The human olfactory receptor gene family

Competitive and noncompetitive odorant interactions in the early neural coding of odorant mixtures

Most olfactory receptor neurons (ORNs) express a single type of olfactory receptor that is differentially sensitive to a wide variety of odorant molecules. The diversity of possible odorant-receptor interactions raises challenging problems for the coding of complex mixtures of many odorants, which make up the vast majority of real world odors. Pure competition, the simplest kind of interaction, arises when two or more agonists can bind to the main receptor site, which triggers receptor activation, although only one can be bound at a time. Noncompetitive effects may result from various mechanisms, including agonist binding to another site, which modifies the receptor properties at the main binding site. Here, we investigated the electrophysiological responses of rat ORNs in vivo to odorant agonists and their binary mixtures and interpreted them in the framework of a quantitative model of competitive interaction between odorants. We found that this model accounts for all concentration-response curves obtained with single odorants and for about half of those obtained with binary mixtures. In the other half, the shifts of curves along the concentration axis and the changes of maximal responses with respect to model predictions, indicate that noncompetitive interactions occur and can modulate olfactory receptors. We conclude that, because of their high frequency, the noncompetitive interactions play a major role in the neural coding of natural odorant mixtures. This finding implies that the CNS activity caused by mixtures will not be easily analyzed into components, and that mixture responses will be difficult to generalize across concentration.

Searching for the ligands of odorant receptors

Through the sense of smell mammals can detect and discriminate between a large variety of odorants present in the surrounding environment. Odorants bind to a large repertoire of odorant receptors located in the cilia of olfactory sensory neurons of the nose. Each olfactory neuron expresses one single type of odorant receptor, and neurons expressing the same type of receptor project their axons to one or a few glomeruli in the olfactory bulb, creating a map of odorant receptor inputs. The information is then passed on to other regions of the brain, leading to odorant perception. To understand how the olfactory system discriminates between odorants, it is necessary to determine the odorant specificities of individual odorant receptors. These studies are complicated by the extremely large size of the odorant receptor family and by the poor functional expression of these receptors in heterologous cells. This article provides an overview of the methods that are currently being used to investigate odorant receptor-ligand interactions.

The peripheral olfactory system of the domestic chicken: physiology and development

Olfaction is a ubiquitous sensory system found in all terrestrial vertebrates. Birds use olfaction for several important activities such as feeding and mating; thus, understanding bird biology would also require the systematic study olfaction. In addition, the olfactory system has several unique features that are useful for the study of nervous system function and development, including a large multigene family for olfactory receptor expression, peripheral neurons that regenerate, and a complex system for sensory innervation of the olfactory bulb. We focused on physiological, anatomical and behavioral approaches to study the chick olfactory neurons and the olfactory bulb. Chick olfactory neurons displayed some properties similar to those found in mature neurons of other vertebrate species, and other properties that were unique. Since information from these neurons is initially processed in the olfactory bulb, we also conducted preliminary studies on the developmental timeline of this structure and showed that glomerular structures are organized in ovo during a critical time period, during which embryonic chicks can form behavioral associations with odorants introduced in ovo. Lastly, we have shown that chick olfactory neurons can grow and mature in vitro, allowing their use in cell culture studies. These results collectively demonstrate some of the features of the olfactory system that are common to all vertebrates, and some that are unique to birds. These highlight the potential for the use of the physiology and development of the olfactory system as a model system for avian brain neurobiology.

Monoallelic expression of multiple genes in the CNS

The inheritance pattern of a number of major genetic disorders suggests the possible involvement of genes that are expressed from one allele and silent on the other, but such genes are difficult to detect. Since DNA methylation in regulatory regions is often a mark of gene silencing, we modified existing microarray-based assays to detect both methylated and unmethylated DNA sequences in the same sample, a variation we term the MAUD assay. We probed a 65 Mb region of mouse Chr 7 for gene-associated sequences that show two distinct DNA methylation patterns in the mouse CNS. Selected genes were then tested for allele-specific expression in clonal neural stem cell lines derived from reciprocal F(1) (C57BL/6xJF1) hybrid mice. In addition, using a separate approach, we directly analyzed allele-specific expression of a group of genes interspersed within clusters of OlfR genes, since the latter are subject to allelic exclusion. Altogether, of the 500 known genes in the chromosomal region surveyed, five show monoallelic expression, four identified by the MAUD assay (Agc1, p (pink-eyed dilution), P4ha3 and Thrsp), and one by its proximity to OlfR genes (Trim12). Thrsp (thyroid hormone responsive SPOT14 homolog) is expressed in hippocampus, but the human protein homolog, S14, has also been implicated in aggressive breast cancer. Monoallelic expression of the five genes is not coordinated at a chromosome-wide level, but rather regulated at individual loci. Taken together, our results suggest that at least 1% of previously untested genes are subject to allelic exclusion, and demonstrate a dual approach to expedite their identification.

A nonfunctioning single nucleotide polymorphism in olfactory receptor gene family is associated with the forced expiratory volume in the first second/the forced vital capacity values of pulmonary function test in a Japanese population

The forced expiratory volume in the first second (FEV1.0)/the forced vital capacity (FVC) is an important index of a single forced expiration. Ectopic expression of the human olfactory receptor (OR) gene family in the lungs has suggested its potential involvement of respiratory physiology. We hypothesized that the individual variability of FEV1.0/FVC value may be attributed to the genetic variance of the OR gene family caused by the nonfunctioning SNPs (nSNPs). We conducted quantitative trait locus (QTL) analyses of population having the 7 OR gene nSNPs and FEV1.0/FVC values by ANOVA, in 2970 samples in the Yamagata Takahata cohort. We found significant association of one nSNP [rs10838851, OR, family 4, subfamily X, member 1 (OR4X1) gene, Tyr273Ter*] with FEV1.0/FVC (%) (P = 0.008). The FEV1.0/FVC value (%) of population having OR4X1 gene nSNP Ter*/Ter*, Ter*/Tyr, and Tyr/Tyr were 78.9 +/- 0.2, 78.2 +/- 0.2, and 77.7 +/- 0.4, respectively. Haplotype-based analysis of the OR4X1 gene with FEV1.0/FVC values demonstrated that two exclusive haplotypes [Hap-1/Hap-2 (frequency 0.669/0.330): SNP1 (rs7106648)T/A-SNP2 (rs871249)G/A-SNP3 (rs713325)G/A-SNP4 (rs10838851)A (Ter*)/T (Tyr)-SNP5 (rs4752923)G/A-SNP6 (rs960640)G/A] were significantly associated with FEV1.0/FVC values (global P = 0.005). These results suggest that OR4X1 may be one of the genes that contribute to the individual variability of FEV1.0/FVC value in pulmonary function test.

