Analysis of penetrance and expressivity during ontogenesis supports a stochastic choice of zebrafish odorant receptors from predetermined groups of receptor genes

Expression of olfactory receptor genes in non-olfactory tissues in the developing and adult zebrafish

Since the discovery of olfactory receptor (OR) genes, their expression in non-olfactory tissues have been reported in rodents and humans. For example, mouse OR23 (mOR23) is expressed in sperm and muscle cells and has been proposed to play a role in chemotaxis and muscle migration, respectively. In addition, mouse mesencephalic dopaminergic neurons express various ORs, which respond to corresponding ligands. As the OR genes comprise the largest multigene family of G protein-coupled receptors in vertebrates (over 400 genes in human and 1000 in rodents), it has been difficult to categorize the extent of their diverse expression in non-olfactory tissues making it challenging to ascertain their function. The zebrafish genome contains significantly fewer OR genes at around 140 genes, and their expression pattern can be easily analyzed by carrying out whole mount in situ hybridization (ISH) assay in larvae. In this study, we found that 31 out of 36 OR genes, including or104-2, or108-1, or111-1, or125-4, or128-1, or128-5, 133-4, or133-7, or137-3 are expressed in various tissues, including the trunk, pharynx, pancreas and brain in the larvae. In addition, some OR genes are expressed in distinct brain regions such as the hypothalamus and the habenula in a dynamic temporal pattern between larvae, juvenile and adult zebrafish. We further confirmed that OR genes are expressed in non-olfactory tissues by RT-PCR in larvae and adults. These results indicate tight regulation of OR gene expression in the brain in a spatial and temporal manner and that the expression of OR genes in non-olfactory tissues are conserved in vertebrates. This study provides a framework to start investigating the function of ORs in the zebrafish brain.

A novel-odour exploration test for measuring anxiety in adult and larval zebrafish

BACKGROUND

Existing methods to assess anxiety in zebrafish are mostly based on visual exploration. However, evidence suggests that zebrafish are more attuned to olfactory than visual stimuli. We developed a novel-odour exploration test (NOEt) for zebrafish.

NEW METHOD

Adult zebrafish were exposed to a stimulus sponge soaked with olfactory cue and a control sponge with no cue, placed at the extremities of a narrow, rectangular tank. We scored time spent close to the two sponges to calculate the attraction towards the olfactory cue. In experiment 1, we tested adult zebrafish in the NOEt using various olfactory cues. In experiment 2, we tested larvae. In experiment 3, we compared the NOEt with the most used method to assess anxiety, the open-field test.

RESULTS

In experiment 1, zebrafish responded markedly to cues, by either approaching or avoiding the soaked sponge according to the type of cue. The temporal pattern of exploration toward the cue was similar to that of novel objects' exploration in this species. In experiment 2, larvae responded to novel odours, but differently from adults. In experiment 3, we found a relationship between the NOEt and the open-field test.

COMPARISON WITH EXISTING METHOD(S)

Compared to existing tests, the NOEt has the advantage of exploiting the preferred sensory modality of zebrafish. Moreover, it can be used in early stages because olfactory receptors develop early in this species.

CONCLUSIONS

The NOEt is a simple, rapid and low-cost test to study anxiety in zebrafish using the spontaneous exploration of novel olfactory cues.

Nucleobase-containing compounds evoke behavioural, olfactory, and transcriptional responses in model fishes

The sensory system of animals detects a massive and unknown array of chemical cues that evoke a diversity of physiological and behavioural responses. One group of nitrogen-containing carbon ring chemicals—nucleobases—are thought to be involved in numerous behaviours yet have received little attention. We took a top-down approach to examine responses evoked by nucleobases at behavioural, tissue, and gene expression levels. Fish generally avoided nucleobases, and this behaviour, when observed, was driven by purines but not pyrimidines. At the tissue level, olfactory neuron generator potential responses tended to be concentration specific and robust at concentrations lower than amino acid detection ranges. In terms of gene expression, more than 2000 genes were significantly upregulated following nucleobase exposure, some of which were expected (e.g., genes involved in purine binding) and some of which were not (e.g., tubulin-related genes). Humanized RNA pathway analysis showed that we had exposed the animal to a nucleobase. Our data indicate that responses to nucleobase-containing compounds may be highly structure based and are evident from changes in behaviour to mRNA expression. Many of these responses were surprising, and all provide numerous routes for further research endeavour.

