Widespread ectopic expression of olfactory receptor genes

Sensory perception and aging in model systems: from the outside in

Sensory systems provide organisms from bacteria to humans with the ability to interact with the world. Numerous senses have evolved that allow animals to detect and decode cues from sources in both their external and internal environments. Recent advances in understanding the central mechanisms by which the brains of simple organisms evaluate different cues and initiate behavioral decisions, coupled with observations that sensory manipulations are capable of altering organismal lifespan, have opened the door for powerful new research into aging. Although direct links between sensory perception and aging have been established only recently, here we discuss these initial discoveries and evaluate the potential for different forms of sensory processing to modulate lifespan across taxa. Harnessing the neurobiology of simple model systems to study the biological impact of sensory experiences will yield insights into the broad influence of sensory perception in mammals and may help uncover new mechanisms of healthy aging.

A new function for odorant receptors: MOR23 is necessary for normal tissue repair in skeletal muscle

Myofibers with an abnormal branching cytoarchitecture are commonly found in various neuromuscular diseases as well as after severe muscle injury. These aberrant myofibers are fragile and muscles containing a high percentage of these myofibers are weaker and more prone to injury. To date the mechanisms and molecules regulating myofiber branching have been obscure. Recent work analyzing the role of mouse odorant receptor 23 (MOR23) in muscle regeneration revealed that MOR23 is necessary for proper skeletal muscle regeneration in mice as loss of MOR23 leads to increased myofiber branching. Further studies demonstrated that MOR23 expression is induced when muscle cells were extensively fusing and plays an important role in controlling cell migration and adhesion. These data demonstrate a novel role for an odorant receptor in tissue repair and identify the first molecule with a functional role in myofiber branching.

Chemosensory Ca2+ dynamics correlate with diverse behavioral phenotypes in human sperm

In the female reproductive tract, mammalian sperm undergo a regulated sequence of prefusion changes that "prime" sperm for fertilization. Among the least understood of these complex processes are the molecular mechanisms that underlie sperm guidance by environmental chemical cues. A "hard-wired" Ca(2+) signaling strategy that orchestrates specific motility patterns according to given functional requirements is an emerging concept for regulation of sperm swimming behavior. The molecular players involved, the spatiotemporal characteristics of such motility-associated Ca(2+) dynamics, and the relation between a distinct Ca(2+) signaling pattern and a behavioral sperm phenotype, however, remain largely unclear. Here, we report the functional characterization of two human sperm chemoreceptors. Using complementary molecular, physiological, and behavioral approaches, we comparatively describe sperm Ca(2+) responses to specific agonists of these novel receptors and bourgeonal, a known sperm chemoattractant. We further show that individual receptor activation induces specific Ca(2+) signaling patterns with unique spatiotemporal dynamics. These distinct Ca(2+) dynamics are correlated to a set of stimulus-specific stereotyped behavioral responses that could play vital roles during various stages of prefusion sperm-egg chemical communication.

Untargeted metabolomics identifies enterobiome metabolites and putative uremic toxins as substrates of organic anion transporter 1 (Oat1)

Untargeted metabolomics on the plasma and urine from wild-type and organic anion transporter-1 (Oat1/Slc22a6) knockout mice identified a number of physiologically important metabolites, including several not previously linked to Oat1-mediated transport. Several, such as indoxyl sulfate, derive from Phase II metabolism of enteric gut precursors and accumulate in chronic kidney disease (CKD). Other compounds included vitamins (pantothenic acid, 4-pyridoxic acid), urate, and metabolites in the tryptophan and nucleoside pathways. Three metabolites, indoxyl sulfate, kynurenine, and xanthurenic acid, were elevated in the plasma and interacted strongly and directly with Oat1 in vitro with IC50 of 18, 12, and 50 μM, respectively. A pharmacophore model based on several identified Oat1 substrates was used to screen the NCI database and candidate compounds interacting with Oat1 were validated in an in vitro assay. Together, the data suggest a complex, previously unidentified remote communication between the gut microbiome, Phase II metabolism in the liver, and elimination via Oats of the kidney, as well as indicating the importance of Oat1 in the handling of endogenous toxins associated with renal failure and uremia. The possibility that some of the compounds identified may be part of a larger remote sensing and signaling pathway is also discussed.

