Evolution and origin of vomeronasal-type odorant receptor gene repertoire in fishes

Recent advances in the crosstalk between adipose, muscle and bone tissues in fish

Control of tissue metabolism and growth involves interactions between organs, tissues, and cell types, mediated by cytokines or direct communication through cellular exchanges. Indeed, over the past decades, many peptides produced by adipose tissue, skeletal muscle and bone named adipokines, myokines and osteokines respectively, have been identified in mammals playing key roles in organ/tissue development and function. Some of them are released into the circulation acting as classical hormones, but they can also act locally showing autocrine/paracrine effects. In recent years, some of these cytokines have been identified in fish models of biomedical or agronomic interest. In this review, we will present their state of the art focusing on local actions and inter-tissue effects. Adipokines reported in fish adipocytes include adiponectin and leptin among others. We will focus on their structure characteristics, gene expression, receptors, and effects, in the adipose tissue itself, mainly regulating cell differentiation and metabolism, but in muscle and bone as target tissues too. Moreover, lipid metabolites, named lipokines, can also act as signaling molecules regulating metabolic homeostasis. Regarding myokines, the best documented in fish are myostatin and the insulin-like growth factors. This review summarizes their characteristics at a molecular level, and describes both, autocrine effects and interactions with adipose tissue and bone. Nonetheless, our understanding of the functions and mechanisms of action of many of these cytokines is still largely incomplete in fish, especially concerning osteokines (i.e., osteocalcin), whose potential cross talking roles remain to be elucidated. Furthermore, by using selective breeding or genetic tools, the formation of a specific tissue can be altered, highlighting the consequences on other tissues, and allowing the identification of communication signals. The specific effects of identified cytokines validated through in vitro models or in vivo trials will be described. Moreover, future scientific fronts (i.e., exosomes) and tools (i.e., co-cultures, organoids) for a better understanding of inter-organ crosstalk in fish will also be presented. As a final consideration, further identification of molecules involved in inter-tissue communication will open new avenues of knowledge in the control of fish homeostasis, as well as possible strategies to be applied in aquaculture or biomedicine.

Remarkable diversity of vomeronasal type 2 receptor (OlfC) genes of basal ray-finned fish and its evolutionary trajectory in jawed vertebrates

The vomeronasal type 2 receptor (V2R, also called OlfC) multigene family is found in a broad range of jawed vertebrates from cartilaginous fish to tetrapods. V2Rs encode receptors for food-related amino acids in teleost fish, whereas for peptide pheromones in mammals. In addition, V2Rs of teleost fish are phylogenetically distinct from those of tetrapods, implying a drastic change in the V2R repertoire during terrestrial adaptation. To understand the process of diversification of V2Rs in vertebrates from "fish-type" to "tetrapod-type", we conducted an exhaustive search for V2Rs in cartilaginous fish (chimeras, sharks, and skates) and basal ray-finned fish (reedfish, sterlet, and spotted gar), and compared them with those of teleost, coelacanth, and tetrapods. Phylogenetic and synteny analyses on 1897 V2Rs revealed that basal ray-finned fish possess unexpectedly higher number of V2Rs compared with cartilaginous fish, implying that V2R gene repertoires expanded in the common ancestor of Osteichthyes. Furthermore, reedfish and sterlet possessed various V2Rs that belonged to both "fish-type" and "tetrapod-type", suggesting that the common ancestor of Osteichthyes possess "tetrapod-type" V2Rs although they inhabited underwater environments. Thus, the unexpected diversity of V2Rs in basal ray-finned fish may provide insight into how the olfaction of osteichthyan ancestors adapt from water to land.

Transcriptome Analysis of Zebrafish Olfactory Epithelium Reveal Sexual Differences in Odorant Detection

Animals have evolved a large number of olfactory receptor genes in their genome to detect numerous odorants in their surrounding environments. However, we still know little about whether males and females possess the same abilities to sense odorants, especially in fish. In this study, we used deep RNA sequencing to examine the difference of transcriptome between male and female zebrafish olfactory epithelia. We found that the olfactory transcriptomes between males and females are highly similar. We also found evidence of some genes showing differential expression or alternative splicing, which may be associated with odorant-sensing between sexes. Most chemosensory receptor genes showed evidence of expression in the zebrafish olfactory epithelium, with a higher expression level in males than in females. Taken together, our results provide a comprehensive catalog of the genes mediating olfactory perception and pheromone-evoked behavior in fishes.

Expansion of vomeronasal receptor genes (OlfC) in the evolution of fright reaction in Ostariophysan fishes

Ostariophysans are the most diverse group of freshwater fishes and feature a pheromone-elicited fright reaction. However, the genetic basis of fright reaction is unclear. Here, we compared vomeronasal type 2 receptor-like (OlfC) genes from fishes having and lacking fright reaction, to provide insight into evolution of pheromonal olfaction in fishes. We found OlfC genes expanded remarkably in ostariophysans having fright reaction compared with fishes lacking fright reaction. Phylogenetic analysis indicates OlfC subfamily 9 expanded specifically in ostariophysans having fright reaction. Principle component and phylogenetic logistic regression analysis partitioned fishes by ecotype (having or lacking fright reaction) and identified OlfC subfamily 9 as being an important factor for fright reaction. Expression levels of expanded OlfC subfamily genes after fright reaction in zebrafish changed more than did genes that had not expanded. Furthermore, evidence of positive selection was found in the expanded OlfC proteins in ostariophysan fishes having fright reaction. These results provide new insight into the genetic basis of fright reaction in ostariophysan fish and will enable future research into the mechanism of action of OlfC proteins.

