications and functional innovations are shown for both the cephalochordate and the vertebrate lineages. The names of duplicated genes and gene families are indicated for both cephalochordates and vertebrates and several functional innovations resulting from the evolution of novel protein functions are proposed. The “?” highlights that additional studies assessing the biochemical and functional properties of the cephalochordate retinoid and steroid machineries are required to provide experimental support for the hypotheses derived from our evolutionary analyses.