The sense of smell: molecular basis of odorant recognition

Most animal species rely on odorant compounds to locate food, predators, or toxins. The sense of smell is also involved in animal communication, and revealing the underlying mechanisms will therefore facilitate a deeper understanding of animal behaviour. Since the 1940s different theories have speculated on the fundamental basis of olfaction. It was assumed that odorant molecules were recognized by selective protein receptors in the nose, triggering a nervous signal processed by the brain. The discovery of these receptors in the early 1990s allowed great progress in understanding the physiological and biochemical principles of olfaction. An overview of the different mechanisms involved in the coding of odour character as well as odour intensity is presented here, focusing on the biochemical basis of odorant recognition. Despite the enormous progress achieved in recent years, details of odorant-receptor interaction at the molecular level and the mechanisms of olfactory receptor activation are poorly understood. The likely role of metal ions in odorant recognition is discussed, and also the perireceptor events involved in odorant transport and biotransformation, with a view to providing a comprehensive overview of mammalian olfaction to guide future computational structural models and the design of functional experiments. Recent studies have analysed the olfactory genome of several species, providing information about the evolution of olfaction. The role of the olfactory system in animal communication is also described.

Co-regulation of a large and rapidly evolving repertoire of odorant receptor genes

The olfactory system meets niche- and species-specific demands by an accelerated evolution of its odorant receptor repertoires. In this review, we describe evolutionary processes that have shaped olfactory and vomeronasal receptor gene families in vertebrate genomes. We emphasize three important periods in the evolution of the olfactory system evident by comparative genomics: the adaptation to land in amphibian ancestors, the decline of olfaction in primates, and the delineation of putative pheromone receptors concurrent with rodent speciation. The rapid evolution of odorant receptor genes, the sheer size of the repertoire, as well as their wide distribution in the genome, presents a developmental challenge: how are these ever-changing odorant receptor repertoires coordinated within the olfactory system? A central organizing principle in olfaction is the specialization of sensory neurons resulting from each sensory neuron expressing only ~one odorant receptor allele. In this review, we also discuss this mutually exclusive expression of odorant receptor genes. We have considered several models to account for co-regulation of odorant receptor repertoires, as well as discussed a new hypothesis that invokes important epigenetic properties of the system.

Extensive gains and losses of olfactory receptor genes in mammalian evolution

Odor perception in mammals is mediated by a large multigene family of olfactory receptor (OR) genes. The number of OR genes varies extensively among different species of mammals, and most species have a substantial number of pseudogenes. To gain some insight into the evolutionary dynamics of mammalian OR genes, we identified the entire set of OR genes in platypuses, opossums, cows, dogs, rats, and macaques and studied the evolutionary change of the genes together with those of humans and mice. We found that platypuses and primates have <400 functional OR genes while the other species have 800–1,200 functional OR genes. We then estimated the numbers of gains and losses of OR genes for each branch of the phylogenetic tree of mammals. This analysis showed that (i) gene expansion occurred in the placental lineage each time after it diverged from monotremes and from marsupials and (ii) hundreds of gains and losses of OR genes have occurred in an order-specific manner, making the gene repertoires highly variable among different orders. It appears that the number of OR genes is determined primarily by the functional requirement for each species, but once the number reaches the required level, it fluctuates by random duplication and deletion of genes. This fluctuation seems to have been aided by the stochastic nature of OR gene expression.

Differences in (-)citronellal binding to various odorant receptors

To test the hypothesis that olfactory receptors (ORs) recognize different molecular features of odor molecules termed "odotypes", we studied receptor-ligand interactions of two human and two mouse ORs, recognizing (-)citronellal. Structurally similar receptors provide identical binding pockets (OLFR43, OR1A1, and OR1A2), and have comparable EC(50) values. Other ORs with lower sequence identity bind (-)citronellal in a different way, leading to different EC(50) values.

Promotor elements governing the clustered expression pattern of odorant receptor genes

Odorant receptor (OR) genes of family mOR262 are only expressed in olfactory sensory neurons (OSNs) segregated in a central patch of the nasal turbinates; they comprise conserved DNA elements upstream of their transcription start sites that are proposed to govern the distinct expression pattern. In mouse lines with a transgene containing the coding sequence and a short upstream region of the mOR262-12 gene, expression was restricted to OSNs that were segregated in the characteristic central patch, although the number of cells varied considerably. Only in one line, the transgene was also expressed in OSNs ectopically positioned outside the patch. The axons of transgene-expressing OSNs co-converged with those expressing the endogenous gene. The transgene was found to be expressed in a mutually exclusive manner and from only one allele indicating that the conserved upstream DNA elements play a critical role in controlling the specific expression pattern of these genes.

Ligand screening system using fusion proteins of G protein-coupled receptors with G protein alpha subunits

G protein-coupled receptors (GPCRs) constitute one of the largest families of genes in the human genome, and are the largest targets for drug development. Although a large number of GPCR genes have recently been identified, ligands have not yet been identified for many of them. Various assay systems have been employed to identify ligands for orphan GPCRs, but there is still no simple and general method to screen for ligands of such GPCRs, particularly of G(i)-coupled receptors. We have examined whether fusion proteins of GPCRs with G protein alpha subunit (Galpha) could be utilized for ligand screening and showed that the fusion proteins provide an effective method for the purpose. This article focuses on the followings: (1) characterization of GPCR genes and GPCRs, (2) identification of ligands for orphan GPCRs, (3) characterization of GPCR-Galpha fusion proteins, and (4) identification of ligands for orphan GPCRs using GPCR-Galpha fusion proteins.

