A unified nomenclature for vertebrate olfactory receptors

A family of olfactory receptors uniquely expanded in marsupial and monotreme genomes are expressed by a T cell subset also unique to marsupials and monotremes

Olfactory receptors (OR), expressed on olfactory neurons, mediate the sense of smell. Recently, OR have also been shown to be expressed in non-olfactory tissues, including cells of the immune system. An analysis of single-cell transcriptomes of splenocytes of the grey short-tailed opossum (Monodelphis domestica) found OR are expressed on a subset of T cells, the γμ T cells, that are unique to marsupials and monotremes. A majority of opossum γμ T cells transcriptomes contain OR family 14 transcripts, specifically, from the OR14C subfamily. Amongst the mammals, the OR14 gene family is expanded in the genomes of marsupials and monotremes, and rarer or absent in placental mammals. In summary, here we demonstrate the intriguing correlation that a family of OR genes, abundant in the genomes of marsupials and monotremes, are ectopically expressed in a particular subset of T cells unique to the marsupials and monotremes.

Role of Ectopic Olfactory Receptors in the Regulation of the Cardiovascular-Kidney-Metabolic Axis

Olfactory receptors (ORs) represent one of the largest yet least investigated families of G protein-coupled receptors in mammals. While initially believed to be functionally restricted to the detection and integration of odors at the olfactory epithelium, accumulating evidence points to a critical role for ectopically expressed ORs in the regulation of cellular homeostasis in extranasal tissues. This review aims to summarize the current state of knowledge on the expression and physiological functions of ectopic ORs in the cardiovascular system, kidneys, and primary metabolic organs and emphasizes how altered ectopic OR signaling in those tissues may impact cardiovascular-kidney-metabolic health.

The Olfactory Trail of Neurodegenerative Diseases

Alterations in olfactory functions are proposed as possible early biomarkers of neurodegenerative diseases. Parkinson's and Alzheimer's diseases manifest olfactory dysfunction as a symptom, which is worth mentioning. The alterations do not occur in all patients, but they can serve to rule out neurodegenerative pathologies that are not associated with small deficits. Several prevalent neurodegenerative conditions, including impaired smell, arise in the early stages of Parkinson's and Alzheimer's diseases, presenting an attractive prospect as a snitch for early diagnosis. This review covers the current knowledge on the link between olfactory deficits and Parkinson's and Alzheimer's diseases. The review also covers the emergence of olfactory receptors as actors in the pathophysiology of these diseases. Olfactory receptors are not exclusively expressed in olfactory sensory neurons. Olfactory receptors are widespread in the human body; they are expressed, among others, in the testicles, lungs, intestines, kidneys, skin, heart, and blood cells. Although information on these ectopically expressed olfactory receptors is limited, they appear to be involved in cell recognition, migration, proliferation, wound healing, apoptosis, and exocytosis. Regarding expression in non-chemosensory regions of the central nervous system (CNS), future research should address the role, in both the glia and neurons, of olfactory receptors. Here, we review the limited but relevant information on the altered expression of olfactory receptor genes in Parkinson's and Alzheimer's diseases. By unraveling how olfactory receptor activation is involved in neurodegeneration and identifying links between olfactory structures and neuronal death, valuable information could be gained for early diagnosis and intervention strategies in neurodegenerative diseases.

A phylogenetics-based nomenclature system for steroid receptors in teleost fishes

Teleost fishes have emerged as tractable models for studying the neuroendocrine regulation of social behavior via molecular genetic techniques, such as CRISPR/Cas9 gene editing. Moreover, teleosts provide an opportunity to investigate the evolution of steroid receptors and their functions, as species within this lineage possess novel steroid receptor paralogs that resulted from a teleost-specific whole genome duplication. Although teleost fishes have grown in popularity as models for behavioral neuroendocrinology, there is not a consistent nomenclature system for steroid receptors and their genes, which may impede a clear understanding of steroid receptor paralogs and their functions. Here, we used a phylogenetic approach to assess the relatedness of protein sequences encoding steroid receptor paralogs in 18 species from 12 different orders of the Infraclass Teleostei. While most similarly named sequences grouped based on the established phylogeny of the teleost lineage, our analysis revealed several inconsistencies in the nomenclature of steroid receptor paralogs, particularly for sequences encoding estrogen receptor beta (ERβ). Based on our results, we propose a nomenclature system for teleosts in which Greek symbols refer to proteins and numbers refer to genes encoding different subtypes of steroid receptors within the five major groups of this nuclear receptor subfamily. Collectively, our results bridge a critical gap by providing a cohesive naming system for steroid receptors in teleost fishes, which will serve to improve communication, promote collaboration, and enhance our understanding of the evolution and function of steroid receptors across vertebrates.

Sensommatic: an efficient pipeline to mine and predict sensory receptor genes in the era of reference-quality genomes

SUMMARY

Sensory receptor gene families have undergone extensive expansion and loss across vertebrate evolution, leading to significant variation in receptor counts between species. However, due to their species-specific nature, conventional reference-based annotation tools often underestimate the true number of sensory receptors in a given species. While there has been an exponential increase in the taxonomic diversity of publicly available genome assemblies in recent years, only ∼30% of vertebrate species on the NCBI database are currently annotated. To overcome these limitations, we developed 'Sensommatic', an automated and accessible sensory receptor annotation pipeline. Sensommatic implements BLAST and AUGUSTUS to mine and predict sensory receptor genes from whole genome assemblies, adopting a one-to-many gene mapping approach. While designed for vertebrates, Sensommatic can be extended to run on non-vertebrate species by generating customized reference files, making it a scalable and generalizable tool.