Transcriptome sequencing of olfactory-related genes in olfactory transduction of large yellow croaker (Larimichthy crocea) in response to bile salts

Fish produce and release bile salts as chemical signalling substances that act as sensitive olfactory stimuli. To investigate how bile salts affect olfactory signal transduction in large yellow croaker (Larimichthy crocea), deep sequencing of olfactory epithelium was conducted to analyse olfactory-related genes in olfactory transduction. Sodium cholates (SAS) have typical bile salt chemical structures, hence we used four different concentrations of SAS to stimulate L. crocea, and the fish displayed a significant behavioural preference for 0.30% SAS. We then sequenced olfactory epithelium tissues, and identified 9938 unigenes that were significantly differentially expressed between SAS-stimulated and control groups, including 9055 up-regulated and 883 down-regulated unigenes. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses found eight categories linked to the olfactory transduction pathway that was highly enriched with some differentially expressed genes (DEGs), including the olfactory receptor (OR), Adenylate cyclase type 3 (ADCY3) and Calmodulin (CALM). Genes in these categories were analysed by RT-qPCR, which revealed aspects of the pathway transformation between odor detection, and recovery and adaptation. The results provide new insight into the effects of bile salt stimulation in olfactory molecular mechanisms in fishes, and expands our knowledge of olfactory transduction, and signal generation and decline.

The Chemosensory Receptor Repertoire of a True Shark Is Dominated by a Single Olfactory Receptor Family

Throughout the animal kingdom chemical senses are one of the primary means by which organisms make sense of their environment. To achieve perception of complex chemosensory stimuli large repertoires of olfactory and gustatory receptors are employed in bony vertebrates, which are characterized by high evolutionary dynamics in receptor repertoire size and composition. However, little is known about their evolution in earlier diverging vertebrates such as cartilaginous fish, which include sharks, skates, rays, and chimeras. Recently, the olfactory repertoire of a chimera, elephant shark, was found to be curiously reduced in odorant receptor number. Elephant sharks rely heavily on electroreception to localize prey; thus, it is unclear how representative their chemosensory receptor repertoire sizes would be for cartilaginous fishes in general. Here, we have mined the genome of a true shark, Scyliorhinus canicula (catshark) for olfactory and gustatory receptors, and have performed a thorough phylogenetic study to shed light on the evolution of chemosensory receptors in cartilaginous fish. We report the presence of several gustatory receptors of the TAS1R family in catshark and elephant shark, whereas TAS2R receptors are absent. The catshark olfactory repertoire is dominated by V2R receptors, with 5–8 receptors in the other three families (OR, ORA, TAAR). Species-specific expansions are mostly limited to the V2R family. Overall, the catshark chemosensory receptor repertoires are generally similar in size to those of elephant shark, if somewhat larger, showing similar evolutionary tendencies across over 400 Myr of separate evolution between catshark and elephant shark.

Overlapping but distinct topology for zebrafish V2R-like olfactory receptors reminiscent of odorant receptor spatial expression zones

Background

The sense of smell is unrivaled in terms of molecular complexity of its input channels. Even zebrafish, a model vertebrate system in many research fields including olfaction, possesses several hundred different olfactory receptor genes, organized in four different gene families. For one of these families, the initially discovered odorant receptors proper, segregation of expression into distinct spatial subdomains within a common sensory surface has been observed both in teleost fish and in mammals. However, for the remaining three families, little to nothing was known about their spatial coding logic. Here we wished to investigate, whether the principle of spatial segregation observed for odorant receptors extends to another olfactory receptor family, the V2R-related OlfC genes. Furthermore we thought to examine, how expression of OlfC genes is integrated into expression zones of odorant receptor genes, which in fish share a single sensory surface with OlfC genes.

Results

To select representative genes, we performed a comprehensive phylogenetic study of the zebrafish OlfC family, which identified a novel OlfC gene, reduced the number of pseudogenes to 1, and brought the total family size to 60 intact OlfC receptors. We analyzed the spatial pattern of OlfC-expressing cells for seven representative receptors in three dimensions (height within the epithelial layer, horizontal distance from the center of the olfactory organ, and height within the olfactory organ). We report non-random distributions of labeled neurons for all OlfC genes analysed. Distributions for sparsely expressed OlfC genes are significantly different from each other in nearly all cases, broad overlap notwithstanding. For two of the three coordinates analyzed, OlfC expression zones are intercalated with those of odorant receptor zones, whereas in the third dimension some segregation is observed.

Conclusion

Our results show that V2R-related OlfC genes follow the same spatial logic of expression as odorant receptors and their expression zones intermingle with those of odorant receptor genes. Thus, distinctly different expression zones for individual receptor genes constitute a general feature shared by teleost and tetrapod V2R/OlfC and odorant receptor families alike.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4740-8) contains supplementary material, which is available to authorized users.

Identification of olfactory receptor genes in the Japanese grenadier anchovy Coilia nasus

Olfaction is essential for fish to detect odorant elements in the environment and plays a critical role in navigating, locating food and detecting predators. Olfactory function is produced by the olfactory transduction pathway and is activated by olfactory receptors (ORs) through the binding of odorant elements. Recently, four types of olfactory receptors have been identified in vertebrate olfactory epithelium, including main odorant receptors (MORs), vomeronasal type receptors (VRs), trace-amine associated receptors (TAARs) and formyl peptide receptors (FPRs). It has been hypothesized that migratory fish, which have the ability to perform spawning migration, use olfactory cues to return to natal rivers. Therefore, obtaining OR genes from migratory fish will provide a resource for the study of molecular mechanisms that underlie fish spawning migration behaviors. Previous studies of OR genes have mainly focused on genomic data, however little information has been gained at the transcript level. In this study, we identified the OR genes of an economically important commercial fish Coilia nasus through searching for olfactory epithelium transcriptomes. A total of 142 candidate MOR, 52 V2R/OlfC, 32 TAAR and two FPR putative genes were identified. In addition, through genomic analysis we identified several MOR genes containing introns, which is unusual for vertebrate MOR genes. The transcriptome-scale mining strategy proved to be fruitful in identifying large sets of OR genes from species whose genome information is unavailable. Our findings lay the foundation for further research into the possible molecular mechanisms underlying the spawning migration behavior in C. nasus.