Structural determinants of odorant recognition by the human olfactory receptors OR1A1 and OR1A2

An interaction of odorants with olfactory receptors is thought to be the initial step in odorant detection. However, ligands have been reported for only 6 out of 380 human olfactory receptors, with their structural determinants of odorant recognition just beginning to emerge. Guided by the notion that amino acid positions that interact with specific odorants would be conserved in orthologs, but variable in paralogs, and based on the prediction of a set of 22 of such amino acid positions, we have combined site-directed mutagenesis, rhodopsin-based homology modelling, and functional expression in HeLa/Olf cells of receptors OR1A1 and OR1A2. We found that (i) their odorant profiles are centred around citronellic terpenoid structures, (ii) two evolutionary conserved amino acid residues in transmembrane domain 3 are necessary for the responsiveness of OR1A1 and the mouse ortholog Olfr43 to (S)-(-)-citronellol, (iii) changes at these two positions are sufficient to account for the differential (S)-(-)-citronellol responsiveness of the paralogs OR1A1 and OR1A2, and (iv) the interaction sites for (S)-(-)-citronellal and (S)-(-)-citronellol differ in both human receptors. Our results show that the orientation of odorants within a homology modelling-derived binding pocket of olfactory receptor orthologs is defined by evolutionary conserved amino acid positions.

SenseLab: new developments in disseminating neuroscience information

This article presents the latest developments in neuroscience information dissemination through the SenseLab suite of databases: NeuronDB, CellPropDB, ORDB, OdorDB, OdorMapDB, ModelDB and BrainPharm. These databases include information related to: (i) neuronal membrane properties and neuronal models, and (ii) genetics, genomics, proteomics and imaging studies of the olfactory system. We describe here: the new features for each database, the evolution of SenseLab's unifying database architecture and instances of SenseLab database interoperation with other neuroscience online resources.

Enterochromaffin cells of the human gut: sensors for spices and odorants

BACKGROUND & AIMS

Release of serotonin from mucosal enterochromaffin cells triggered by luminal substances is the key event in the regulation of gut motility and secretion. We were interested to know whether nasal olfactory receptors are also expressed in the human gut mucosa by enterochromaffin cells and whether their ligands and odorants present in spices, fragrances, detergents, and cosmetics cause serotonin release.

METHODS

Receptor expression was studied by the reverse-transcription polymerase chain reaction method in human mucosal enterochromaffin cells isolated by laser microdissection and in a cell line derived from human enterochromaffin cells. Activation of the cells by odorants was investigated by digital fluorescence imaging using the fluorescent Ca(2+) indicator Fluo-4. Serotonin release was measured in culture supernatants by a serotonin enzyme immunoassay and amperometry using carbon fiber microelectrodes placed on single cells.

RESULTS

We found expression of 4 olfactory receptors in microdissected human mucosal enterochromaffin cells and in a cell line derived from human enterochromaffin cells. Ca(2+) imaging studies revealed that odorant ligands of the identified olfactory receptors cause Ca(2+) influx, elevation of intracellular free Ca(2+) levels, and, consequently, serotonin release.

CONCLUSIONS

Our results show that odorants present in the luminal environment of the gut may stimulate serotonin release via olfactory receptors present in human enterochromaffin cells. Serotonin controls both gut motility and secretion and is implicated in pathologic conditions such as vomiting, diarrhea, and irritable bowel syndrome. Thus, olfactory receptors are potential novel targets for the treatment of gastrointestinal diseases and motility disorders.

Genetic component of identification, intensity and pleasantness of odours: a Finnish family study

Although potential odorant receptor genes have been identified, the precise genetic component of perception of odours is still obscure. Although there is some evidence for heritability of a few olfactory-related traits, no genome-wide search for loci harboring underlying genes has been published to date. We performed a genome-wide scan to identify loci affecting the identification, intensity and pleasantness of 12 odours (cinnamon, turpentine, lemon, smoke, chocolate, rose, paint thinner, banana, pineapple, gasoline, soap, onion) using 146 Finnish adults from 26 families. Several of these traits showed heritable variation in the families. Suggestive evidence of linkage was found for the pleasantness of cinnamon odour (h(2)=61%) on chromosome 4q32.3 (multipoint logarithm of the odds (LOD) score 3.01), as well as for the perceived intensity of paint thinner odour (h(2)=31%) on chromosome 2p14 (multipoint LOD score 2.55). As these loci do not contain any known human odorant receptor genes, they may rather harbor genes that affect the central processing than the peripheral detection of the odour signal. Thus, perception of odours is potentially modified by genes other than those encoding odorant receptors.

Olfactory sensitivity through the course of psychosis: Relationships to olfactory identification, symptomatology and the schizophrenia odour

There is some evidence for an unusual body odour in schizophrenia that has been linked to a hexenoic acid derivative (trans-3-methyl-2-hexenoic acid; MHA). Poor body odour has been linked to increased negative symptoms and reduced olfactory identification ability. However, the relationship between these findings and MHA, including olfactory sensitivity for MHA, has not been examined. Olfactory sensitivity thresholds were assessed for MHA and n-butyl-alcohol (NBA), in normal controls (CTL; n=24), patients with chronic schizophrenia (CHR; n=32) and a first-episode psychosis cohort (FE; n=31). In addition, forced choice detection of the pheromonal steroids 5-alpha-androst-16-en-3-one, androsterone-sulphate and estrone-3-sulphate was performed along with a measure of olfactory identification. CHR patients had significantly reduced sensitivity to MHA, but not NBA, compared to FE and CTL subjects. While sensitivity to pheromones was not different between the groups, CHR patients who could not detect them also showed poorer sensitivity to MHA. Further, the CHR group showed a significant association between reduced MHA sensitivity and greater levels of disorganised and negative symptoms. No relationships between identification and sensitivity for any substance were found. Our findings are the first to report reduced sensitivity for MHA in chronic schizophrenia patients, in the absence of similar impairment for more traditionally used substances. This may be linked to olfactory habituation effects, abnormal chemical processing or a genetic predisposition.

