Biology subjects

Matsunami, H.

Publications and source records attributed to Matsunami, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Allosteric Gating Mechanism Regulates Odorant Selectivity and Antagonism in Odorant Receptors

Odorant receptors (ORs) belong to class A G protein coupled receptors that detect diverse small molecules, yet the steps that link odorant association to receptor mediated selectivity remains incompletely defined. Here we combined 1.26 milliseconds of all-atom odorant association Molecular Dynamics simulations with Markov state modeling and cell-based cAMP measurements to examine two human ORs receptors that recognize chemically distinct odorants. In the class I receptor OR51E2, propionate associates via two extracellular pathways gated for selectivity by residues in the extracellular loop 2 and 3. The longer alkyl chain heptanoate occupies this gate and reduces propionate association and signaling which is consistent with the observed antagonist behavior of heptanoate. Pocket-expanding mutations at F155 and L158 allosterically regulate ECL2-ECL3 gate by permitting longer-chain fatty acids to adopt fully inserted poses that support gate closure, while also attenuating propionate responses. In the class II receptor OR1A1, hydrophobic odorants partition into the membrane and reach the orthosteric site mostly through multiple transmembrane paths. A mutational scan of gating residues and analysis of intermediate-state occupancies suggest that an orthosteric substitution at G108 can allosterically bias odorant association path choice. Together, these results support a model in which odorant association paths and gate residence, together with allosteric coupling between the orthosteric site and entry gates, contribute to odorant specificity and antagonism in odorant receptors.

biophysics↗

bioRxiv2026

Rapid odorant metabolism organizes identity- and timing-based odor representations by olfactory bulb inputs and outputs

Sensory neurons encode information about external stimuli in the form of stimulus-specific patterns of activity across their population. In the mammalian olfactory system, olfactory sensory neurons (OSNs) encode odor identity with odorant-specific combinatorial patterns that are temporally structured by inhalation. We investigated the stimulus features that determine these inhalation-linked patterns, leveraging receptor- and functionally-defined OSN populations in awake mice. We found that both the chemical tuning and temporal dynamics of many odorant-evoked responses deviate from prevailing models of receptor-ligand binding and sensitivity-based timing relationships. These deviations were well-explained by rapid metabolism of odorants within the olfactory mucosa, which generates secondary odorants that activate additional OSNs within a single breath. This process fundamentally reshapes odor representations at naturally-occurring concentrations and timescales relevant to perception. Importantly, we found that timing features robustly discriminate inhaled from metabolism-generated odorants, and that these timing differences persist at the level of olfactory bulb output. Our results suggest a novel role for inhalation-linked timing in odor coding - to disambiguate inhaled odorants from those generated internally - and raise the possibility that the nervous system may differentially process external and internally-sourced olfactory stimuli on the basis of their temporal dynamics.

neuroscience↗

bioRxiv2026

Decoding Smell from Receptor Structure

Olfaction enables animals to detect and discriminate a vast array of chemicals, yet how odorant receptors (ORs) encode ligand selectivity remains unclear. Although recent advances in protein structure prediction have expanded access to OR structures, linking these to function at scale has been challenging. Here, we combined AlphaFold3-predicted receptor structures with protein language model embeddings and in vivo pS6-IP-Seq measurements of olfactory sensory neuron activation across a chemically diverse odor panel to train a deep learning model of OR-ligand interactions. The resulting framework predicts receptor responses, organizes receptors by functional similarity independent of sequence, and identifies structural determinants of ligand selectivity. These findings establish a structure-based map of OR function and provide a foundation for predictive and interpretable models of olfactory coding.

molecular biology↗

bioRxiv2025

Evolutionary diversity and function of odorant receptors in birds

Abstract: Odorant receptors (ORs) form among the largest gene families in vertebrates; most mammals have hundreds of intact OR genes. Although birds display diverse behavior and ecology, they were long thought to rely minimally on olfaction. We reexamine this idea by using genomic data to uncover diverse and variable OR repertoires in birds, including the nocturnal kiwi (Apteryx mantelli), which possesses the largest number of ORs known (3,750). We reveal that widespread gene conversion is shaping the evolution of bird ORs, reflecting a novel mechanism for generating functional diversity. We show that ORs are expressed in avian olfactory sensory neurons and show responses to defined, ecologically relevant odorants. Our results demonstrate the importance and functional mechanisms underlying olfaction in birds.