Remote communication through solute carriers and ATP binding cassette drug transporter pathways: an update on the remote sensing and signaling hypothesis

Recent data from knockouts, human disease, and transport studies suggest that solute carrier (SLC) and ATP binding cassette (ABC) multispecific "drug" transporters maintain effective organ and body fluid concentrations of key nutrients, signaling molecules, and antioxidants. These processes involve transcellular movement of solutes across epithelial barriers and fluid compartments (e.g., blood, cerebrospinal fluid, urine, bile) via "matching" or homologous sets of SLC (e.g., SLC21, SLC22, SLC47) and ABC transporters. As described in the "Remote Sensing and Signaling Hypothesis" (Biochem Biophys Res Commun 323:429-436, 2004; Biochem Biophys Res Commun 351:872-876, 2006; J Biol Chem 282:23841-23853, 2007; Nat Clin Pract Nephrol 3:443-448, 2007; Mol Pharmacol 76:481-490, 2009), highly regulated transporter networks with overlapping substrate preferences are involved in sensing and signaling to maintain homeostasis in response to environmental changes (e.g., substrate imbalance and injury). They function in parallel with (and interact with) the endocrine and autonomic systems. Uric acid (urate), carnitine, prostaglandins, conjugated sex steroids, cGMP, odorants, and enterobiome metabolites are discussed here as examples. Xenobiotics hitchhike on endogenous carrier systems, sometimes leading to toxicity and side effects. By regulation of the expression and/or function of various remote organ multispecific transporters after injury, the overall transport capacity of the remote organ to handle endogenous toxins, metabolites, and signaling molecules may change, aiding in recovery. Moreover, these transporters may play a role in communication between organisms. The specific cellular components involved in sensing and altering transporter abundance or functionality depend upon the metabolite in question and probably involve different types of sensors as well as epigenetic regulation.

Human male superiority in olfactory sensitivity to the sperm attractant odorant bourgeonal

Recent studies have shown that sperm chemotaxis critically involves the human olfactory receptor OR1D2, which is activated by the aromatic aldehyde bourgeonal. Given that both natural and sexual selection may act upon the expression of receptors, we hypothesized that human males are more sensitive than human females for bourgeonal. Using a 3-alternative forced-choice test procedure, olfactory detection thresholds were determined for a total of 500 subjects, 250 males, and 250 females between 18 and 40 years of age. We found that male subjects detected bourgeonal at significantly lower concentrations (mean value: 13 ppb) compared with female subjects (mean value: 26 ppb), whereas no such gender difference in olfactory sensitivity was found with helional, a structural analog of bourgeonal, and with n-pentyl acetate, an aliphatic ester, which were tested in parallel. Males and females did not differ in their frequency of specific anosmia for any of the 3 odorants. The frequency distributions of olfactory detection thresholds were monomodal with all 3 odorants in both genders. Olfactory detection thresholds did not differ significantly between pre- and postovulatory females with any of the 3 odorants. To the best of our knowledge, this is the first study ever to find a human male superiority in olfactory sensitivity. Single nucleotide polymorphisms and/or copy number variations in genes coding for olfactory receptors may be the proximate cause for our finding, whereas a gender difference in the behavioral relevance of bourgeonal may be the ultimate cause.

The diffuse chemosensory system: exploring the iceberg toward the definition of functional roles