Molecular and genomic characterisation of cryptic chromosomal alterations leading to paternal duplication of the 11p15.5 Beckwith-Wiedemann region

BACKGROUND

Beckwith-Wiedemann syndrome (BWS) is an overgrowth disorder with increased risk of paediatric tumours. The aetiology involves epigenetic and genetic alterations affecting the 11p15 region, methylation of the differentially methylated DMR2 region being the most common defect, while less frequent aetiologies include mosaic paternal 11p uniparental disomy (11patUPD), maternally inherited mutations of the CDKN1C gene, and hypermethylation of DMR1. A few patients have cytogenetic abnormalities involving 11p15.5.

METHODS

Screening of 70 trios of BWS probands for 11p mosaic paternal UPD and for cryptic cytogenetic rearrangements using microsatellite segregation analysis identified a profile compatible with paternal 11p15 duplication in two patients.

RESULTS

Fluorescence in situ hybridisation analysis revealed in one case the unbalanced translocation der(21)t(11;21)(p15.4;q22.3) originated from missegregation of a cryptic paternal balanced translocation. The second patient, trisomic for D11S1318, carried a small de novo dup(11)(p15.5p15.5), resulting from unequal recombination at paternal meiosis I. The duplicated region involves only IC1 and spares IC2/LIT1, as shown by fluorescent in situ hybridisation (FISH) mapping of the proximal duplication breakpoint within the amino-terminal part of KvLQT1.

CONCLUSIONS

An additional patient with Wolf-Hirschorn syndrome was shown by FISH studies to carry a der(4)t(4;11)(p16.3;p15.4), contributed by a balanced translocation father. Interestingly, refined breakpoint mapping on 11p and the critical regions on the partner 21q and 4p chromosomal regions suggested that both translocations affecting 11p15.4 are mediated by segmental duplications. These findings of chromosomal rearrangements affecting 11p15.5-15.4 provide a tool to further dissect the genomics of the BWS region and the pathogenesis of this imprinting disorder.

Gene discovery at the human T-cell receptor alpha/delta locus

The human T-cell receptor (TCR) alpha/delta variable loci are interspersed on the chromosome 14q11 and consist of 57 intergenic spaces ranging from 4 to 100 kb in length. To elucidate the evolutionary history of this locus, we searched the intergenic spaces of all TCR alpha/delta variable (TRAV/DV) genes for pseudogenes and potential protein-coding genes. We applied direct open reading frame (ORF) searches, an exon-finding algorithm and comparative genomics. Two TRAV/DV pseudogenes were discovered bearing 80 and 65% sequence similarity to TRAV14DV4 and TRAV9-1/9-2 genes, respectively. A gene bearing 85% sequence identity to B lymphocyte activation-related protein, BC-1514, upstream of TRAV26-2 was also discovered. This ORF (BC-1514tcra) is a member of a gene family whose evolutionary history and function are not known. In total, 36 analogs of this gene exist in the human, the chimpanzee, the Rhesus monkey, the frog and the zebrafish. Phylogenetic analyses show convergent evolution of these genes. Assays for the expression of BC-1514tcra revealed transcripts in the bone marrow, thymus, spleen, and small intestine. These assays also showed the expression of another analog to BC-1514, found on chromosome 5 in the bone marrow and thymus RNA. The existence of at least 17 analogs at various locations in the human genome and in nonsyntenic chromosomes of the chimpanzee suggest that BC-1514tcra, along with its analogs may be transposable elements with evolved function(s). The identification of conserved putative serine phosphorylation sites provide evidence of their possible role(s) in signal transduction events involved in B cell development and differentiation.

[The human olfactory system. Anatomy and physiology]

The sense of smell is one of the phylogenetically oldest human senses. Nevertheless the number of publications regarding olfaction is marginal compared with other sensory systems. In recent years, however, there have been enormous advances in understanding the main olfactory processes. These range from the first contact of odorants with receptor cells in the nasal mucosa to the olfactory signal cascade to the processing of olfactory stimuli in the central nervous system. This article focuses on anatomy and physiology of the human sense of smell, which consists mostly of sensory input from two neural systems--the olfactory and trigeminal systems. It considers recent biomolecular experiments and functional neuroimaging studies in humans.

Olfactory receptor gene repertoires in mammals

In mammals, olfaction is mediated by two distinct organs that are located in the nasal cavity: the main olfactory epithelium (MOE) that binds volatile odorants is responsible for the conscious perception of odors, and the vomeronasal organ (VNO) that binds pheromones is responsible for various behavioral and neuroendocrine responses between individuals of a same species. Odorants and pheromones bind to seven transmembrane domain G-protein-coupled receptors that permit signal transduction. These receptors are encoded by large multigene families that evolved in mammal species in function of specific olfactory needs.

The repertoire of olfactory C family G protein-coupled receptors in zebrafish: candidate chemosensory receptors for amino acids

Background

Vertebrate odorant receptors comprise at least three types of G protein-coupled receptors (GPCRs): the OR, V1R, and V2R/V2R-like receptors, the latter group belonging to the C family of GPCRs. These receptor families are thought to receive chemosensory information from a wide spectrum of odorant and pheromonal cues that influence critical animal behaviors such as feeding, reproduction and other social interactions.

Results

Using genome database mining and other informatics approaches, we identified and characterized the repertoire of 54 intact "V2R-like" olfactory C family GPCRs in the zebrafish. Phylogenetic analysis – which also included a set of 34 C family GPCRs from fugu – places the fish olfactory receptors in three major groups, which are related to but clearly distinct from other C family GPCRs, including the calcium sensing receptor, metabotropic glutamate receptors, GABA-B receptor, T1R taste receptors, and the major group of V2R vomeronasal receptor families. Interestingly, an analysis of sequence conservation and selective pressure in the zebrafish receptors revealed the retention of a conserved sequence motif previously shown to be required for ligand binding in other amino acid receptors.

Conclusion

Based on our findings, we propose that the repertoire of zebrafish olfactory C family GPCRs has evolved to allow the detection and discrimination of a spectrum of amino acid and/or amino acid-based compounds, which are potent olfactory cues in fish. Furthermore, as the major groups of fish receptors and mammalian V2R receptors appear to have diverged significantly from a common ancestral gene(s), these receptors likely mediate chemosensation of different classes of chemical structures by their respective organisms.