evolutionary biology↗

bioRxiv2023

Engineered odorant receptors illuminate structural principles of odor discrimination

A central challenge in olfaction is understanding how the olfactory system detects and distinguishes odorants with diverse physicochemical properties and molecular configurations. Vertebrate animals perceive odors via G protein-coupled odorant receptors (ORs). In humans, [~]400 ORs enable the sense of smell. The OR family is composed of two major classes: Class I ORs are tuned to carboxylic acids while Class II ORs, representing the vast majority of the human repertoire, respond to a wide variety of odorants. How ORs recognize chemically diverse odorants remains poorly understood. A fundamental bottleneck is the inability to visualize odorant binding to ORs. Here, we uncover fundamental molecular properties of odorant-OR interactions by employing engineered ORs crafted using a consensus protein design strategy. Because such consensus ORs (consORs) are derived from the 17 major subfamilies of human ORs, they provide a template for modeling individual native ORs with high sequence and structural homology. The biochemical tractability of consORs enabled four cryoEM structures of distinct consORs with unique ligand recognition properties. The structure of a Class I consOR, consOR51, showed high structural similarity to the native human receptor OR51E2 and yielded a homology model of a related member of the human OR51 family with high predictive power. Structures of three Class II consORs revealed distinct modes of odorant-binding and activation mechanisms between Class I and Class II ORs. Thus, the structures of consORs lay the groundwork for understanding molecular recognition of odorants by the OR superfamily.

neuroscience↗

bioRxiv2022

Structural basis of odorant recognition by a human odorant receptor

Our sense of smell enables us to navigate a vast space of chemically diverse odor molecules. This task is accomplished by the combinatorial activation of approximately 400 olfactory G protein-coupled receptors (GPCRs) encoded in the human genome1-3. How odorants are recognized by olfactory receptors (ORs) remains mysterious. Here we provide mechanistic insight into how an odorant binds a human olfactory receptor. Using cryogenic electron microscopy (cryo-EM), we determined the structure of active human OR51E2 bound to the fatty acid propionate. Propionate is bound within an occluded pocket in OR51E2 and makes specific contacts critical to receptor activation. Mutation of the odorant binding pocket in OR51E2 alters the recognition spectrum for fatty acids of varying chain length, suggesting that odorant selectivity is controlled by tight packing interactions between an odorant and an olfactory receptor. Molecular dynamics simulations demonstrate propionate-induced conformational changes in extracellular loop 3 to activate OR51E2. Together, our studies provide a high-resolution view of chemical recognition of an odorant by a vertebrate OR, providing insight into how this large family of GPCRs enables our olfactory sense.

biochemistry↗

bioRxiv2022

Antagonistic interactions between odorants alter human odor perception.

The olfactory system detects a vast number of odorants using hundreds of olfactory receptors (ORs), the largest group of the G protein-coupled receptor (GPCR) superfamily. Each OR is activated by specific odorous ligands. Like other GPCRs, activation of ORs may be blocked through antagonism. Recent reports highlight widespread antagonisms in odor mixtures influencing olfactory neuron activities. However, it is unclear if and how these antagonisms influence perception of odor mixtures. Here we show that odorant antagonisms at the receptor level alter odor perception. Using a large-scale heterologous expression, we first identified a set of human ORs that are activated by methanethiol and hydrogen sulfide, two extremely potent volatile sulfur malodors. We then screened odorants that block activation of these ORs and identified a set of antagonists, including {beta}-ionone. Finally, human sensory evaluation revealed that odor intensity and unpleasantness of methanethiol were decreased by {beta}-ionone. Odor intensity of {beta}-ionone itself is not correlated with the degree of suppression of malodor sensation. Suppression was also not observed when methanethiol and {beta}-ionone were simultaneously introduced to different nostrils. Together, our data supports the model that odor sensation is altered through antagonistic interactions at the level of the ORs.

neuroscience↗

bioRxiv2022

Persistent post-COVID-19 smell loss is associated with inflammatory infiltration and altered olfactory epithelial gene expression