Embryology of the VNO and associated structures in the grass snake Natrix natrix (Squamata: Naticinae): a 3D perspective

BACKGROUND

Snakes are considered to be vomerolfaction specialists. They are members of one of the most diverse groups of vertebrates, Squamata. The vomeronasal organ and the associated structures (such as the lacrimal duct, choanal groove, lamina transversalis anterior and cupola Jacobsoni) of adult lizards and snakes have received much anatomical, histological, physiological and behavioural attention. However, only limited embryological investigation into these structures, constrained to some anatomical or cellular studies and brief surveys, has been carried out thus far. The purpose of this study was, first, to examine the embryonic development of the vomeronasal organ and the associated structures in the grass snake (Natrix natrix), using three-dimensional reconstructions based on histological studies, and, second, to compare the obtained results with those presented in known publications on other snakes and lizards.

RESULTS

Five major developmental processes were taken into consideration in this study: separation of the vomeronasal organ from the nasal cavity and its specialization, development of the mushroom body, formation of the lacrimal duct, development of the cupola Jacobsoni and its relation to the vomeronasal nerve, and specialization of the sensory epithelium. Our visualizations showed the VNO in relation to the nasal cavity, choanal groove, lacrimal duct and cupola Jacobsoni at different embryonic stages. We confirmed that the choanal groove disappears gradually, which indicates that this structure is absent in adult grass snakes. On our histological sections, we observed a gradual growth in the height of the columns of the vomeronasal sensory epithelium and widening of the spaces between them.

CONCLUSIONS

The main ophidian taxa (Scolecophidia, Henophidia and Caenophidia), just like other squamate clades, seem to be evolutionarily conservative at some levels with respect to the VNO and associated structures morphology. Thus, it was possible to homologize certain embryonic levels of the anatomical and histological complexity, observed in the grass snake, with adult conditions of certain groups of Squamata. This may reflect evolutionary shift in Squamata from visually oriented predators to vomerolfaction specialists. Our descriptions offer material useful for future comparative studies of Squamata, both at their anatomical and histological levels.

Deep sequencing of the olfactory epithelium reveals specific chemosensory receptors are expressed at sexual maturity in the European eel Anguilla anguilla

Vertebrate genomes encode a diversity of G protein-coupled receptor (GPCR) that belong to large gene families and are used by olfactory systems to detect chemical cues found in the environment. It is not clear however, if individual receptors from these large gene families have evolved roles that are specific to certain life stages. Here, we used deep sequencing to identify differentially expressed receptor transcripts in the olfactory epithelia (OE) of freshwater, seawater and sexually mature male eels (Anguilla anguilla). This species is particularly intriguing because of its complex life cycle, extreme long-distance migrations and early-branching position within the teleost phylogeny. In the A. anguillaOE, we identified full-length transcripts for 13, 112, 6 and 38 trace amine-associated receptors, odorant receptors (OR) and type I and type II vomeronasal receptors (V1R and V2R). Most of these receptors were expressed at similar levels at different life stages and a subset of OR and V2R-like transcripts was more abundant in sexually mature males suggesting that ORs and V2R-like genes are important for reproduction. We also identified a set of GPCR signal transduction genes that were differentially expressed indicating that eels make use of different GPCR signal transduction genes at different life stages. The finding that a diversity of chemosensory receptors is expressed in the olfactory epithelium and that a subset is differentially expressed suggests that most receptors belonging to large chemosensory gene families have functions that are important at multiple life stages, while a subset has evolved specific functions at different life stages.

Insights into the origin of nematode chemosensory GPCRs: putative orthologs of the Srw family are found across several phyla of protostomes

Nematode chemosensory GPCRs in Caenorhabditis elegans (NemChRs) are classified into 19 gene families, and are initially thought to have split from the ancestral Rhodopsin family of GPCRs. However, earlier studies have shown that among all 19 NemChR gene families, only the srw family has a clear sequence relationship to the ancestral Rhodopsin GPCR family. Yet, the phylogenetic relationships between the srw family of NemChRs and the Rhodopsin subfamilies are not fully understood. Also, a widespread search was not previously performed to check for the presence of putative srw family-like sequences or the other 18 NemChR families in several new protostome species outside the nematode lineage. In this study, we have investigated for the presence of 19 NemChR families across 26 eukaryotic species, covering basal eukaryotic branches and provide the first evidence that the srw family of NemChRs is indeed present across several phyla of protostomes. We could identify 29 putative orthologs of the srw family in insects (15 genes), molluscs (11 genes) and Schistosoma mansoni (3 genes). Furthermore, using HMM-HMM profile based comparisons and phylogenetic analysis we show that among all Rhodopsin subfamilies, the peptide and SOG (somatostatin/opioid/galanin) subfamilies are phylogenetically the closest relatives to the srw family of NemChRs. Taken together, we demonstrate that the srw family split from the large Rhodopsin family, possibly from the peptide and/or SOG subfamilies, well before the split of the nematode lineage, somewhere close to the divergence of the common ancestor of protostomes. Our analysis also suggests that the srsx family of NemChRs shares a clear sequence homology with the Rhodopsin subfamilies, as well as with few of the vertebrate olfactory receptors. Overall, this study provides further insights into the evolutionary events that shaped the GPCR chemosensory system in protostome species.