Testis-specific expression and genomic multiplicity of the rat Rtdpoz genes that encode bipartite TRAF- and POZ/BTB-domain proteins

Based on bioinformatics analysis, we previously hypothesized the existence of a bipartite TDPOZ protein family members of which carry the TRAF domain (TD) and POZ/BTB [Huang, C.-J., Chen, C.-Y., Chen, H.-H., Tsai, S.-F., Choo, K.-B., 2004. TDPOZ, a family of bipartite animal and plant proteins that contain the TRAF (TD) and POZ/BTB domains. Gene 324, 117-127.]. Conservation in animals and plants suggests important biological functions for the putative TDPOZ proteins. In this work, we report testis-specific expression of two new Tdpoz members, Rtdpoz-T1 and -T2, of the rat genome; the result clearly indicates that members of the hypothetical gene family are, indeed, expressed. T1 and T2 cDNA sequences were derived by rapid amplification of cDNA ends (RACE). The exons of the genes were determined by queries of the rat genome sequence draft and selectively confirmed in splicing assays. The results indicate that T1 and T2 share a common leader exon indicative of alternative splicing, and that the genes are uninterrupted by introns in their respective coding sequences. Database interrogations also reveal a combined 297 hits of Rtdpoz-like sequences on 7 chromosomes; however, the bulk of the hits (264) and 26 putative TDPOZ-encoding genes, including T1 and T2, are found in a approximately 2.5 Mb cluster in the Rn2_2148 supercontig on chromosome 2. Our data signify retrotransposition in the generation and expansion of the Rtdpoz repertoire in the rat genome. We also anticipate spatio-temporal-specific expression of many more TDPOZ members in the rat or other animals and plants.

Novel function of β-arrestin2 in the nucleus of mature spermatozoa

A growing number of proteins originally found in endocytic structures of the plasma membrane appear to be able to traffic into the nucleus, but the cellular function of this translocation remains unclear. We have found that β-arrestin2, which typically shows a cytoplasmic localization owing to constitutive nuclear export, appears in the nucleus after stimulation of the G-protein-coupled odorant receptor hOR17-4. In the nucleus, β-arrestin2 was involved in transcriptional regulation as shown by a Gal4-based transactivation assay. Moreover, we discovered that β-arrestin2 and hOR17-4, a receptor known to have a role in sperm-egg communication, colocalize in the midpiece of mature human spermatozoa. Stimulation of hOR17-4 in spermatozoa induced PKA-dependent translocation of β-arrestin2 to the nucleus and nuclear accumulation of phosphorylated MAPKs. Analysis of the interaction partners of β-arrestin2 indicates that odorant receptor signaling in spermatozoa may be important for the regulation of gene expression during the early processes of fertilization.

Accessory chemosignaling mechanisms in primates

Accessory olfaction is defined as the chemoreceptive system that employs the vomeronasal complex (VNC) and its distinct central projections to the accessory olfactory bulb (AOB) and limbic/cortical systems. Comparisons of the structural and functional features of primate accessory olfaction can now be made at many levels. Advances in the understanding of molecular mechanisms of odorant transfer and detection, physiological analyses of signal processing, and appreciation of ontogenetic timetables have clarified the contribution of accessory chemoreception to the sensory map. Two principal functions dominate: the decoding of social information through the uptake of signals (often fluid-borne), and the provision of an essential pathway for the "migration" of presumptive neurocrine (GnRH) cells from the olfactory placode to the hypothalamus. VN "smelling" (vomerolfaction) is now seen to overlap with primary olfaction. Both systems detect signal compounds along the spectrum of volatility/molecular weight, and neither is an exclusive sensor. Both main and accessory chemoreception seem to require collaborative molecular devices to assist in odorant transfer (binding proteins) and (for the VNO) signal recognition (MHC1 proteins). Most adaptive-selective features of primate chemocommunication variously resemble those of other terrestrial mammals. VN function, along with its genome, has been maintained within the Strepsirrhines and tarsiers, reduced in Platyrrhines, and nearly extinguished at the Catarrhine up to hominin levels. It persists as an intriguing ancient sense that retains key features of past evolutionary events.

Ric-8B promotes functional expression of odorant receptors

Odorants are detected by a large family of odorant receptors (ORs) expressed in the nose. The information provided by the ORs is transmitted to specific regions of the brain, leading to odorant perception. The determination of the odorant specificities of the different ORs will contribute to the understanding of how odorants are discriminated by the olfactory system. However, to date only a few ORs have been linked to odorants they recognize, because ORs are poorly expressed on the cell surface of heterologous cells. Here we show that Ric-8B, a putative guanine nucleotide exchange factor for Galphaolf, promotes efficient heterologous expression of ORs. Our results also show that Ric-8B enhances accumulation of Galphaolf at the cell periphery, indicating that it promotes functional OR expression by improving the efficiency of OR coupling to Galphaolf. Expression systems containing Galphaolf and Ric-8B should contribute to the functional characterization of ORs.

G-protein-coupled receptor heterodimers: pharmacology, function and relevance to drug discovery

The growing recognition that members of the rhodopsin-like family A G-protein-coupled receptors (GPCRs) exist and function as dimers or higher-order oligomers, and that GPCR hetero-dimers and -oligomers are present in physiological tissues, offers novel opportunities for drug discovery. Differential pharmacology, function and regulation of GPCR hetero-dimers and -oligomers suggest means to selectively target GPCRs in different tissues and hint that the mechanism of function of several pharmacological agents might be different in vivo than anticipated from simple ligand-screening programmes that rely on heterologous expression of a single GPCR.

Formation of glomerular maps in the olfactory system

Sensory perception relies on the decoding of external stimuli into an internal neuronal representation, which requires precise connections between the periphery and the brain. In the olfactory system the axons of chemosensory neurons with the same odorant receptor coalesce into common glomeruli in the olfactory bulb, forming a receptor-topic map. The creation of this map begins prenatally when axons navigate towards the bulb, resort in a receptor-specific manner and terminate in a broad area interdigitated with other axon populations; distinct glomeruli form postnatally. While the initial process of glomerulization requires mainly molecular determinants, activity-dependent processes lead to a refinement of glomerular organization.