Most human subjects infected by SARS-CoV-2 report an acute alteration in their sense of smell, and more than 25% of COVID patients report lasting olfactory dysfunction. While animal studies and human autopsy tissues have suggested mechanisms underlying acute loss of smell, the pathophysiology that underlies persistent smell loss remains unclear. Here we combine objective measurements of smell loss in patients suffering from post-acute sequelae of SARS-CoV-2 infection (PASC) with single cell sequencing and histology of the olfactory epithelium (OE). This approach reveals that the OE of patients with persistent smell loss harbors a diffuse infiltrate of T cells expressing interferon-gamma; gene expression in sustentacular cells appears to reflect a response to inflammatory signaling, which is accompanied by a reduction in the number of olfactory sensory neurons relative to support cells. These data identify a persistent epithelial inflammatory process associated with PASC, and suggests mechanisms through which this T cell-mediated inflammation alters the sense of smell.

neuroscience↗

bioRxiv2021

Encoding of odors by mammalian olfactory receptors

O_LIIdentified ligands for > 500 mouse ORs C_LIO_LIORs are specifically tuned towards individual odorants and their molecular properties C_LIO_LIOdor molecular properties are informative of odor responses C_LIO_LIPredictive modeling and convergent evolution analyses suggest specific residues within a canonical location for odorant binding C_LI Olfactory receptors (ORs) constitute the largest multi-gene family in the mammalian genome, with hundreds to thousands of loci in humans and mice respectively1. The rapid expansion of this massive family of genes has been generated by numerous duplication and diversification events throughout evolutionary history. This size, similarity, and diversity has made it challenging to define the principles by which ORs encode olfactory stimuli. Here, we performed a broad surveying of OR responses, using an in vivo strategy, against a diverse panel of odorants. We then used the resulting interaction profiles to uncover relationships between OR responses, odorants, odor molecular properties, and OR sequences. Our data and analyses revealed that ORs generally exhibited sparse tuning towards odorants and their molecular properties. Odor molecular property similarity between pairs of odorants was informative of odor response similarity. Finally, ORs sharing response to an odorant possessed amino acids at poorly conserved sites that exhibited both, predictive power towards odorant selectivity and convergent evolution. The localization of these residues occurred primarily at the interface of the upper halves of the transmembrane domains, implying that canonical positions govern odor selectivity across ORs. Altogether, our results provide a basis for translating odorants into receptor neuron responses for the unraveling of mammalian odor coding.

neuroscience↗

bioRxiv2021

Decoding the olfactory map: targeted transcriptomics link olfactory sensory neurons to glomeruli

Sensory processing in vertebrate olfactory systems is organized across olfactory bulb glomeruli, wherein axons of peripheral sensory neurons expressing the same olfactory receptor co-terminate to transmit receptor-specific activity to central neurons. Understanding how receptors map to glomeruli is therefore critical to understanding olfaction. High-throughput spatial transcriptomics is a rapidly advancing field, but low-abundance olfactory receptor expression within glomeruli has previously precluded high-throughput mapping of receptors to glomeruli. Here we combined spatial sectioning along the anteroposterior, dorsoventral, and mediolateral axes with target capture enrichment sequencing to overcome low-abundance target expression. This strategy allowed us to spatially map 86% of olfactory receptors across the olfactory bulb and uncover a relationship between OR sequence and glomerular position. ONE SENTENCE SUMMARYTargeted enrichment of olfactory receptor mRNA in olfactory bulb sections determines spatial positions for murine glomeruli.

neuroscience↗

bioRxiv2021

Genetic and functional odorant receptor variation in the Homo lineage

Using ancient DNA sequences, we explored the function of olfactory receptor genes in the genus Homo. Humans, Neandertals, and Denisovans independently adapted to a wide range of geographic environments and the odours produced by their food. Variations in their odorant receptor protein sequence and structure resulted in variation in detection and perception. Studying thirty olfactory receptor genes, we found our relatives showed highly conserved receptor structures, but Homo sapiens did not. Variants led to changes in sensitivity to some odors, but no change in specificity, indicating a common olfactory repertoire in our genus. Diversity of geographic adaptations in H. sapiens may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. One-Sentence SummaryUsing ancient DNA we studied the sense of smell in our extinct ancestors and in our relatives, Denisovans and Neanderthals

evolutionary biology↗

bioRxiv2021

Aging-related olfactory loss is associated with olfactory stem cell transcriptional alterations in humans