The diffuse chemosensory system (DCS) is an anatomical structure composed of solitary chemosensory cells (SCCs, also called solitary chemoreceptor cells), which have analogies with taste cells but are not aggregated in buds. The concept of DCS has been advanced, after the discovery that cells similar to gustatory elements are present in several organs. The elements forming the DCS share common morphological and biochemical characteristics with the taste cells located in taste buds of the oro-pharyngeal cavity but they are localized in internal organs. In particular, they may express molecules of the chemoreceptorial cascade (e.g. trans-membrane taste receptors, the G-protein alpha-gustducin, PLCbeta2, TRPM5). This article will focus on the mammalian DCS in apparatuses of endodermic origin (i.e. digestive and respiratory systems), which is composed of an enormous number of sensory elements and presents a multiplicity of morphological aspects. Recent research has provided an adequate description of these elements, but the functional role for the DCS in these apparatuses is unknown. The initial findings led to the definition of a DCS structured like an iceberg, with a mysterious "submerged" portion localized in the distal part of endodermic apparatuses. Recent work has focussed on the discovery of this submerged portion, which now appears less puzzling. However, the functional roles of the different cytotypes belonging to the DCS are not well known. Recent studies linked chemosensation of the intraluminal content to local control of absorptive and secretory (exocrine and endocrine) processes. Control of the microbial population and detection of irritants seem to be other possible functions of the DCS. In the light of these new findings, the DCS might be thought to be involved in a wide range of diseases of both the respiratory (e.g. asthma, chronic obstructive pulmonary disease, cystic fibrosis) and digestive apparatuses (absorptive or secretive diseases, dysmicrobism), as well as in systemic diseases (e.g. obesity, diabetes). A description of the functional roles of the DCS might be a first step toward the discovery of therapeutic approaches which target chemosensory mechanisms.

MOR23 promotes muscle regeneration and regulates cell adhesion and migration

Odorant receptors (ORs) in the olfactory epithelium bind to volatile small molecules leading to the perception of smell. ORs are expressed in many tissues but their functions are largely unknown. We show multiple ORs display distinct mRNA expression patterns during myogenesis in vitro and muscle regeneration in vivo. Mouse OR23 (MOR23) expression is induced during muscle regeneration when muscle cells are extensively fusing and plays a key role in regulating migration and adhesion of muscle cells in vitro, two processes common during tissue repair. A soluble ligand for MOR23 is secreted by muscle cells in vitro and muscle tissue in vivo. MOR23 is necessary for proper skeletal muscle regeneration as loss of MOR23 leads to increased myofiber branching, commonly associated with muscular dystrophy. Together these data identify a functional role for an OR outside of the nose and suggest a larger role for ORs during tissue repair.

YY1's DNA-binding motifs in mammalian olfactory receptor genes

BACKGROUND

YY1 is an epigenetic regulator for a large number of mammalian genes. While performing genome-wide YY1 binding motif searches, we discovered that the olfactory receptor (OLFR) genes have an unusual cluster of YY1 binding sites within their coding regions. The statistical significance of this observation was further analyzed.

RESULTS

About 45% of the olfactory genes in the mouse have a range of 4-8 YY1 binding sites within their respective 1 kb coding regions. Statistical analyses indicate that this enrichment of YY1 motifs has likely been driven by unknown selection pressures at the DNA level, but not serendipitously by some peptides enriched within the OLFR genes. Similar patterns are also detected in the OLFR genes of all mammals analyzed, but not in the OLFR genes of the fish lineage, suggesting a mammal-specific phenomenon.

CONCLUSION

YY1, or YY1-related transcription factors, may help regulate olfactory receptor genes. Furthermore, the protein-coding regions of vertebrate genes can contain cis-regulatory elements for transcription factor binding as well as codons.

RNA profiles of rat olfactory epithelia: individual and age related variations

Background

Mammalian genomes contain a large number (~1000) of olfactory receptor (OR) genes, many of which (20 to 50%) are pseudogenes. OR gene transcription is not restricted to the olfactory epithelium, but is found in numerous tissues. Using microarray hybridization and RTqPCR, we analyzed the mRNA profiles of the olfactory epithelium of male and female Brown Norway rats of different origins and ages (newborn, adult and old).

Results

(1) We observed very little difference between males and females and between rats from two different suppliers. (2) Different OR genes were expressed at varying levels, rather than uniformly across the four endoturbinates. (3) A large proportion of the gene transcripts (2/3 of all probes) were detected in all three age groups. Adult and older rats expressed similar numbers of OR genes, both expressing more OR genes than newborns. (4) Comparisons of whole transcriptomes or transcription profiles of expressed OR genes only showed a clear clustering of the samples as a function of age. (5) Most OR genes were expressed at lower levels at birth than in older animals, but a small number of OR genes were expressed specifically or were overexpressed in newborns.