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.

Coordination of olfactory receptor choice with guidance receptor expression and function in olfactory sensory neurons

Olfactory sensory neurons choose to express a single odorant receptor (OR) from a large gene repertoire and extend axons to reproducible, OR-specific locations within the olfactory bulb. This developmental process produces a topographically organized map of odorant experience in the brain. The axon guidance mechanisms that generate this pattern of connectivity, as well as those that coordinate OR choice and axonal guidance receptor expression, are incompletely understood. We applied the powerful approach of single-cell RNA-seq on newly born olfactory sensory neurons (OSNs) in young zebrafish larvae to address these issues. Expression profiles were generated for 56 individual Olfactory Marker Protein (OMP) positive sensory neurons by single-cell (SC) RNA-seq. We show that just as in mouse OSNs, mature zebrafish OSNs typically express a single predominant OR transcript. Our previous work suggests that OSN targeting is related to the OR clade from which a sensory neuron chooses to express its odorant receptor. We categorized each of the mature cells based on the clade of their predominantly expressed OR. Transcripts expressed at higher levels in each of three clade-related categories were identified using Penalized Linear Discriminant Analysis (PLDA). A genome-wide approach was used to identify membrane-associated proteins that are most likely to have guidance-related activity. We found that OSNs that choose to express an OR from a particular clade also express specific subsets of potential axon guidance genes and transcription factors. We validated our identification of candidate axon guidance genes for one clade of OSNs using bulk RNA-seq from a subset of transgene-labeled neurons that project to a single protoglomerulus. The differential expression patterns of selected candidate guidance genes were confirmed using fluorescent in situ hybridization. Most importantly, we observed axonal mistargeting in knockouts of three candidate axonal guidance genes identified in this analysis: nrp1a, nrp1b, and robo2. In each case, targeting errors were detected in the subset of axons that normally express these transcripts at high levels, and not in the axons that express them at low levels. Our findings demonstrate that specific, functional, axonal guidance related genes are expressed in subsets of OSNs that that can be categorized by their patterns of OR expression.

Olfactory sensory axons target specific protoglomeruli in the olfactory bulb of zebrafish

Background

The axons of Olfactory Sensory Neurons (OSNs) project to reproducible target locations within the Olfactory Bulb (OB), converting odorant experience into a spatial map of neural activity. We characterized the initial targeting of OSN axons in the zebrafish, a model system suitable for studying axonal targeting early in development. In this system the initial targets of OSN axons are a small number of distinct, individually identifiable neuropilar regions called protoglomeruli. Previously, Olfactory Marker Protein-expressing and TRPC2-expressing classes of OSNs were shown to project to specific, non-overlapping sets of protoglomeruli, indicating that particular subsets of OSNs project to specific protoglomerular targets. We set out to map the relationship between the classical Odorant Receptor (OR) an OSN chooses to express and the protoglomerulus its axon targets.

Methods

A panel of BACs were recombineered so that the axons of OSNs choosing to express modified ORs were fluorescently labeled. Axon projections were followed into the olfactory bulb to determine the protoglomeruli in which they terminated.

Results

RNA-seq demonstrates that OSNs express a surprisingly wide variety of ORs and Trace Amine Associated Receptors (TAARs) very early when sensory axons are arriving in the bulb. Only a single OR is expressed in any given OSN even at these early developmental times. We used a BAC expression technique to map the trajectories of OSNs expressing specific odorant receptors. ORs can be divided into three clades based upon their sequence similarities. OSNs expressing ORs from two of these clades project to the CZ protoglomerulus, while OSNs expressing ORs from the third clade project to the DZ protoglomerulus. In contrast, OSNs expressing a particular TAAR project to multiple protoglomeruli. Neither OR choice nor axonal targeting are related to the position an OSN occupies within the olfactory pit.