Presbyosmia, or aging related olfactory loss, occurs in a majority of humans over age 65 years, yet remains poorly understood, with no specific treatment options. The olfactory epithelium (OE) in the nasal fossa is the peripheral organ for olfaction, and is subject to acquired damage, suggesting a likely site of pathology in aging. OE basal stem cells reconstitute the neuroepithelium in response to cell loss under normal conditions. In aged OE, patches of respiratory-like metaplasia have been observed histologically, consistent with a failure in normal neuroepithelial homeostasis or repair. Accordingly, we have focused on identifying cellular and molecular changes in presbyosmic OE. Combining psychophysical testing with olfactory mucosa biopsy analysis, single cell RNA-sequencing (scRNA-seq), and human olfactory culture studies, we identified evidence for inflammation-associated changes in the OE stem cells of presbyosmic patients. The presbyosmic basal stem cells exhibited increased expression of genes involved in response to cytokines or stress, or the regulation of proliferation and differentiation. To facilitate further study of human OE stem cells, we developed an adult human basal cell culture model. Characterization of cultures using scRNA-seq confirmed maintenance of a reserve stem cell-like phenotype, and brief cytokine exposure in basal cell cultures resulted in increased expression of TP63, a transcription factor acting to prevent OE stem cell differentiation. Our data are consistent with a process by which aging-related inflammatory changes in OE stem cells may contribute to presbyosmia, via the disruption of normal epithelial homeostasis, suggesting that OE stem cells may represent a rational therapeutic target for restoration of olfaction. One Sentence SummarySingle cell profiling suggests that inflammatory-associated olfactory epithelial stem cell dysfunction is associated with presbyosmia in humans.

neuroscience↗

bioRxiv2021

A sex chromosome drives the emergence of vocal learning following hormonal manipulation in female zebra finches

Zebra finches are sexually dimorphic vocal learners. Males learn to sing by imitating mature conspecifics, but females do not. Absence of song in females is associated with partial atrophy and apparent repression of several vocal learning brain regions during development. However, atrophy can be prevented and vocal learning retained in females when given early pharmacological estrogen treatment. To screen for candidate drivers of this sexual dimorphism, we performed an unbiased transcriptomic analysis of song learning nuclei specializations relative to the surrounding regions from either sex, treated with vehicle or estrogen until 30 days old when divergence between the sexes becomes anatomically apparent. Analyses of transcriptomes by RNA sequencing identified song nuclei-specialized gene expressed modules associated with sex and estrogen manipulation. Female HVC and Area X gene modules were specialized by estrogen supplementation, exhibiting a subset of the transcriptomic specializations observed in males. Female RA and LMAN specialized modules were less dependent on estrogen. The estrogen-induced gene modules in females were enriched for anatomical development functions and strongly correlated to the expression of several Z sex chromosome genes. We present a hypothesis where reduced dosage and expression of these Z chromosome genes suppresses the full development of the song system and thus song learning behavior, which is partially rescued by estrogen treatment.

neuroscience↗

bioRxiv2020

Transcriptome analysis for the development of cell-type specific labeling to study olfactory circuits

In each sensory system of the brain, mechanisms exist to extract distinct features from stimuli to generate a variety of behavioural repertoires. These often correspond to different cell types at some stage in sensory processing. In the mammalian olfactory system, complex information processing starts in the olfactory bulb, whose output is conveyed by mitral and tufted cells (MCs and TCs). Despite many differences between them, and despite the crucial position they occupy in the information hierarchy, little is known how these two types of projection neurons differ at the mRNA level. Here, we sought to identify genes that are differentially expressed between MCs and TCs, with an ultimate goal to generate a cell-type specific Cre-driver line, starting from a transcriptome analysis using a large and publicly available single-cell RNA-seq dataset (Zeisel et al., 2018). Despite many genes showing differential expressions, we identified only a few that were abundantly and consistently expressed only in MCs. After further validating these putative markers using in-situ hybridization, two genes, namely Pkib and Lbdh2, remained as promising candidates. Using CRISPR/Cas9-mediated gene editing, we generated Cre-driver lines and analysed the resulting recombination patterns. This analysis indicated that our new inducible Cre-driver line, Lbhd2-CreERT2, can be used to genetically label MCs in a tamoxifen dose-dependent manner, as assessed by soma locations, projection patterns and sensory-evoked responses. Hence this line is a promising tool for future investigations of cell-type specific contributions to olfactory processing and demonstrates the power of publicly accessible data in accelerating science.

neuroscience↗

bioRxiv2020

Estrogen and sex-dependent loss of the vocal learning system in female zebra finches