Conclusion

Not all OR genes are expressed at a detectable level. Pups expressed fewer OR genes than adult rats, and generally at a lower level; however, a small subset of OR genes were more strongly expressed in these newborn rats. The reasons for these differences are not understood. However, the specific expression of some OR genes in newborn olfactory epithelia may be related to the blindness and deafness of pups at birth, when these pups are heavily reliant on olfaction and their mother.

Genomics of olfactory receptors

In many species, the sense of smell plays important roles in locating food, detecting predators, navigating, and communicating social information. The olfactory system has evolved complex repertoires of odor receptors (ORs) to fulfill these functions. Through computational data mining, OR repertoires of multiple species were identified, revealing a surprisingly large OR gene family in rodents and evolutionary fluctuation among different organisms. Characteristics of OR genes were explored through computational and experimental methods, showing a complicated gene structure and special genomic distribution. Utilizing high-throughput OR microarrays, expression profiles of the mouse and human OR repertoire were examined, their olfactory functions verified, and their zonal, ectopic and developmental expression determined. Variation in human smelling abilities results from different functional OR repertoires, variable expressional levels and polymorphisms in the copy number of the OR genes. These genomic approaches have both provided new data and generated new questions.

Dual activities of odorants on olfactory and nuclear hormone receptors

We have screened an odorant compound library and discovered molecules acting as chemical signals that specifically activate both G-protein-coupled olfactory receptors (ORs) on the cell surface of olfactory sensory neurons and the human nuclear estrogen receptor alpha (ER) involved in transcriptional regulation of cellular differentiation and proliferation in a wide variety of tissues. Hence, these apparent dual active odorants induce distinct signal transduction pathways at different subcellular localizations, which affect both neuronal signaling, resulting in odor perception, and the ER-dependent transcriptional control of specific genes. We demonstrate these effects using fluorescence-based in vitro and cellular assays. Among these odorants, we have identified synthetic sandalwood compounds, an important class of molecules used in the fragrance industry. For one estrogenic odorant we have also identified the cognate OR. This prompted us to compare basic molecular recognition principles of odorants on the two structurally and apparent functionally non-related receptors using computational modeling in combination with functional assays. Faced with the increasing evidence that ORs may perform chemosensory functions in a number of tissues outside of the nasal olfactory epithelium, the unraveling of these molecular ligand-receptor interaction principles is of critical importance. In addition the evidence that certain olfactory sensory neurons naturally co-express ORs and ERs may provide a direct functional link between the olfactory and hormonal systems in humans. Our results are therefore useful for defining the structural and functional characteristics of ER-specific odorants and the role of odorant molecules in cellular processes other than olfaction.

Mammalian olfactory receptors

Perception of chemical stimuli from the environment is essential to most animals; accordingly, they are equipped with a complex olfactory system capable of receiving a nearly unlimited number of odorous substances and pheromones. This enormous task is accomplished by olfactory sensory neurons (OSNs) arranged in several chemosensory compartments in the nose. The sensitive and selective responsiveness of OSNs to odorous molecules and pheromones is based on distinct receptors in their chemosensory membrane; consequently, olfactory receptors play a key role for a reliable recognition and an accurate processing of chemosensory information. They are therefore considered as key elements for an understanding of the principles and mechanisms underlying the sense of smell. The repertoire of olfactory receptors in mammals encompasses hundreds of different receptor types which are highly diverse and expressed in distinct subcompartments of the nose. Accordingly, they are categorized into several receptor families, including odorant receptors (ORs), vomeronasal receptors (V1Rs and V2Rs), trace amine-associated receptors (TAARs), formyl peptide receptors (FPRs), and the membrane guanylyl cyclase GC-D. This large and complex receptor repertoire is the basis for the enormous chemosensory capacity of the olfactory system.

