Biology subjects

de March, C. A.

Publications and source records attributed to de March, C. A..

9 recordsLinked to original sources

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↗

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↗

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

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↗

bioRxiv2019

Divergence from conserved residues underlies intracellular retention of mammalian odorant receptors

Mammalian odorant receptors are a diverse and rapidly evolving set of G protein-coupled receptors expressed in olfactory cilia membranes. Most odorant receptors show little to no cell surface expression in non-olfactory cells due to endoplasmic reticulum retention, which has slowed down biochemical studies. Here, we provide evidence that structural instability and divergence from conserved residues of individual odorant receptors underlie intracellular retention using a combination of large-scale screening of odorant receptors cell surface expression in heterologous cells, point mutations, structural modeling, and machine learning techniques. We demonstrate the importance of conserved residues by synthesizing "consensus" odorant receptors that show high levels of cell surface expression similar to conventional G protein-coupled receptors. Furthermore, we associate in silico structural instability with poor cell surface expression using molecular dynamics simulations. We propose an enhanced evolutionary capacitance of olfactory sensory neurons that enable the functional expression of odorant receptors with cryptic mutations. Significance StatementOdor detection in mammals depends on the largest family of G protein-coupled receptors, the odorant receptors, which represent [~]2% of our protein-coding genes. The vast majority of odorant receptors are trapped within the cell when expressed in non-olfactory cells. The underlying causes of why odorant receptors cannot be functionally expressed in non-olfactory cells have remained enigmatic for over 20 years. Our study points to divergence from a consensus sequence as a key factor in a receptors inability to function in non-olfactory cells, which in turn, helps explain odorant receptors exceptional functional diversity and rapid evolution. We also show the success of protein engineering strategies for promoting odorant receptor cell surface expression.

cell biology↗