Sex hormones alter the organization of the brain during early development and coordinate various behaviors throughout life. In zebra finches, song learning is limited to males, and the associated song learning brain pathway only matures in males and atrophies in females. This atrophy can be reversed by giving females exogenous estrogen during early post-hatch development, but whether normal male song system development requires estrogen is uncertain. For the first time in songbirds, we administered exemestane, a potent third generation estrogen synthesis inhibitor, from the day of hatching until adulthood. We examined the behavior, brain, and transcriptome of individual song nuclei of these pharmacologically manipulated animals. We found that males with long-term exemestane treatment had diminished male-specific plumage, impaired song learning, but retained normal song nuclei sizes and most, but not all, of their specialized transcriptome. Consistent with prior findings, females with long-term estrogen treatment retained a functional song system, and we further observed their song nuclei had specialized gene expression profiles similar, but not identical to males. We also observed that different song nuclei responded to estrogen manipulation differently, with Area X in the striatum being the most altered by estrogen modulation. These findings support the hypothesis that song learning is an ancestral trait in both sexes, which was subsequently suppressed in females of some species, and that estrogen has come to play a critical role in modulating this suppression as well as refinement of song learning.

neuroscience↗

bioRxiv2020

Functions of olfactory receptors are decoded from their sequence

G protein-coupled receptors (GPCRs) conserve common structural folds and activation mechanisms, yet their ligand spectra and functions are highly diversified. This work investigated how the functional variations in olfactory GPCRs (ORs)-the largest GPCR family-are encoded in the primary sequence. With the aid of site-directed mutagenesis and molecular simulations, we built machine learning models to predict OR-ligand pairs as well as basal activity of ORs. In vitro functional assay confirmed 20 new OR-odorant pairs, including 9 orphan ORs. Residues around the odorant-binding pocket dictate the odorant selectivity/specificity of the ORs. Residues that encode the varied basal activities of the ORs were found to mostly surround the conserved motifs as well as the binding pocket. The machine learning approach, which is readily applicable to mammalian OR families, will accelerate OR-odorant mapping and the decoding of combinatorial OR codes for odors.

bioinformatics↗

bioRxiv2019

Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic

AbstractUnderstanding how genes and experiences work in concert to generate phenotypic variability will provide a better understanding of individuality. Here, we considered this in the context of the main olfactory epithelium, a chemosensory structure with over a thousand distinct cell-types, in mice. We identified a subpopulation of at least three types of olfactory sensory neurons, defined by receptor expression, whose abundances were sexually dimorphic. This subpopulation of olfactory sensory neurons was over-represented in sex-separated female mice and responded robustly to the male-specific semiochemicals 2-sec-butyl-4,5-dihydrothaizole and (methylthio)methanethiol. Sex-combined housing led to a robust attenuation of the female over-representation. Testing of Bax null mice revealed a Bax-dependence in generating the sexual dimorphism in sex-separated mice. Altogether, our results suggest a profound role of experience in influencing homeostatic neural lifespan mechanisms to generate a robust sexually dimorphic phenotype in the main olfactory epithelium.

neuroscience↗

bioRxiv2019

Modulation of the combinatorial code of odorant receptor response patterns in odorant mixtures

The perception of odors relies on combinatorial codes consisting of odorant receptor (OR) response patterns to encode odor identity. The modulation of these patterns by odorant interactions at ORs potentially explains several olfactory phenomena: mixture suppression, unpredictable sensory outcomes, and the perception of odorant mixtures as unique objects. We determined OR response patterns to 4 odorants and 3 binary mixtures in vivo in mice, identifying 30 responsive ORs. These patterns typically had a few strongly responsive ORs and a greater number of weakly responsive ORs. The ORs responsive to an odorant were often unrelated sequences distributed across several OR subfamilies. Mixture responses predicted pharmacological interactions between odorants, which were tested in vitro by heterologous expression of ORs in cultured cells. These tests provided independent evidence confirming odorant agonists for 13 ORs and identified both suppressive and additive effects of mixing odorants. This included 11 instances of antagonism of ORs by an odorant, 1 instance of additive responses to a binary mixture, 1 instance of suppression of a strong agonist by a weak agonist, and the discovery of an inverse agonist for an OR. These findings demonstrate that interactions between odorants at ORs are common.

cell biology↗