Promoter motifs of olfactory receptor genes expressed in distinct topographic patterns

Novel olfactory receptor-encoding genes that are expressed in olfactory sensory neurons arranged in a clustered pattern in the nasal epithelium, typical of the mOR262 (approved gene symbol Olfr) family, were identified. The genes share sequence motifs upstream of their transcription start sites that are highly related to those previously identified as characteristic of the mOR262 genes, suggesting that these regulatory elements may contribute to governing their unique expression pattern. Promoter analyses of genes encoding class I receptors that are expressed in the dorsal region of the epithelium revealed a different, but again common set of sequence motifs. A prominent feature of the class I gene promoters are multiple O/E-like binding sites, and O/E-type transcription factors that bind to the putative promoter region of class I OR genes were in fact identified. The findings support the concept that common elements in the promoter region of these OR genes may determine their congenic expression pattern in the epithelium.

Evolution of the "OR37" subfamily of olfactory receptors: a cross-species comparison

Genes encoding the olfactory receptors of the "OR37" subfamily of the mouse are characterized by special features including a clustered expression pattern, assembly in two distinct gene clusters, and highly conserved putative promoter motifs. Mining the rat and dog databases revealed that these two species possess highly conserved clusters of OR37 genes at two syntenic genomic loci. In a prototherian mammal, the platypus (Ornithorhynchus anatinus), none of the characteristic OR37 genes were found. Examination of a metatherian mammal, the gray short-tailed opossum (Monodelphis domestica) revealed seven canonical OR37 genes, all phylogenetically related to cluster II genes and also organized similar to cluster II of eutherian species. In addition, their 5' upstream regions comprised sequence motifs related to the putative regulatory sequences of cluster II genes. Typical cluster I OR37 genes were identified only in the eutherian mammals examined, including the evolutionary ancient anteater, wherein OR37 genes related to both clusters were present. Together, these results reveal novel information concerning the phylogenetic origin and important evolutionary steps of the mammalian-specific OR37 olfactory receptor family.

Concerted and birth-and-death evolution of multigene families

Until around 1990, most multigene families were thought to be subject to concerted evolution, in which all member genes of a family evolve as a unit in concert. However, phylogenetic analysis of MHC and other immune system genes showed a quite different evolutionary pattern, and a new model called birth-and-death evolution was proposed. In this model, new genes are created by gene duplication and some duplicate genes stay in the genome for a long time, whereas others are inactivated or deleted from the genome. Later investigations have shown that most non-rRNA genes including highly conserved histone or ubiquitin genes are subject to this type of evolution. However, the controversy over the two models is still continuing because the distinction between the two models becomes difficult when sequence differences are small. Unlike concerted evolution, the model of birth-and-death evolution can give some insights into the origins of new genetic systems or new phenotypic characters.

Enantioselective Syntheses of Georgyone, Arborone, and Structural Relatives. Relevance to the Molecular-Level Understanding of Olfaction

Georgyone (1) and arborone (2), powerful woody odorants, have been synthesized enantioselectively along with their enantiomers. Several structural relatives of 1 and 2 have also been made enantioselectivity in order to probe the molecular details of the binding of 1 and 2 to the olfactory G-protein-coupled receptors which they activate. These studies have led to a number of conclusions regarding the structural requirements for woody odor, including absolute configuration, critical methyl substitution, and the spatial orientation of the key methyl groups. Odorants 1 and 2 bind to at least 10 mouse olfactory receptors, lending support to the combinatorial model for odor perception/differentiation. The implications of this work with regard to possible receptor binding modes are discussed.

The odorant receptor repertoire of teleost fish

BACKGROUND

Vertebrate odorant receptors comprise three types of G protein-coupled receptors: the OR, V1R and V2R receptors. The OR superfamily contains over 1,000 genes in some mammalian species, representing the largest gene superfamily in the mammalian genome.

RESULTS

To facilitate an informed analysis of OR gene phylogeny, we identified the complete set of 143 OR genes in the zebrafish genome, as well as the OR repertoires in two pufferfish species, fugu (44 genes) and tetraodon (42 genes). Although the genomes analyzed here contain fewer genes than in mammalian species, the teleost OR genes can be grouped into a larger number of major clades, representing greater overall OR diversity in the fish.

CONCLUSION

Based on the phylogeny of fish and mammalian repertoires, we propose a model for OR gene evolution in which different ancestral OR genes or gene families were selectively lost or expanded in different vertebrate lineages. In addition, our calculations of the ratios of non-synonymous to synonymous codon substitutions among more recently expanding OR subgroups in zebrafish implicate residues that may be involved in odorant binding.

Odor and chemesthesis from brief exposures to TXIB

An experiment explored ability of subjects to detect vapors of the plasticizer TXIB (2,2,4-trimethyl-1,3-pentanediol diisobutyrate) and ethanol via olfaction and via ocular and nasal chemesthesis, i.e. chemically stimulated feel. Testing, tailored to the sensitivity of each subject, produced psychometric functions for individuals. Olfactory detection of TXIB began at concentrations below 1 ppb (v/v), with 50% correct detection at 1.2 ppb. (Comparable detection for ethanol occurred almost two orders of magnitude higher.) Chemesthetic detection of TXIB began at about 500 ppb, with 50% correct detection at 2.1 ppm for the eye and 4.6 ppm for the nose, both close to saturated vapor concentration. (Comparable detection for ethanol occurred essentially three orders of magnitude higher.) Suggestions that TXIB plays a role in generation of irritative symptoms at concentrations in the range of parts-per-billion need to reckon with a conservatively estimated 200-fold gap between the levels putatively 'responsible' for the symptoms and those even minimally detectable via chemesthesis. Neither the variable of exposure duration nor that of mixing offers a likely explanation. Inclusion of ethanol in the study allowed comparisons pertinent to issues of variability in human chemoreception. An interpretation of the psychometric functions for individuals across materials and perceptual continua led to the conclusion that use of concentration as the metric of detection in olfaction inflates individual differences.