Lineage-specific expansion of vomeronasal type 2 receptor-like (OlfC) genes in cichlids may contribute to diversification of amino acid detection systems

Fish use olfaction to sense a variety of nonvolatile chemical signals in water. However, the evolutionary importance of olfaction in species-rich cichlids is controversial. Here, we determined an almost complete sequence of the vomeronasal type 2 receptor-like (OlfC: putative amino acids receptor in teleosts) gene cluster using the bacterial artificial chromosome library of the Lake Victoria cichlid, Haplochromis chilotes. In the cluster region, we found 61 intact OlfC genes, which is the largest number of OlfC genes identified among the seven teleost fish investigated to date. Data mining of the Oreochromis niloticus (Nile tilapia) draft genome sequence, and genomic Southern hybridization analysis revealed that the ancestor of all modern cichlids had already developed almost the same OlfC gene repertoire, which was accomplished by lineage-specific gene expansions. Furthermore, comparison of receptor sequences showed that recently duplicated paralogs are more variable than orthologs of different species at particular sites that were predicted to be involved in amino acid selectivity. Thus, the increase of paralogs through gene expansion may lead to functional diversification in detection of amino acids. This study implies that cichlids have developed a potent capacity to detect a variety of amino acids (and their derivatives) through OlfCs, which may have contributed to the extraordinary diversity of their feeding habitats.

Neural circuits mediating olfactory-driven behavior in fish

The fish olfactory system processes odor signals and mediates behaviors that are crucial for survival such as foraging, courtship, and alarm response. Although the upstream olfactory brain areas (olfactory epithelium and olfactory bulb) are well-studied, less is known about their target brain areas and the role they play in generating odor-driven behaviors. Here we review a broad range of literature on the anatomy, physiology, and behavioral output of the olfactory system and its target areas in a wide range of teleost fish. Additionally, we discuss how applying recent technological advancements to the zebrafish (Danio rerio) could help in understanding the function of these target areas. We hope to provide a framework for elucidating the neural circuit computations underlying the odor-driven behaviors in this small, transparent, and genetically amenable vertebrate.

Identification of chemosensory receptor genes from vertebrate genomes

Chemical senses are essential for the survival of animals. In vertebrates, mainly three different types of receptors, olfactory receptors (ORs), vomeronasal receptors type 1 (V1Rs), and vomeronasal receptors type 2 (V2Rs), are responsible for the detection of chemicals in the environment. Mouse or rat genomes contain >1,000 OR genes, forming the largest multigene family in vertebrates, and have >100 V1R and V2R genes as well. Recent advancement in genome sequencing enabled us to computationally identify nearly complete repertories of OR, V1R, and V2R genes from various organisms, revealing that the numbers of these genes are highly variable among different organisms depending on each species' living environment. Here I would explain bioinformatic methods to identify the entire repertoires of OR, V1R, and V2R genes from vertebrate genome sequences.

Vertebrate extracellular calcium-sensing receptor evolution: selection in relation to life history and habitat

Ionic calcium (Ca(2+)) supports essential functions within physiological systems, and consequently its concentration is homeostatically regulated within narrow bounds in the body fluids of animals through endocrine effects at ion-transporting osmoregulatory tissues. In vertebrates, extracellular Ca(2+) is detected at the cell surface by the extracellular calcium-sensing receptor (CaSR), a member of the G protein-coupled receptor (GPCR) superfamily. Interestingly, the taxonomic distribution of CaSRs is restricted to vertebrates, with some CaSR-like receptors apparently present in non-vertebrate chordates. Since bone is a known Ca(2+) storage site and is characteristically restricted to the vertebrate lineage, we hypothesized a functional association of CaSR with vertebrate skeleton that may have an ancient origin. Protein sequence alignment and phylogenetic analysis of vertebrate CaSRs and related GPCRs of the glutamate receptor-like family expose similarities and indel differences among these receptors, and reveal the evolutionary history of CaSRs. Evolutionary selection was tested statistically by evaluating the relationship between non-synonymous (replacement, dN) versus synonymous (silent, dS) amino acid substitution rates (as dN/dS) of protein-coding DNA sequences among branches of the estimated protein phylogeny. On a background of strong purifying selection (dN/dS<1) in the CaSR phylogeny, statistical evidence for adaptive evolution (dN/dS>1) was detected on some branches to major clades in the CaSR phylogeny, especially to the tetrapod vertebrate CaSRs and chordate CaSR-like branches. Testing also revealed overall purifying selection at the codon level. At some sites relaxation from strong purifying selection was seen, but evidence for adaptive evolution was not detected for individual sites. The results suggest purifying selection of CaSRs, and of adaptive evolution among some major vertebrate clades, reflecting clade specific differences in natural history and organismal biology, including skeletal involvement in calcium homeostasis.

Characterization of squamate olfactory receptor genes and their transcripts by the high-throughput sequencing approach

The olfactory receptor (OR) genes represent the largest multigene family in the genome of terrestrial vertebrates. Here, the high-throughput next-generation sequencing (NGS) approach was applied to characterization of OR gene repertoires in the green anole lizard Anolis carolinensis and the Japanese four-lined ratsnake Elaphe quadrivirgata. Tagged polymerase chain reaction (PCR) products amplified from either genomic DNA or cDNA of the two species were used for parallel pyrosequencing, assembling, and screening for errors in PCR and pyrosequencing. Starting from the lizard genomic DNA, we accurately identified 56 of 136 OR genes that were identified from its draft genome sequence. These recovered genes were broadly distributed in the phylogenetic tree of vertebrate OR genes without severe biases toward particular OR families. Ninety-six OR genes were identified from the ratsnake genomic DNA, implying that the snake has more OR gene loci than the anole lizard in response to an increased need for the acuity of olfaction. This view is supported by the estimated number of OR genes in the Burmese python's draft genome (∼280), although squamates may generally have fewer OR genes than terrestrial mammals and amphibians. The OR gene repertoire of the python seems unique in that many class I OR genes are retained. The NGS approach also allowed us to identify candidates of highly expressed and silent OR gene copies in the lizard's olfactory epithelium. The approach will facilitate efficient and parallel characterization of considerable unbiased proportions of multigene family members and their transcripts from nonmodel organisms.