Comparison of rat olfactory mucosal responses to carcinogenic and non-carcinogenic chloracetanilides

Alachlor and butachlor are chloracetanilide herbicides that induce olfactory tumors in rats, whereas propachlor does not. The mechanism by which alachlor induces tumors is distinct from many other nasal carcinogens, in that alachlor induces a gradual de-differentiation of the olfactory mucosa (OM) to a more respiratory-like epithelium, in contrast to other agents that induce cytotoxicity, followed by an aberrant regenerative response. We studied biochemical and genomic effects of these compounds to identify processes that occur in common between alachlor- and butachlor-treated rats. Because we have previously shown that matrix metalloproteinase-2 (MMP2) is activated in OM by alachlor, in the present studies we evaluated both MMP2 activation and changes in OM gene expression in response to carcinogenic and non-carcinogenic chloracetanilide treatments. All three chloracetanilides activated MMP2, and >300 genes were significantly up- or downregulated between control and alachlor-treated rats. The most significantly regulated gene was vomeromodulin, which was dramatically upregulated by alachlor and butachlor treatment (>60-fold), but not by propachlor treatment. Except for similar gene responses in alachlor- and butachlor-treated rats, we did not identify clear-cut differences that would predict OM carcinogenicity in this study.

Activation of an olfactory receptor inhibits proliferation of prostate cancer cells

Olfactory receptors (ORs) are expressed not only in the sensory neurons of the olfactory epithelium, where they detect volatile substances, but also in various other tissues where their potential functions are largely unknown. Here, we report the physiological characterization of human OR51E2, also named prostate-specific G-protein-coupled receptor (PSGR) due to its reported up-regulation in prostate cancer. We identified androstenone derivatives as ligands for the recombinant receptor. PSGR can also be activated with the odorant beta-ionone. Activation of the endogenous receptor in prostate cancer cells by the identified ligands evoked an intracellular Ca2+ increase. Exposure to beta-ionone resulted in the activation of members of the MAPK family and inhibition of cell proliferation. Our data give support to the hypothesis that because PSGR signaling could reduce growth of prostate cancer cells, specific receptor ligands might therefore be potential candidates for prostate cancer treatment.

Olfactory receptors: G protein-coupled receptors and beyond

Sensing the chemical environment is critical for all organisms. Diverse animals from insects to mammals utilize highly organized olfactory system to detect, encode, and process chemostimuli that may carry important information critical for health, survival, social interactions and reproduction. Therefore, for animals to properly interpret and react to their environment it is imperative that the olfactory system recognizes chemical stimuli with appropriate selectivity and sensitivity. Because olfactory receptor proteins play such an essential role in the specific recognition of diverse stimuli, understanding how they interact with and transduce their cognate ligands is a high priority. In the nearly two decades since the discovery that the mammalian odorant receptor gene family constitutes the largest group of G protein-coupled receptor (GPCR) genes, much attention has been focused on the roles of GPCRs in vertebrate and invertebrate olfaction. However, is has become clear that the 'family' of olfactory receptors is highly diverse, with roles for enzymes and ligand-gated ion channels as well as GPCRs in the primary detection of olfactory stimuli.

A signature of evolutionary constraint on a subset of ectopically expressed olfactory receptor genes

Olfactory receptor (OR) genes constitute the basis for the sense of smell. It has long been observed that a subset of mammalian OR genes are expressed in nonolfactory tissues, in addition to their expression in the olfactory epithelium. However, it is unknown whether OR genes have alternative functions in the nonolfactory tissues. Using a dedicated microarray, we surveyed OR gene expression in olfactory epithelium as well as a number of nonolfactory tissues, in human and chimpanzee. Our observations suggest that ectopically expressed OR orthologous genes are expressed in the same nonolfactory tissues in human and chimpanzee more often than expected by chance alone. Moreover, we found that the subset of orthologous OR genes with conserved ectopic expression evolve under stronger evolutionary constraint than OR genes expressed exclusively in the olfactory epithelium. Thus, although we cannot provide direct functional data, our observations are consistent with the notion that a subset of ectopically expressed OR genes have additional functions in nonolfactory tissues.