PRACTICAL IMPLICATIONS

This study indicated that the plasticizer TXIB could contribute odor at concentrations in the range of parts-per-billion, but could hardly contribute sensory irritation per se, as alleged in reports of some field studies where TXIB has existed amongst many other organic compounds.

Selectionism and neutralism in molecular evolution

Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism. Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions. This suggestion generated an intense controversy over selectionism and neutralism. This controversy is partially caused by Kimura's definition of neutrality, which was too strict (|2Ns|< or =1). If we define neutral mutations as the mutations that do not change the function of gene products appreciably, many controversies disappear because slightly deleterious and slightly advantageous mutations are engulfed by neutral mutations. The ratio of the rate of nonsynonymous nucleotide substitution to that of synonymous substitution is a useful quantity to study positive Darwinian selection operating at highly variable genetic loci, but it does not necessarily detect adaptively important codons. Previously, multigene families were thought to evolve following the model of concerted evolution, but new evidence indicates that most of them evolve by a birth-and-death process of duplicate genes. It is now clear that most phenotypic characters or genetic systems such as the adaptive immune system in vertebrates are controlled by the interaction of a number of multigene families, which are often evolutionarily related and are subject to birth-and-death evolution. Therefore, it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is some similarity between phenotypic and molecular evolution with respect to functional or environmental constraints and evolutionary rate. It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels.

Structural activation pathways from dynamic olfactory receptor-odorant interactions

We have simulated an odor ligand's dynamic behavior in the binding region of an olfactory receptor (OR). Our short timescale computational studies (up to 200 ps) have helped identify unprecedented postdocking ligand behavior of ligands. From in vacuo molecular dynamics simulations of interactions between models of rat OR I7 and 10 aldehyde ligands, we have identified a dissociative pathway along which the ligand exits and enters the OR-binding pocket--a transit event. The ligand's transit through the receptor's binding region may mark the beginning of a signal transduction cascade leading to odor recognition. We have graphically traced the rotameric changes in key OR amino acid side chains during the transit. Our results have helped substantiate or refute previously held notions of amino acid contribution to ligand stability in the binding pocket. Our observations of ligand activity when compared to those of experimental (electroolfactogram response) OR-activation studies provide a view to predicting the stability of ligands in the binding pocket as a precursor to OR activation by the ligand.

PSGR2, a novel G-protein coupled receptor, is overexpressed in human prostate cancer

The G-protein coupled receptors (GPCRs) recognize a large variety of extracellular molecules (such as hormones, neurotransmitters, growth and developmental factors) and several sensory messages (such as light, odors and pain). GPCRs and their signal transduction pathway represent important specific targets for a variety of human diseases. To investigate the potential roles of GPCRs in human normal prostate and prostate cancers, we identified and characterized a novel human G-protein coupled receptor, PSGR2, which is highly overexpressed in human prostate cancers. Although PSGR2 shares sequence homology with human olfactory G-protein coupled receptors, the expression of PSGR2 is highly restricted to human prostate tissue, and no expression was detected in 22 normal and 10 tumor tissues examined using Northern blot and PCR analysis. Furthermore, we investigated the expression levels of PSGR2 in 133 human prostate samples with real-time quantitative reverse transcription-PCR and in situ hybridization method. We demonstrated that PSGR2 expression increased significantly in human high grade prostate intraepithelial neoplasia (PIN) and prostate cancers (approximately 10-fold) as compared to normal and BPH (benign prostatic hyperplasia) tissues (p < 0.001), suggesting PSGR2 may play an important role in human prostate cancer development and progression. Together, our results suggest that PSGR2 is a novel prostate specific G-protein coupled receptor and may be useful as a tissue marker and molecular target for the early detection and treatment of human prostate cancers.

The dog and rat olfactory receptor repertoires

BACKGROUND

Dogs and rats have a highly developed capability to detect and identify odorant molecules, even at minute concentrations. Previous analyses have shown that the olfactory receptors (ORs) that specifically bind odorant molecules are encoded by the largest gene family sequenced in mammals so far.

RESULTS

We identified five amino acid patterns characteristic of ORs in the recently sequenced boxer dog and brown Norway rat genomes. Using these patterns, we retrieved 1,094 dog genes and 1,493 rat genes from these shotgun sequences. The retrieved sequences constitute the olfactory receptor repertoires of these two animals. Subsets of 20.3% (for the dog) and 19.5% (for the rat) of these genes were annotated as pseudogenes as they had one or several mutations interrupting their open reading frames. We performed phylogenetic studies and organized these two repertoires into classes, families and subfamilies.

CONCLUSION

We have established a complete or almost complete list of OR genes in the dog and the rat and have compared the sequences of these genes within and between the two species. Our results provide insight into the evolutionary development of these genes and the local amplifications that have led to the specific amplification of many subfamilies. We have also compared the human and rat ORs with the human and mouse OR repertoires.

Test of the Binding Threshold Hypothesis for olfactory receptors: explanation of the differential binding of ketones to the mouse and human orthologs of olfactory receptor 912-93

We tested the Binding Threshold Hypothesis (BTH) for activation of olfactory receptors (ORs): To activate an OR, the odorant must bind to the OR with binding energy above some threshold value. The olfactory receptor (OR) 912-93 is known experimentally to be activated by ketones in mouse, but is inactive to ketones in human, despite an amino acid sequence identity of approximately 66%. To investigate the origins of this difference, we used the MembStruk first-principles method to predict the tertiary structure of the mouse OR 912-93 (mOR912-93), and the HierDock first-principles method to predict the binding site for ketones to this receptor. We found that the strong binding of ketones to mOR912-93 is dominated by a hydrogen bond of the ketone carbonyl group to Ser105. All ketones predicted to have a binding energy stronger than EBindThresh = 26 kcal/mol were observed experimentally to activate this OR, while the two ketones predicted to bind more weakly do not. In addition, we predict that 2-undecanone and 2-dodecanone both bind sufficiently strongly to activate mOR912-93. A similar binding site for ketones was predicted in hOR912-93, but the binding is much weaker because the human ortholog has a Gly at the position of Ser105. We predict that mutating this Gly to Ser in human should lead to activation of hOR912-93 by these ketones. Experimental substantiations of the above predictions would provide further tests of the validity of the BTH, our predicted 3D structures, and our predicted binding sites for these ORs.