Conclusions

Our results demonstrate that it is not the choice of a particular OR, but of one from a category of ORs, that is related to initial OSN target location within the olfactory bulb. These choices are not related to OSN position within the olfactory epithelium.

The peripheral olfactory system of vertebrates: molecular, structural and functional basics of the sense of smell

The sense of smell provides people and animals with an abundance of information about their environment, helping them to navigate, detect potential threats, control food intake, choose sexual partners and significantly influence intraspecies social behav­ior. The perception of odors begins with the binding of odor molecules to specialized olfactory receptor proteins, which nearly all be­long to the superfamily of G protein-coupled receptors. Altogether, five different olfactory receptor gene families have been described to date, among them the largest gene family in the genome with over 1000 genes in rodents. The signal transduction cascade coupled to the receptors has already been well characterized for this family. Three different classes of receptor neurons-ciliated, microvillous and crypt receptor neurons-can be distinguished by their anatomical and molecular characteristics. Generally, an individual receptor neuron expresses only a single olfactory receptor gene, and olfactory receptor neurons that express the same receptor converge into a common target structure, a glomerulus, which generates a receptotop­ic map in the first olfactory brain region, the olfactory bulb. This review article provides a general overview of the peripheral detection of odorants on the one hand, while on the other it focuses on recent advances in the field, including new findings on the peripher­al modulation of olfactory signals.

Experience-dependent versus experience-independent postembryonic development of distinct groups of zebrafish olfactory glomeruli

Olfactory glomeruli are innervated with great precision by the axons of different olfactory sensory neuron types and act as functional units in odor information processing. Approximately 140 glomeruli are present in each olfactory bulb of adult zebrafish; these units consist of either highly stereotypic large glomeruli or smaller anatomically indistinguishable glomeruli. In the present study, we investigated developmental differences among these types of glomeruli. We observed that 10 large and individually identifiable glomeruli already developed before hatching, at 72 h after fertilization, in configurations that resembled their mature organization. However, the cross-sectional area of these glomeruli increased throughout larval development, and they eventually comprised the largest units in postlarval olfactory bulbs. In contrast, small and anatomically indistinguishable glomeruli formed only after hatching, apparently by segregating from five larger precursors that were identifiable during embryonic development. The differentiation of these small glomeruli proceeded with conspicuous variation in number and arrangement, both among larvae and between olfactory bulbs of the same individuals. To determine factors that might contribute to this variability, we investigated the effects of olfactory enrichment on the development of amino acid-responsive lateral glomeruli, which include both large and small units. Larvae reared in an amino acid-enriched environment had normal large lateral glomeruli, but the small lateral glomeruli were more numerous and displayed reduced cross-sectional areas compared with glomeruli in control animals. Our results suggest that large and small glomeruli mature via distinct developmental processes that may be differentially influenced by sensory experience.

Functional development of the olfactory system in zebrafish

The olfactory system has become a popular model to study the function of neuronal circuits and the molecular and cellular mechanisms underlying the development of neurons and their connections. An excellent model to combine studies of function and development is the zebrafish because it not only permits sophisticated molecular and genetic analyses of development, but also functional measurements of neuronal activity patterns in the intact brain. This article reviews insights into the functional development of the olfactory system that have been obtained in zebrafish. The focus is on the specification of olfactory sensory neurons (OSNs), the mechanisms controlling odorant receptor expression and OSN identity, the pathfinding of OSN axons towards target glomeruli in the olfactory bulb (OB), the development of glomeruli and functional topographic maps in the OB, and the development of inhibitory interneurons in the OB.