The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity

Chemosensory receptors are essential for the survival of organisms that range from bacteria to mammals. Recent studies have shown that the numbers of functional chemosensory receptor genes and pseudogenes vary enormously among the genomes of different animal species. Although much of the variation can be explained by the adaptation of organisms to different environments, it has become clear that a substantial portion is generated by genomic drift, a random process of gene duplication and deletion. Genomic drift also generates a substantial amount of copy-number variation in chemosensory receptor genes within species. It seems that mutation by gene duplication and inactivation has important roles in both the adaptive and non-adaptive evolution of chemosensation.

Identification of neuronal target genes for CCAAT/enhancer binding proteins

CCAAT/Enhancer Binding Proteins (C/EBPs) play pivotal roles in the development and plasticity of the nervous system. Identification of the physiological targets of C/EBPs (C/EBP target genes) should therefore provide insight into the underlying biology of these processes. We used unbiased genome-wide mapping to identify 115 C/EBPbeta target genes in PC12 cells that include transcription factors, neurotransmitter receptors, ion channels, protein kinases and synaptic vesicle proteins. C/EBPbeta binding sites were located primarily within introns, suggesting novel regulatory functions, and were associated with binding sites for other developmentally important transcription factors. Experiments using dominant negatives showed C/EBPbeta to repress transcription of a subset of target genes. Target genes in rat brain were subsequently found to preferentially bind C/EBPalpha, beta and delta. Analysis of the hippocampal transcriptome of C/EBPbeta knockout mice revealed dysregulation of a high percentage of transcripts identified as C/EBP target genes. These results support the hypothesis that C/EBPs play non-redundant roles in the brain.

Common null variant, Arg192Stop, in a G-protein coupled receptor, olfactory receptor 1B1, associated with decreased serum cholinesterase activity

AIM

Non-functioning single nucleotide polymorphisms (nSNPs) that result in premature termination codons, that is null-alleles of the respective genes, may have phenotypic effects on clinical parameters. We conducted association studies involving several G-protein coupled receptors (GPCRs) that harbor nSNPs, using clinical parameters of liver function in a general population consisting of 2969 Japanese adults.

METHODS

SNP typings were performed with TaqMan and Invader assays. Quantitative associations between genotypes and clinical parameters were analyzed by analysis of variance. Linkage disequilibrium (LD) was tested by Haploview Version 3.3. Haplotype-based association was performed using the haplo.stats program.

RESULTS

A significant correlation (P = 0.0057) was identified between serum cholinesterase activity (CHE) and an nSNP (Arg192Stop) in the olfactory receptor (OR) 1B1 gene, a member of the GPCR gene family. This nSNP was associated with decreased serum CHE (P = 0.0013). LD analysis based on eight selected SNPs at the locus revealed three LD blocks. The Arg192Stop nSNP was located on the second LD block, which covered one-third of the 3'-portion of the gene.

CONCLUSION

These results suggested that the null-allele of OR1B1 might affect metabolism of serum cholinesterase in carriers of this nSNP.

DA and Xiao-two giant and composite LTR-retrotransposon-like elements identified in the human genome

We discovered two new complex elements while studying large genomic rearrangements and segmental duplications in the human genome. Both resemble bacterial composite DNA transposon Tn9, consisting of a core flanked by mobile elements, except that the flanking element is not a DNA transposon but instead is long terminal repeat retrotransposon-like with human endogenous retrovirus and satellite sequences. Based on the core size, we named them Xiao ( approximately 30 kb) and DA ( approximately 280 kb), meaning small and big, respectively, in Chinese. Xiao originated from a 19p region encoding olfactory receptor 7E members after the human/ape divergence from Old World monkeys, while DA likely evolved from a Xiao by inserting approximately 200 kb of chimeric sequence from 16p and 21q into the Xiao core, resulting in a target site duplication of 3.4 kb. DA/Xiao was identified in 30 loci on 12 chromosomes, and only DAs mediated intrachromosomal rearrangements, based on our reconstructed human-mouse-rat ancestral genome and the rhesus macaque genome.

