Mammalian Olfactory Receptors

Molecular Mechanisms of Odorant Detection, 3D-Modeling, and Structure-Activity Relationships

Marie-Annick Persuy*; Guenhaël Sanz*; Anne Tromelin┼; Thierry Thomas-Danguin┼; Jean-François Gibrat╬; Edith Pajot-Augy*,1    * INRA UR 1197 NeuroBiologie de l'Olfaction, Domaine de Vilvert, Jouy-en-Josas, France
┼ INRA UMR 1129 Flaveur, Vision et Comportement du Consommateur, Dijon, France
╬ INRA UR1077 Mathématique Informatique et Génome, Domaine de Vilvert, Jouy-en-Josas, France
1 Corresponding author: email address: edith.pajot@jouy.inra.fr

Abstract

This chapter describes the main characteristics of olfactory receptor (OR) genes of vertebrates, including generation of this large multigenic family and pseudogenization. OR genes are compared in relation to evolution and among species. OR gene structure and selection of a given gene for expression in an olfactory sensory neuron (OSN) are tackled. The specificities of OR proteins, their expression, and their function are presented. The expression of OR proteins in locations other than the nasal cavity is regulated by different mechanisms, and ORs display various additional functions.

A conventional olfactory signal transduction cascade is observed in OSNs, but individual ORs can also mediate different signaling pathways, through the involvement of other molecular partners and depending on the odorant ligand encountered. ORs are engaged in constitutive dimers. Ligand binding induces conformational changes in the ORs that regulate their level of activity depending on odorant dose. When present, odorant binding proteins induce an allosteric modulation of OR activity.

Since no 3D structure of an OR has been yet resolved, modeling has to be performed using the closest G-protein-coupled receptor 3D structures available, to facilitate virtual ligand screening using the models. The study of odorant binding modes and affinities may infer best-bet OR ligands, to be subsequently checked experimentally. The relationship between spatial and steric features of odorants and their activity in terms of perceived odor quality are also fields of research that development of computing tools may enhance.

Keywords

Olfactory receptor proteins

Mammals

Odorant binding proteins

Odorant ligands

Dimerization

Allosteric modulation

3D-modeling

Screening

3D-QSAR modeling

1 Mammalian Olfactory Receptors: From Genes to Proteins

Olfactory receptors are predominantly expressed in the main olfactory epithelium located in the nasal cavity. They are the gateways, located across the plasma membranes of olfactory sensory neurons (OSN) cilia, through which the message conveyed by the odorant molecules in the ambient air transit, before being transduced into an electrical signal.

1.1 Genes and pseudogenes

In mammals, there exist several hundred (up to several thousand) OR genes accounting for 1-3% of estimated mammalian gene repertoire,1,2 and representing the largest gene superfamily.

The number of OR genes exceeds 1700 in the rat and is around 860 in humans.3 This abundance is justified by the number of physiological functions in which olfaction is involved (food intake and preferences, search for prey, predator avoidance, social behaviors, mother-young relationships, spatial orientation, stress, etc.), even though this chemical sense was for a while considered to be a minor sense relative to vision. ORs being GPCRs are characterized by seven-transmembrane helices (TMHs), participating in the transmission of the olfactory message carried by the volatile odorant compounds of the environment.4-6 Because ORs are involved in the detection of chemical messages from the environment of animals, their genes have undergone selection pressure, inducing the evolution of the olfactory repertoires of the various species. Some OR genes evolved to nonfunctional pseudogenes7 in varying proportions depending on the species, from ~ 20% in the mouse and dog8,9 to ~ 50-60% in primates and humans1,3,10 (for review, see Ref. 11). Indeed, if the number of OR genes differs from species to species (133 ORs in zebrafish to 1300 in pigs,12 2129 in cows, 4200 in African elephants13) the amount of pseudogenes is also variable. Some primates have less than 400 types of functional ORs (humans and chimpanzees, orangutans, and macaques even less14,15) compared to over 1000 for pigs, rodents and dogs,12,16,17 and 1948 in African elephants.13 However, the cognitive power of these species, i.e., the ability to process olfactory data, allows them to integrate information from complex olfactory environments, beyond simply the number of functional ORs that can be activated.18

Mammalian OR genes are organized in a large number of clusters distributed on many chromosomes e.g., 9 chromosomes for mice,19 all chromosomes except 20, and Y for humans.7 Potentially, coding sequences may predominate on some chromosomes (7, 16, and 17 in humans, for instance7). OR pseudogenes are interspersed with full-length OR genes. Closely located OR genes within a cluster tend to be closely related evolutionarily, while duplication of whole OR gene clusters appears to be rare.20 Generation of this large and diverse multigenic family involved in a key biological function may result from successive duplications of large genomic regions during evolution,11,21 followed by an accumulation of mutations. Moreover, evolutionarily distantly related genes may be found in a given OR gene cluster, and OR genes with a close evolutionary relationship may be located at different clusters or chromosomes,20 suggesting additional chromosomal rearrangements within OR gene clusters and shuffling of the genes from different clusters.

In different species, a number of OR genes exhibit sequence identities above 90%, for instance in dogs and humans,22 humans and other primates,7,14,23-25 rats and mice.25 Man et al.26 showed that orthologs (coded by genes deriving from the same ancestor by speciation) were more similar than paralogs (coded by genes deriving from the same ancestor gene by duplication) when measuring amino acid similarity, using either the whole coding sequence or the 22 amino acids predicted to be involved in ligand binding. In closely related species, orthologs tend to present similar ligand selectivity but important differences in receptor potency (EC50) to a given ligand. However, while paralogous ORs within the same species respond to a common ligand only 33% of the time, orthologous ORs respond to a common ligand 82% of the time on average (from 93% for human-chimpanzee orthologs to 83% for human-mouse orthologs).25 Moreover, the genetic variation in the coding region of OR genes may contribute to the variation in odor perception among individuals.

Mammalian OR genes are divided into two classes. Class I was initially ascribed to fish OR genes for which OR proteins mostly bind hydrophilic odorants (amino acids), while Class II was related to mammalian OR genes with OR proteins binding hydrophobic odorants. In fact, recent studies show that Class I ORs can be subdivided into several groups, among which the a group is proposed to encode ORs specific to airborne odorants, while the d, ?, ?, and ? group genes appear to primarily detect water-soluble odorants. Only the a group of Class I is present in mammals, together with the Class II genes (which consists only of ? group genes).27 Fishes encode only Class I genes, of groups d, ?, ?, and ?, and in amphibians OR genes are found from both Classes (Fig. 1). Interestingly, both in the human and mouse genomes, all Class I OR genes (thus of the a group) are encoded in a single genomic cluster, contrary to Class II genes.11,28 Pseudogenes are present in a lower proportion among human Class I ORs (52%) than Class II ORs (77%),1 suggesting that "fish" OR genes still have a functional significance.

OR genes exhibit a relatively well-conserved structure including one or several small untranslated exons at their 5´ termini, followed by a large 3-10 kb intron preceding a single coding exon of...