Molecular biological research on olfactory chemoreception in fishes

This review describes recent molecular biological research on olfactory chemoreception in fishes. The recent rapid development of molecular biological techniques has provided new valuable information on the main and vomeronasal olfactory receptor (OR) genes, the axonal projection from ciliated, microvillous and crypt-olfactory receptor cells to the olfactory bulb, properties of odorant substances and olfactory imprinting and homing in salmon. Many important questions, however, remain unanswered on functional differences among OR genes, on ligand binding to each OR and on the molecular biological mechanisms underlying olfactory imprinting and homing in salmon. Olfactory chemoreception is believed to be the oldest sensory cue for both animal survival and adaptation to various different environments. Further intensive molecular biological research on olfactory memory formation and remembrance should be carried out to clarify the fundamental process of olfactory chemoreception in fishes.

The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage

Background

In gnathostomes, chemosensory receptors (CR) expressed in olfactory epithelia are encoded by evolutionarily dynamic gene families encoding odorant receptors (OR), trace amine-associated receptors (TAAR), V1Rs and V2Rs. A limited number of OR-like sequences have been found in invertebrate chordate genomes. Whether these gene families arose in basal or advanced vertebrates has not been resolved because these families have not been examined systematically in agnathan genomes.

Results

Petromyzon is the only extant jawless vertebrate whose genome has been sequenced. Known to be exquisitely sensitive to several classes of odorants, lampreys detect fewer amino acids and steroids than teleosts. This reduced number of detectable odorants is indicative of reduced numbers of CR gene families or a reduced number of genes within CR families, or both, in the sea lamprey. In the lamprey genome we identified a repertoire of 59 intact single-exon CR genes, including 27 OR, 28 TAAR, and four V1R-like genes. These three CR families were expressed in the olfactory organ of both parasitic and adult life stages.

Conclusion

An extensive search in the lamprey genome failed to identify potential orthologs or pseudogenes of the multi-exon V2R family that is greatly expanded in teleost genomes, but did find intact calcium-sensing receptors (CASR) and intact metabotropic glutamate receptors (MGR). We conclude that OR and V1R arose in chordates after the cephalochordate-urochordate split, but before the diversification of jawed and jawless vertebrates. The advent and diversification of V2R genes from glutamate receptor-family G protein-coupled receptors, most likely the CASR, occurred after the agnathan-gnathostome divergence.

The repertoire of G-protein-coupled receptors in Xenopus tropicalis

Background

The G-protein-coupled receptor (GPCR) superfamily represents the largest protein family in the human genome. These proteins have a variety of physiological functions that give them well recognized roles in clinical medicine. In Xenopus tropicalis, a widely used animal model for physiology research, the repertoire of GPCRs may help link the GPCR evolutionary history in vertebrates from teleost fish to mammals.

Results

We have identified 1452 GPCRs in the X. tropicalis genome. Phylogenetic analyses classified these receptors into the following seven families: Glutamate, Rhodopsin, Adhesion, Frizzled, Secretin, Taste 2 and Vomeronasal 1. Nearly 70% of X. tropicalis GPCRs are represented by the following three types of receptors thought to receive chemosensory information from the outside world: olfactory, vomeronasal 1 and vomeronasal 2 receptors.

Conclusion

X. tropicalis shares a more similar repertoire of GPCRs with mammals than it does with fish. An examination of the three major groups of receptors related to olfactory/pheromone detection shows that in X. tropicalis, these groups have undergone lineage specific expansion. A comparison of GPCRs in X. tropicalis, teleost fish and mammals reveals the GPCR evolutionary history in vertebrates.

Extracellular calcium-sensing receptor distribution in osmoregulatory and endocrine tissues of the tilapia

The extracellular calcium-sensing receptor (CaSR) serves an important detector function in vertebrate Ca(2+) homeostasis. In this study, we surveyed using immunohistochemistry the tissue and cellular distribution of the CaSR protein in the Mozambique tilapia (Oreochromis mossambicus) and the Japanese eel (Anguilla japonica). Specifically, we examined receptor expression in ion-transporting barrier tissues that may be directly responsive to extracellular Ca(2+) levels, and in tissues that are implicated in endocrine signaling to homeostatic effectors such as Ca(2+)-transporting epithelia. In tilapia osmoregulatory tissues, CaSR protein is strongly expressed in proximal segments of renal tubule, but not in distal segments (where Na(+),K(+)-ATPase is prominently expressed) or in glomeruli. The receptor was also localized in the ion-transporting mitochondria-rich cells of gill and in ion- and nutrient-transporting epithelia of middle and posterior intestine. Consistent with our earlier RT-PCR assessment of mRNA expression in tilapia, CaSR protein expression was salinity dependent in some osmoregulatory tissues. In tilapia pituitary gland, CaSR expression was observed in the rostral pars distalis (containing prolactin-secreting cells, and in the pars intermedia (containing somatolactin-secreting and melanocyte-stimulating hormone-secreting cells), with notably greater expression in the latter. In the eel, weak immunostaining was seen in the stanniocalcin-secreting cells of the corpuscles of Stannius. Olfactory lobe CaSR expression suggests an environment-sensing role for the receptor. Altogether, these findings support the involvement of CaSR in piscine Ca(2+) homeostasis at the levels of environmental sensing, of integrative endocrine signaling through both hypercalcemic (prolactin, and perhaps somatolactin) and hypocalcemic (stanniocalcin) hormones, and of direct local regulation of Ca(2+)-transporting tissues.

