The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision

Abstract

Recently, much progress has been made in elucidating the chemistry and metabolism of retinoids and carotenoids, as well as the structures of processing proteins related to vision. Carotenoids and their retinoid metabolites are isoprenoids, so only a limited number of chemical transformations are possible, and just a few of these occur naturally. Although there is an intriguing evolutionary conservation of the key components involved in the production and recycling of chromophores, these genes have also adapted to the specific requirements of insect and vertebrate vision. These 'ancestral footprints' in animal genomes bear witness to the common origin of the chemistry of vision, and will further stimulate research across evolutionary boundaries.

Box 1, Figure I. Key components (highlighted in blue) in the pathways for chromophore production are well conserved between flies and mammals.

Figure 1. Key enzymatic steps in carotenoid/retinoid metabolism in insects and mammals

A comparison of the chemical transformations of carotenoids and their retinoid metabolites in the pathways for chromophore production in different animal classes. These include oxidative cleavage of double bonds, oxidation of alcohols to aldehydes and aldehydes to acids and aldehyde reduction to alcohols, esterification of alcohols, hydroxylation of carbons in ionone ring structures, and trans-to-cis isomerization of carbon-carbon double bonds. A) In insects, [i] carotenoids such as zeaxanthin are converted to one molecule of 11-cis and one molecule of all-trans-3-hydroxy-retinal in an isomerooxygenase reaction. [ii] all-trans-3-hydroxy-Retinal is converted to all-trans-3-hydroxy-retinol. [iii] all-trans-3-hydroxy-Retinol is light-dependently isomerized to 11-cis-3-hydroxy-retinol. [iv] 11-cis-3-hydroxy-Retinol is oxidized to 11-cis-3-hydroxy-retinal. B) In mammals, [i] β,β-carotene is symmetrically cleaved to two molecules of all-trans-retinal. [ii] all-trans-Retinal is reduced to all-trans-retinol (vitamin A). [iii] all-trans-Retinol is converted to retinyl esters for storage or [iv] formation of 11-cis-retinol. [v] 11-cis-Retinol is oxidized to 11-cis-retinal. [vi] all-trans-Retinal can be also oxidized to retinoic acid.

Figure 2. The visual cycle regenerates 11-cis-RAL

In rod cells, 11-cis-retinal couples to a protein opsin, forming rhodopsin. Absorption of a photon of light by rhodopsin causes photoisomerization of 11-cis-RAL to all-trans-RAL leading to release of all-trans-RAL from the chromophore-binding pocket of opsin [i]. [ii] All-trans-RAL is reduced to all-trans-retinol in a reversible reaction catalyzed by an NADPH-dependent all-trans-RDH. [iii] All-trans-ROL diffuses into the RPE where it is esterified in a reaction catalyzed by LRAT. [iv] There all-trans-RE is the substrate for RPE65 that converts it to 11-cis-ROL, which is further oxidized back to 11-cis-RAL by RDH5, RDH11 and other RDHs [v]. [vi] 11-cis-RAL formed in the RPE diffuses back into the ROS and COS, where it completes the cycle by recombining with opsins to form rhodopsin and cone pigments.

Figure 3. Crystal structures of proteins involved in the visual cycle, retinoid transport and phototransduction

A variety of protein folds are utilized in nature to bind retinoids for metabolism, transport and signal transduction. In panels A-F and H, β strands and α helices are colored blue and green, respectively. A) Apocarotenoid oxygenase (ACO) from Synechocystis (PDB ID: 2BIW). B) 65 kDa retinal pigment epithelium-specific protein (RPE65, retinoid isomerase) from Bos taurus (PDB ID: 3FSN). The arrow indicates an insertion found in vertebrate members of the carotenoid cleavage enzyme family but not in cyanobacterial members. Despite the overall similar architecture of A) and B), the proteins catalyze fundamentally different reactions and have only about 22% sequence identity. C) Human serum retinol-binding protein (PDB ID: 1RBP). D) Cellular retinol-binding protein from Rattus norvegicus (PDB ID: 1CRP). E) Module two of Xenopus laevis interphotoreceptor retinoid-binding protein (PDB ID: 1J7X). F) Human cellular retinaldehyde-binding protein (PDB ID: 3HY5). Proteins that preferentially bind all-trans-retinol (C and D) have retinoid binding sites composed exclusively of β strands whereas those proteins that bind 11-cis-retinal (E and F) are composed of a mixture of α helices and β sheets. G) Structural superpositioning of the C-terminal domain of CRALBP and the B domain of IRBP module 2 reveals similar chain folds. Superimposed structures of the C-terminal domain of CRALBP consisting of residues 132-306 (in blue) and the B domain of IRBP module two consisting of residues 89-169, 194-240 and 275-303 (in green) are shown. The bound 11-cis-retinal ligand in the CRALBP structure is shown as orange sticks. Both domains exhibit asymmetric αβα sandwich folds that superimpose with an RMSD of 3.5 Å over 107 matched Cα positions. This observation might indicate that the 11-cis-retinoid-binding site of IRBP resides in the B domain. The superposition was performed with the DALI server (http://ekhidna.biocenter.helsinki.fi/dali_server/). H) Ground-state rhodopsin from Bos taurus (PDB ID: 1U19). The retinylidene binding site is composed entirely of α helices.

Figure 4. Observed and hypothetical mechanisms by which retinoid isomerization occurs

A) Photoisomerization. Here energy from visible light temporarily reduces the π bond order through generation of anti-bonding orbitals of the polyene chain that allow rotation about the σ bonds. This mechanism is found throughout nature for both trans to cis and cis to trans isomerization reactions. B) Putative unimolecular nucleophilic substitution. In this mechanism, dissociation of a leaving group that may be promoted by a Lewis acid (LA) creates a retinyl carbocation with a lowered π bond order. Consequently, the activation energy for geometric isomerization is reduced. C) Putative bimolecular nucleophilic substitution. Here substitution of an active site nucleophile (Nu:) for the terminal retinoid R group and the consequent rearrangement of double bonds results in an enzyme-retinoid covalent intermediate with a single bond connecting the retinyl C11 and C12 atoms. After low energy rotation, a strong nucleophile, such as hydroxide, attacks the retinyl C15 atom, which rearranges the double bonds locking the C11-C12 in a cis configuration and leading to expulsion of the enzyme-linked nucleophile. D) Saturation/desaturation. Here, reduction of a π bond by addition of two hydrogen atoms allows free rotation of the C11-C12 sigma bond. Subsequent removal of H₂ locks C11-C12 in the cis configuration.