Onset and dynamic expression of S100 proteins in the olfactory organ and the lateral line system in zebrafish development

In the zebrafish olfactory epithelium, three morphologically distinct olfactory neurons express different marker proteins. We utilize this feature to access developmental dynamics of one of the neuron types, the crypt cells, to determine whether they are differentiated at a stage similar to other olfactory neurons. Immunohistochemical studies using an S100 antibody that specifically recognizes crypt cells showed that S100-positive cells appear in olfactory rosettes as early as at 2day postfertilization (dpf). However, some of the rosettes did not have any S100-positive cells until 4 dpf. The number of S100-positive cells in individual rosettes increased steadily over the next 3days before it decreased significantly. There were 7.8 S100-positive cells per rosettes on average in larvae at 7 dpf. The number reduced to 2.2 at 9 dpf. A recovery to a pre-reduction level was detected in 12 dpf larvae. We also observed S100-positive cells in neuromasts of the lateral line system in 2 dpf larvae, suggesting that the crypt cells and sensory cells in the neuromasts have similar onsets of differentiation. Our data have provided a time line of differentiation of crypt cells in development of the olfactory system and demonstrated that this type of cell is differentiated at a stage similar to ciliated and microvillous olfactory neurons. A nonlinear growth trajectory of the crypt cell population in the first nine days of zebrafish development implicates a possible functional significance of crypt cells in early life stages of zebrafish.

The sense of scents: olfactory behaviors in the zebrafish

The olfactory sensory system is perhaps the most intriguing of the sensory systems making up the peripheral nervous system. Understanding how olfactory sensory stimuli result in behaviors relevant to the animal is made complicated by the fact that olfactory stimuli are more difficult to quantify than light and sound stimuli. Furthermore, in all vertebrates the olfactory sensory neurons regenerate throughout life, presenting a fascinating problem of how both the functional repertoire of olfactory sensory neurons and fidelity of connections to the central nervous system are maintained. Olfactory behaviors are crucial for feeding and reproduction and the olfactory information essential to these behaviors appears to be processed separately in distinct regions of the central nervous system. Zebrafish represent an excellent model system in which the strength of genetics and development can be combined with neuroethological techniques to unravel the mechanisms underlying olfactory behaviors in vertebrate animals.

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.

Early functional development of interneurons in the zebrafish olfactory bulb

In the adult olfactory bulb (OB) of vertebrates, local GABAergic interneurons (INs) mediate recurrent and lateral inhibition between the principal neurons of the OB, the mitral cells (MCs), and play pivotal roles in the processing of odor-evoked activity patterns. The properties and functions of INs in the developing OB are, however, not well understood. We studied the functional development of INs in the OB of living zebrafish larvae 3-6 days postfertilization using anatomical techniques and in-vivo two-photon Ca2+ imaging. We identified MCs and INs by cell-type-specific expression of transgenic fluorescent markers and found that the IN:MC ratio was lower than in the adult fish. Moreover, the fraction of INs responding with Ca2+ signals to a set of natural odors was substantially lower than in adults. Odors of different chemical classes evoked overlapping patterns of Ca2+ signals that were concentrated in the center of the IN layer. The GABA(A) receptor agonists GABA and muscimol strongly suppressed odor responses, whereas a GABA(A) receptor antagonist enhanced responses and altered the spatial distribution of odor-evoked activity. These results indicate that IN odor responses at early developmental stages are sparse and exhibit no obvious chemotopic organization. Nevertheless, GABAergic signaling is already inhibitory at early stages of OB development and strongly influences odor-evoked activity patterns. Hence, INs already participate in the processing of odor information at very early stages of OB development even though the majority of INs emerge only at later stages.