Genomic organization and evolution of the vomeronasal type 2 receptor-like (OlfC) gene clusters in Atlantic salmon, Salmo salar

There are three major multigene superfamilies of olfactory receptors (OR, V1R, and V2R) in mammals. The ORs are expressed in the main olfactory organ, whereas the V1Rs and V2Rs are located in the vomeronasal organ. Fish only possess one olfactory organ in each nasal cavity, the olfactory rosette; therefore, it has been proposed that their V2R-like genes be classified as olfactory C family G protein-coupled receptors (OlfC). There are large variations in the sizes of OR gene repertoires. Previous studies have shown that fish have between 12 and 46 functional V2R-like genes, whereas humans have lost all functional V2Rs, and frog sp. have more than 240. Pseudogenization of V2R genes is a prevalent event across species. In the mouse and frog genomes, there are approximately double the number of pseudogenes compared with functional genes. An oligonucleotide probe was designed from a conserved sequence from four Atlantic salmon OlfC genes and used to screen the Atlantic salmon bacterial artificial chromosome (BAC) library. Hybridization-positive BACs were matched to fingerprint contigs, and representative BACs were shotgun cloned and sequenced. We identified 55 OlfC genes. Twenty-nine of the OlfC genes are classified as putatively functional genes and 26 as pseudogenes. The OlfC genes are found in two genomic clusters on chromosomes 9 and 20. Phylogenetic analysis revealed that the OlfC genes could be divided into 10 subfamilies, with nine of these subfamilies corresponding to subfamilies found in other teleosts and one being salmon specific. There is also a large expansion in the number of OlfC genes in one subfamily in Atlantic salmon. Subfamily gene expansions have been identified in other teleosts, and these differences in gene number reflect species-specific evolutionary requirements for olfaction. Total RNA was isolated from the olfactory epithelium and other tissues from a presmolt to examine the expression of the odorant genes. Several of the putative OlfC genes that we identified are expressed only in the olfactory epithelium, consistent with these genes encoding odorant receptors.

Extraordinary diversity of chemosensory receptor gene repertoires among vertebrates

Chemosensation (smell and taste) is important to the survival and reproduction of vertebrates and is mediated by specific bindings of odorants, pheromones, and tastants by chemoreceptors that are encoded by several large gene families. This review summarizes recent comparative genomic and evolutionary studies of vertebrate chemoreceptor genes. It focuses on the remarkable diversity of chemoreceptor gene repertoires in terms of gene number and gene sequence across vertebrates and the evolutionary mechanisms that are responsible for generating this diversity. We argue that the great among-species variation of chemoreceptor gene repertoires is a result of adaptations of individual species to their environments and diets.

The molecular evolution of teleost olfactory receptor gene families

Four olfactory receptor gene families, all of them G protein-coupled receptors, have been identified and characterized in mammals--the odorant (OR), vomeronasal (V1R and V2R) and trace amine-associated (TAARs) receptors. Much less attention has been directed towards non-mammalian members of these families. Since a hallmark of mammalian olfactory receptors is their remarkable species specificity, an evaluation of the non-mammalian olfactory receptors is instructive both for comparative purposes and in its own right. In this review I have compiled the results currently available for all four olfactory gene families and discuss their phylogenomic properties in relation to their mammalian counterparts. Representatives of all four families are found in cartilaginous fish and/or jawless fish, allowing a minimal estimate for the evolutionary origin as preceding the segregation between cartilaginous and bony fish or cartilaginous and jawless fish, respectively. Gene repertoires of teleost olfactory receptors are smaller in size (OR, ORA), comparable (olfC), or even larger (TAAR) than the corresponding mammalian gene repertoires. Despite their smaller repertoire size, the teleost OR and ORA families show much larger divergence than their mammalian counterparts. Evolutionary rates vary greatly between families, with evidence for positive selection in teleost OR genes, whereas the ora genes are subject to strong negative selection, and in fact are being conserved among all teleost species investigated. With one exception, ligands are unknown for any of the four teleost olfactory receptor gene families, and so the considerable knowledge about the odor responses of the olfactory epithelium and the olfactory bulb can only be linked indirectly to the receptor repertoires.

Evolutionary patterns and selective pressures of odorant/pheromone receptor gene families in teleost fishes

Background

Teleost fishes do not have a vomeronasal organ (VNO), and their vomeronasal receptors (V1Rs, V2Rs) are expressed in the main olfactory epithelium (MOE), as are odorant receptors (ORs) and trace amine-associated receptors (TAARs). In this study, to obtain insights into the functional distinction among the four chemosensory receptor families in teleost fishes, their evolutionary patterns were examined in zebrafish, medaka, stickleback, fugu, and spotted green pufferfish.

Methodology/Principal Findings

Phylogenetic analysis revealed that many lineage-specific gene gains and losses occurred in the teleost fish TAARs, whereas only a few gene gains and losses have taken place in the teleost fish vomeronasal receptors. In addition, synonymous and nonsynonymous nucleotide substitution rate ratios (K_A/K_S) in TAARs tended to be higher than those in ORs and V2Rs.

Conclusions/Significance

Frequent gene gains/losses and high K_A/K_S in teleost TAARs suggest that receptors in this family are used for detecting some species-specific chemicals such as pheromones. Conversely, conserved repertoires of V1R and V2R families in teleost fishes may imply that receptors in these families perceive common odorants for teleosts, such as amino acids. Teleost ORs showed intermediate evolutionary pattern between TAARs and vomeronasal receptors. Many teleost ORs seem to be used for common odorants, but some ORs may have evolved to recognize lineage-specific odors.