Effects of RNA degradation on gene expression analysis of human postmortem tissues

The Affymetrix GeneChip platform was used to build a gene expression database of the normal human body. Postmortem human tissues represent a valuable source of biological materials for this type of study, but their use entails some delays before harvesting such tissues. We first evaluated the RNA quality obtained from tissues obtained 3-5 h postmortem and found variations that were both tissue and donor-dependent. RNAs extracted from brain regions were of higher quality than those obtained from the gut, while the cause of death was a significant factor in donor-dependent differences. To avoid these variables, we used rat duodenum to determine the effects of RNA degradation on the analysis of gene expression. Surprisingly, even samples exhibiting significant RNA degradation yielded robust gene expression results, comparable to those obtained using intact samples at a certain signal intensity cutoff. We extended these findings to our human expression database and obtained similar results, indicating that the Affymetrix platform, which is biased to the 3' end of transcripts for detection, can tolerate significant RNA degradation, while still yielding high quality expression data. Our resulting body index expression database is a valuable research tool. As examples of potential uses, we report novel expression sites for four potential therapeutic targets--CCL27, GPR22, GPR113 and GPR128--and as well as a set of thymus-specific genes, including three not previously associated with the thymus.

A comparison of the human and chimpanzee olfactory receptor gene repertoires

Olfactory receptor (OR) genes constitute the basis of the sense of smell and are encoded by the largest mammalian gene superfamily, with >1000 members. In humans, but not in mice or dogs, the majority of OR genes have become pseudogenes, suggesting that OR genes in humans evolve under different selection pressures than in other mammals. To explore this further, we compare the OR gene repertoire of human with its closest living evolutionary relative, by taking advantage of the recently sequenced genome of the chimpanzee. In agreement with previous reports based on a small number of ORs, we find that humans have a significantly higher proportion of OR pseudogenes than chimpanzees. Moreover, we can reject the possibility that humans have been accumulating OR pseudogenes at a constant neutral rate since the divergence of human and chimpanzee. The comparison of the two repertoires reveals two chimpanzee-specific OR subfamily expansions and three expansions specific to humans. It also suggests that a subset of OR genes are under positive selection in either the human or the chimpanzee lineage. Thus, although overall there is relaxed constraint on human olfaction relative to chimpanzee, species-specific sensory requirements appear to have shaped the evolution of the functional OR gene repertoires in both species.

Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods

Olfaction, which is an important physiological function for the survival of mammals, is controlled by a large multigene family of olfactory receptor (OR) genes. Fishes also have this gene family, but the number of genes is known to be substantially smaller than in mammals. To understand the evolutionary dynamics of OR genes, we conducted a phylogenetic analysis of all functional genes identified from the genome sequences of zebrafish, pufferfish, frogs, chickens, humans, and mice. The results suggested that the most recent common ancestor between fishes and tetrapods had at least nine ancestral OR genes, and all OR genes identified were classified into nine groups, each of which originated from one ancestral gene. Eight of the nine group genes are still observed in current fish species, whereas only two group genes were found from mammalian genomes, showing that the OR gene family in fishes is much more diverse than in mammals. In mammals, however, one group of genes, gamma, expanded enormously, containing approximately 90% of the entire gene family. Interestingly, the gene groups observed in mammals or birds are nearly absent in fishes. The OR gene repertoire in frogs is as diverse as that in fishes, but the expansion of group gamma genes also occurred, indicating that the frog OR gene family has both mammal- and fish-like characters. All of these observations can be explained by the environmental change that organisms have experienced from the time of the common ancestor of all vertebrates to the present.

Unveiling Health Attitudes and Creating Good-For-You Foods: The Genomics Metaphor, Consumer Innovative Web-Based Technologies

This article presents an integrated analysis of three emerging knowledge bases in the nutrition and consumer products industries, and how they may effect the food industry. These knowledge bases produce new vistas for corporate product development, especially with respect to those foods that are positioned as 'good for you.' Couched within the current thinking of state-of-the-art knowledge and information, this article highlights how today's thinking about accelerated product development can be introduced into the food and health industries to complement these three research areas. The 3 knowledge bases are: the genomics revolution, which has opened new insights into understanding the interactions of personal needs of individual consumers with nutritionally relevant components of the foods; the investigation of food choice by scientific studies; the development of large scale databases (mega-studies) about the consumer mind. These knowledge bases, combined with new methods to understand the consumer through research, make possible a more focused development. The confluence of trends outlined in this article provides the corporation with the beginnings of a new path to a knowledge-based, principles-grounded product-development system. The approaches hold the potential to create foods based upon people's nutritional requirements combined with their individual preferences. Integrating these emerging knowledge areas with new consumer research techniques may well reshape how the food industry develops new products to satisfy consumer needs and wants.

Functional characterization of two human olfactory receptors expressed in the baculovirus Sf9 insect cell system

Olfactory receptors (ORs) are the largest member of the G-protein-coupled receptors which mediate early olfactory perception in discriminating among thousands of odorant molecules. Assigning odorous ligands to ORs is a prerequisite to gaining an understanding of the mechanisms of odorant recognition. The functional expression of ORs represents a critical step in addressing this issue. Due to limitations in heterologous expression, very few mammal ORs have been characterized, and so far only one is from human origin. Consequently, OR function still remains poorly understood, especially in humans, whose genome encodes a restricted chemosensory repertoire compared with most mammal species. In this study, we have designed cassette baculovirus vectors to coexpress human OR 17-209 or OR 17-210 with either G(alpha olf) or G(alpha16) proteins in Sf9 cells. Each OR was found to be expressed at the cell surface and colocalized with both G(alpha) proteins. Using Ca2+ imaging, we showed that OR 17-209 and OR 17-210 proteins are activated by esters and ketones respectively. Odorant-induced calcium response was increased when ORs were coexpressed with G(alpha16) protein, whereas coexpression with G(alpha olf) abolished calcium signaling. This strategy has been found to overcome most of the limitations encountered when expressing an OR protein and has permitted odorant screening of functional ORs. Our approach could thus be of interest for further expression and ligand assignment of other orphan receptor proteins.