Taste receptor genes

In the past several years, tremendous progress has been achieved with the discovery and characterization of vertebrate taste receptors from the T1R and T2R families, which are involved in recognition of bitter, sweet, and umami taste stimuli. Individual differences in taste, at least in some cases, can be attributed to allelic variants of the T1R and T2R genes. Progress with understanding how T1R and T2R receptors interact with taste stimuli and with identifying their patterns of expression in taste cells sheds light on coding of taste information by the nervous system. Candidate mechanisms for detection of salts, acids, fat, complex carbohydrates, and water have also been proposed, but further studies are needed to prove their identity.

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.

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.

Sympatric speciation as intrinsic property of the expanding population

Sympatric speciation is still debatable, though some well documented empirical data that support it already exist. Our computer modeling reveals that sympatric speciation is an intrinsic property of the expanding populations with differentiated inbreeding-higher at the edges and lower inside the territory. At the edges of expanding populations, the probability of forming deleterious phenotypes by placing two defective alleles in the corresponding loci is relatively high even with low genetic load. Thus, the winning strategy is to use rather the complementary haplotypes to form zygotes. This strategy leads to a very fast sympatric speciation and specific distribution of recombination activity along the chromosomes-higher at the subtelomeric regions (close to the ends of chromosomes) and lower in the middle of chromosomes, which is also observed in all human chromosomes (excluding Y).

Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray

BACKGROUND

Olfactory receptor (OR) genes were discovered more than a decade ago, when Buck and Axel observed that, in rats, certain G-protein coupled receptors are expressed exclusively in the olfactory epithelium. Subsequently, protein sequence similarity was used to identify entire OR gene repertoires of a number of mammalian species, but only in mouse were these predictions followed up by expression studies in olfactory epithelium. To rectify this, we have developed a DNA microarray that contains probes for most predicted human OR loci and used that array to examine OR gene expression profiles in olfactory epithelium tissues from three individuals.

RESULTS

We detected expression of 437 (76%) human OR genes in these olfactory epithelia. Interestingly, we detected widespread expression of OR pseudogenes, an observation that may shed light on the mechanism of OR gene choice in the olfactory sensory neurons. To address the hypothesis that OR genes may carry out additional functions, we also characterized the expression of OR genes in a number of non-olfactory tissues.

CONCLUSION

While our results corroborate the functional annotation of the majority of predicted human odorant receptors, we find that a large number of putative human OR genes are expressed in non-olfactory tissues, sometimes exclusively so. Our evolutionary analysis of ectopically expressed human OR genes does not lend support to the hypothesis that these genes have alternative functions.

A probabilistic classifier for olfactory receptor pseudogenes

BACKGROUND

Olfactory receptors (ORs), the largest mammalian gene superfamily (900-1400 genes), has >50% pseudogenes in humans. While most of these inactive genes are identified via coding frame (nonsense) disruptions, seemingly intact genes may also be inactive due to other deleterious (missense) mutations. An ultimate assessment of the actual size of the functional human OR repertoire thus requires an accurate distinction between genes and pseudogenes.

RESULTS

To characterize inactive ORs with intact open reading frame, we have developed a probabilistic Classifier for Olfactory Receptor Pseudogenes (CORP). This algorithm is based on deviations from a functionally crucial consensus, constituting sixty highly conserved positions identified by a comparison of two evolutionarily-constrained OR repertoires (mouse and dog) with a small pseudogene fraction. We used a logistic regression analysis to assign appropriate coefficients to the conserved position and thus achieving maximal separation between active and inactive ORs. Consequently, the algorithms identified only 5% of the mouse functional ORs as pseudogenes, setting an upper limit of 0.05 to the false positive detection. Finally we used this algorithm to classify the 384 purportedly intact human OR genes. Of these, 135 were predicted as likely encoding non-functional proteins, and 38 were segregating between active and inactive forms due to missense polymorphisms.

CONCLUSION

We demonstrated that the CORP algorithm is capable to distinguish between functional and non-functional OR genes with high precision even when the encoded protein would differ by a single amino acid. Using the CORP algorithm, we predict that approximately 70% of human OR genes are likely non-functional pseudogenes, a much higher number than hitherto suspected. The method we present may be employed for better annotation of inactive members in other gene families as well. CORP algorithm is available at: http://bioportal.weizmann.ac.il/HORDE/CORP/