Male-specific protein (MSP): a new gene linked to sexual behavior and aggressiveness of tilapia males

MSP is a male-specific protein initially identified in the serum of sexually active Sarotherodon galilaeus males, and is shown herein to be present in the serum of sexually mature males, but not females, of three other tilapia species. Cloning of the MSP cDNA and analysis of its predicted amino-acid sequence revealed that it is an outlier lipocalin that contains a signal peptide in its N-terminal region. The abundance of highly homologous sequences found in fish and the monophyletic relationship to tetrapod Alpha-1-acid glycoprotein (AGP) places it as a clade XII lipocalin. MSP was shown to undergo major N-glycosylation, characteristic of many lipocalins. The expression pattern of MSP, as determined at both the RNA and protein levels, points to the liver, head kidney and testis as production tissues, and resembles a pattern typical of some hormones. We found that MSP is secreted in urine and seminal fluids, and is present in the skin mucus of socially dominant males. Moreover, we discovered a positive correlation between MSP levels in the serum and the dominance and aggressive behavior displayed by socially dominant males. Based on these data, we suggest that MSP is a novel male-specific lipocalin that may function in intra and inter-sex communication.

Screening the V2R-type putative odorant receptor gene repertoire in bitterling Tanakia lanceolata

Fish odorant receptors comprise several distinct families of G protein-coupled receptors. The repertoires of fish vomeronasal receptor family 2 (V2R) genes differ substantially among species, which seems to be related to the different odor sensitivity among fish species. In this study, the number and diversity of V2R genes in a cyprinid fish, bitterling Tanakia lanceolata, were examined by gene cloning and genomic Southern blot analysis. Fifty-six distinct V2R partial sequences were identified by extensive cloning of degenerate PCR fragments. Phylogenetic analysis of the V2R genes in bitterling and other model fishes showed that the bitterling V2Rs were subdivided into eight subfamilies that diverged before the separation of cyprinids and other fishes. Most bitterling V2Rs belonged to two major subfamilies, while only one or a few genes were identified in the remaining six subfamilies. The repertoire of bitterling V2Rs was quite similar to that of zebrafish, although some bitterling-specific gene expansions have also occurred. Based on the genomic Southern blot analysis, the copy number of the bitterling V2R gene was estimated at least 60, similar to the number of V2R genes found in the zebrafish genome. This also suggests that bitterling has relatively larger number of V2R genes than other model fishes.

Genomic organization and characterization of two vomeronasal 1 receptor-like genes (ora1 and ora2) in Atlantic salmon Salmo salar

Olfactory receptors are encoded by three large multigene superfamilies (OR, V1R and V2R) in mammals. Fish do not possess a vomeronasal system; therefore, it has been proposed that their V1R-like genes be classified as olfactory receptors related to class A G protein-coupled receptors (ora). Unlike mammalian genomes, which contain more than a hundred V1R genes, the five species of teleost fish that have been investigated to date appear to have six ora genes (ora1-6) except for pufferfish that have lost ora1. The common ancestor of salmonid fishes is purported to have undergone a whole genome duplication. As salmonids have a life history that requires the use of olfactory cues to navigate back to their natal habitats to spawn, we set out to determine if ora1 or ora2 is duplicated in a representative species, Atlantic salmon (Salmo salar). We used an oligonucleotide probe designed from a conserved sequence of several teleost ora2 genes to screen an Atlantic salmon BAC library (CHORI-214). Hybridization-positive BACs belonged to a single fingerprint contig of the Atlantic salmon physical map. All were also positive for ora2 by PCR. One of these BACs was chosen for further study, and shotgun sequencing of this BAC identified two V1R-like genes, ora1 and ora2, that are in a head-to-head conformation as is seen in some other teleosts. The gene products, ora1 and ora2, are highly conserved among teleosts. We only found evidence for a single ora1-2 locus in the Atlantic salmon genome, which was mapped to linkage group 6. Fluorescent in situ hybridization (FISH) analysis placed ora1-2 on chromosome 12. Conserved synteny was found surrounding the ora1 and ora2 genes in Atlantic salmon, medaka and three-spined stickleback, but not zebrafish.

Molecular genetic dissection of the zebrafish olfactory system

Zebrafish is now becoming one of the most useful model organisms in neurobiology. In addition to its general advantageous properties (external fertilization, rapid development, transparency of embryos, etc.), the zebrafish is amenable to various genetic engineering technologies such as transgenesis, mutagenesis, gene knockdown, and transposon-mediated gene transfer. A transgenic approach unraveled two segregated neural circuits originating from ciliated and microvillous sensory neurons in the olfactory epithelium to distinct regions of the olfactory bulb, which likely convey different types of olfactory information (e.g., pheromones and odorants) to the higher olfactory centers. Furthermore, the two basic principles identified in mice, so-called one neuron-one receptor rule and convergence of like axons to target glomeruli, are basically preserved also in the zebrafish, rendering this organism a suitable model vertebrate for studies of the olfactory system. This review summarizes recent advances in our knowledge on genetic, molecular, and cellular mechanisms underlying the development and functional architecture of the olfactory neural circuitry in the zebrafish.