Early development of functional spatial maps in the zebrafish olfactory bulb

In the adult olfactory bulb (OB), particular chemical classes of odorants preferentially activate glomeruli within loosely defined regions, resulting in a coarse and fractured "chemotopic" map. In zebrafish, amino acids and bile acids predominantly stimulate glomeruli in the lateral and medial OB, respectively. We studied the development of these spatial response maps in zebrafish. At 3 d postfertilization (dpf), the OB contained protoglomerular structures that became refined and more numerous during subsequent days. In a transgenic zebrafish line expressing the Ca2+ indicator protein inverse pericam, mainly in mitral cells, odor responses in the OB were first detected at 2.5-3 dpf. Already at this stage, amino acids and bile acids evoked activity predominantly in the lateral and medial OB, respectively. Two-photon Ca2+ imaging using a synthetic indicator was used to reconstruct activity patterns at higher resolution in three dimensions. Responses to amino acids and bile acids were detected predominantly in the lateral and medial OB, respectively, with little overlap. Between 2.5 and 6 dpf, the number of odor-responsive units increased, but the overall spatial organization of activity persisted. Hence, a coarse spatial organization of functional activity maps is established very early during OB development when glomeruli are not yet differentiated. This spatial organization is maintained during development and growth of neuronal circuits and may have important functions for odor processing in larvae, for the differentiation of glomeruli, and for the refinement of activity maps at later developmental stages.

3D atlas describing the ontogenic evolution of the primary olfactory projections in the olfactory bulb of Xenopus laevis

The adult Xenopus presents the unique capability to smell odors both in water and air thanks to two different olfactory pathways. Nevertheless, the tadpole can initially perceive only water-borne odorants, as the olfactory receptor neurons (ORN) that will detect air-borne odorants develop later. Such a phenomenon requires major reorganization processes. Here we focused on the precise description of the neuroanatomical modifications occurring in the olfactory bulb (OB) of the tadpole throughout metamorphosis. Using both carbocyanine dyes and lectin staining, we investigated the evolution of ORN projection patterns into the OB from Stages 47 to 66, thus covering the period of time when all the modifications take place. Although our results confirm previous works (Reiss and Burd [1997] Semin Cell Dev Biol 8:171-179), we showed for the first time that the main olfactory bulb (MOB) is subdivided into seven zones at Stage 47 plus the accessory olfactory bulb (AOB). These seven zones receive fibers dedicated to aquatic olfaction ("aquatic fibers") and are conserved until Stage 66. At Stage 48 the first fibers dedicated to the aerial olfaction constitute a new dorsomedial zone that grows steadily, pushing the seven original zones ventrolaterally. Only the part of the OB receiving aquatic fibers is fragmented, reminiscent of the organization described in fish. This raises the question of whether such an organization in zones constitutes a plesiomorphy or is linked to aquatic olfaction. We generated a 3D atlas at several stages which are representative of the reorganization process. This will be a useful tool for future studies of development and function.

Cascades of response vectors of olfactory receptor neurons in Xenopus laevis tadpoles

Olfactory receptor neurons (ORNs) of Xenopus laevis tadpoles respond to water-born stimuli such as amino acids. Their sensitivity spectra with respect to amino acids have recently been shown to become more selective over ontogenetic stages [Manzini & Schild (2004) J. Gen. Physiol., 123, 99-107]. In this paper, we undertake a theoretical analysis of this data set and determine the correlational relationships among odorant responses represented as binary response vectors. We first show that, on the one hand, the number of 204 ORN classes (out of 283 recorded ORNs) cannot be explained by a random expression pattern of olfactory receptors (ORs). On the other hand, this number does not appear to be reconcilable with the idea that individual ORNs express one type of OR each. The covariance matrix of stimulus responses shows that the responses to some stimuli are correlated to those of others. Furthermore, the response vectors show positive as well as negative correlations among each other. While the positive correlations can partly be explained by the differing response frequencies to the odorants used, the negative ones cannot. Finally, we analyse the similarity among responses using the Hamming distance as a distance measure, the result being that most response vectors differ from others by small Hamming distances. Such vectors are shown to form pattern cascades, possibly reflecting a decreasing number of ORs being expressed over ontogenetic stages.