Inferring evolution of fish proteins: the globin case study

Because hemoglobins (Hbs) of all animal species have the same heme group, differences in their properties, including oxygen affinity, electrophoretic mobility, and pH sensitivity, must result from the interaction of the prosthetic group with specific amino acid residues in the primary structure. For this reason, fish globins have been the object of extensive studies in the past few years, not only for their structural characteristics but also because they offer the possibility to investigate the evolutionary history of Hbs in marine and freshwater species living in a large variety of environmental conditions. For such a purpose, phylogenetic analysis of globin sequences can be combined with knowledge of the phylogenetic relationships between species. In addition, Type I functional-divergence analysis is aimed toward predicting the amino acid residues that are more likely responsible for biochemical diversification of different Hb families. These residues, mapped on the three-dimensional Hb structure, can provide insights into functional and structural divergence.

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.

Sensory genes and mate choice: Evidence that duplications, mutations, and adaptive evolution alter variation in mating cue genes and their receptors

Fascinating new data, revealed through gene sequencing, comparative genomics, and genetic engineering, precisely establish which genes are involved in mate choice and mating activity--behaviors that are surprisingly understudied from a genetic perspective. Discussed here are some of the recently identified visual and chemosensory genes that are involved in mate choice and mating behavior. These genes' products are involved in the production, transmission, and receipt of crucial sensory mate-choice cues that affect fitness. This review exposes newfound evidence that alternative splicing, gene-expression pattern changes, and molecular genetic variation in sensory genes are crucial for both intra- and interspecific mate choice and mating success. Many sensory genes have arisen through gene duplications, and data amassed from studies conducted at scales ranging from individual genes to genomic comparisons show that strong, positive Darwinian selection acts on several mating-related genes and that these genes evolve rapidly.

Evolution of Trace Amine–Associated Receptor (TAAR) Gene Family in Vertebrates: Lineage-Specific Expansions and Degradations of a Second Class of Vertebrate Chemosensory Receptors Expressed in the Olfactory Epithelium

The trace amine-associated receptors (TAARs) form a specific family of G protein-coupled receptors in vertebrates. TAARs were initially considered neurotransmitter receptors, but recent study showed that mouse TAARs function as chemosensory receptors in the olfactory epithelium. To clarify the evolutionary dynamics of the TAAR gene family in vertebrates, near-complete repertoires of TAAR genes and pseudogenes were identified from the genomic assemblies of 4 teleost fishes (zebrafish, fugu, stickleback, and medaka), western clawed frogs, chickens, 3 mammals (humans, mice, and opossum), and sea lampreys. Database searches revealed that fishes had many putatively functional TAAR genes (13-109 genes), whereas relatively small numbers of TAAR genes (3-22 genes) were identified in tetrapods. Phylogenetic analysis of these genes indicated that the TAAR gene family was subdivided into 5 subfamilies that diverged before the divergence of ray-finned fishes and tetrapods. In tetrapods, virtually all TAAR genes were located in 1 specific region of their genomes as a gene cluster; however, in fishes, TAAR genes were scattered throughout more than 2 genomic locations. This possibly reflects a whole-genome duplication that occurred in the common ancestor of ray-finned fishes. Expression analysis of zebrafish and stickleback TAAR genes revealed that many TAARs in these fishes were expressed in the olfactory organ, suggesting the relatively high importance of TAARs as chemosensory receptors in fishes. A possible evolutionary history of the vertebrate TAAR gene family was inferred from the phylogenetic and comparative genomic analyses.

Diversification and adaptive evolution of putative sweet taste receptors in threespine stickleback

The threespine stickleback Gasterosteus aculeatus is known to include several morphologically and ecologically divergent forms. Its phenotypic traits related to feeding vary among forms, and are considered to be a result of adaptations to various environments to find foods effectively. To examine whether the diversification of feeding modes in the stickleback involves genetic changes of the sense of taste, taste receptor family 1 (T1R) genes in stickleback were analyzed and compared with those in other model fishes. Ten T1R genes and 2 pseudogenes were identified from the stickleback genomic sequences. In particular, putative sweet taste receptors (T1R2s) highly increased in number in stickleback (8 genes and 2 pseudogenes) compared to other fishes (2-3 genes). Maximum likelihood estimations of nonsynonymous-synonymous nucleotide substitution rate have indicated that stickleback T1R2 are under positive selection. Expression analysis by RT-PCR revealed that most stickleback T1R genes were expressed in the taste organs; however, at least two T1R2 genes were not expressed in the taste organs, suggesting that the expression levels of these T1R2 genes may be fluctuated through the life history. In addition, sequencing analysis showed that several T1R2 genes in an anadromous form stickleback individual collected from the western Pacific (Japan) were substantially different from those in genomic data derived from a freshwater form individual collected in North America. This suggested that intra-specific variations of stickleback T1R2 genes were considerably large. Our results imply that, in stickleback, T1R2s have diversified through adaptation to various environments, probably to perceive substances important for its survival and reproduction.

Mining the gene repertoire and ESTs for G protein-coupled receptors with evolutionary perspective

The purpose of this article was to review recent progress in mining the gene repertoire and expressed sequence tags (ESTs) for the super-family of G protein-coupled receptors (GPCRs) in the form of a proceeding from the Nordic GPCR meeting held at the Nobel Forum, Karolinska Institute in August 2006. We update and give an overview of the expansion of the main families of GPCRs; Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin (GRAFS) in perspective of fully sequenced genomes. We look into the most recent findings including the work that has been carried out on the spotted green puffer fish (Tetraodon nigroviridis), mouse (Mus musculus), chicken (Gallus gallus), slime mold (Dictyostelium discoideum) and the plant pathogenic fungus Magnaporthe grisea. We use examples from our recent work on chicken GPCRs to highlight the importance of detailed assembly and curation of sequences and how that can affect percentage similarity and phylogeny. ESTs can give valuable information about expression patterns. GPCRs have comparatively low numbers of EST suggesting that GPCRs are in generally expressed in lower amount than other genes. We discuss similarities in the evolution of the trace amine associated receptors with other sensory receptors.

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.