AVAILABILITY AND IMPLEMENTATION

Source code and associated files are available at: https://github.com/GMHughes/Sensommatic.

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.

Comparative analyses reveal potential genetic mechanisms for high-altitude adaptation of Schizopygopsis fishes based on chromosome-level genomes

The schizothoracine fishes, widely distributed in the Qinghai-Tibetan Plateau and its adjacent areas, are considered as ideal models for investigation of high-altitude adaptation. Schizophygopsis are one group of the highly specialized schizothoracine fishes, and the genetic basis for their high-altitude adaptation is poorly understood. In this study, we performed comparative genomics analyses to investigate the potential genetic mechanisms for high-altitude adaptation of Schizopygopsis malacanthus and Schizopygopsis pylzovi based on the chromosome-level genomes. Functional enrichment analysis revealed that many expanded gene families in Schizopygopsis were associated with immune response while many contracted gene families were functionally associated with olfaction. Among the 123 positively selected genes (PSGs), angpt2a was detected in HIF-1 signaling pathway and possibly related to the hypoxia adaptation of Schizopygopsis. Furthermore, two PSGs cox15 and ndufb10 were distributed in thermogenesis, and there was a Schizopygopsis-specific missense mutation in cox15 (Gln115Glu), which possibly contributed to the cold temperature adaptation of the Schizopygopsis. Kyoto Encyclopedia of Genes and Genomes enrichment of the PSGs revealed three significant pathways including metabolic pathways, cell cycle, and homologous recombination and Gene Ontology enrichment analysis of the PSGs revealed several categories associated with DNA repair, cellular response to DNA damage stimulus, and metabolic process. Chromosome-scale characterization of olfactory receptor (OR) repertoires indicated that Schizopygopsis had the least number of OR genes, and the OR gene contraction was possibly caused by the limited food variety and the environmental factors such as lower air pressure, lower humidity, and lower temperature. Our study will help expand our understanding of the potential adaptive mechanism of Schizopygopsis to cope with the high-altitude conditions.

Parallel evolution of fish bi-modal breathing and expansion of olfactory receptor (OR) genes: toward a universal ORs nomenclature

Olfactory receptors (ORs) play a key role in the prime sensorial perception, being highly relevant for intra/interspecific interactions. ORs are a subgroup of G-protein coupled receptors that exhibit highly complex subgenomes in vertebrates. However, OR repertoires remain poorly studied in fish lineages, precluding finely retracing their origin, evolution, and diversification, especially in the most basal groups. Here, we conduct an exhaustive gene screening upon 43 high-quality fish genomes exhibiting varied gene repertoires (2-583 genes). While the early vertebrates performed gas exchange through gills, we hypothesize that the emergence of new breathing structures (swim bladder and paired lungs) in early osteichthyans may be associated with expansions in the ORs gene families sensitive to airborne molecules. Additionally, we verify that the OR repertoire of moderns actinopterygians has not increased as expected following a whole genome duplication, likely due to regulatory mechanisms compensating the gene load excess. Finally, we identify 25 distinct OR families, allowing us to propose an updated universal nomenclature for the fish ORs.

The VGNC: expanding standardized vertebrate gene nomenclature

The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 as a sister project to the HUGO Gene Nomenclature Committee, to approve gene nomenclature in vertebrate species without an existing dedicated nomenclature committee. The VGNC aims to harmonize gene nomenclature across selected vertebrate species in line with human gene nomenclature, with orthologs assigned the same nomenclature where possible. This article presents an overview of the VGNC project and discussion of key findings resulting from this work to date. VGNC-approved nomenclature is accessible at https://vertebrate.genenames.org and is additionally displayed by the NCBI, Ensembl, and UniProt databases.

Netrins and Netrin Receptors are Essential for Normal Targeting of Sensory Axons in the Zebrafish Olfactory Bulb

Olfactory sensory neurons that express related odorant receptors specifically target large identifiable neuropils called protoglomeruli when they first reach the olfactory bulb in the zebrafish. This crude odorant receptor-related mapping is further refined as odorant receptor-specific glomeruli segregate from protoglomeruli later in development. Netrins are a prominent class of axon guidance molecules whose contribution to olfactory circuit formation is poorly studied. Morpholino knock down experiments have suggested that Netrin/Dcc signaling is involved in normal protoglomerular targeting. Here we extend these findings with more detailed characterization and modeling of netrin expression, and by examining protoglomerular targeting in mutant lines fornetrin1a (ntn1a), netrin1b (ntn1b), and their receptorsunc5b,dcc, andneo1a. We confirm thatntn1a,ntn1b, anddccare required for normal protoglomerular guidance of a subset of olfactory sensory neurons that are labeled with the Tg(or111-7:IRES:Gal4) transgene. We also observe errors in the targeting of these axons inunc5bmutants, but not inneo1a mutants. Our findings are consistent with ntn1a andntn1bacting primarily as attractants for olfactory sensory neurons targeting the central zone protoglomerulus.

Building the Chordata Olfactory Receptor Database using more than 400,000 receptors annotated by Genome2OR

Olfactory receptors are poorly annotated for most genome-sequenced chordates. To address this deficiency, we developed a nhmmer-based olfactory receptor annotation tool Genome2OR ( https://github.com/ToHanwei/Genome2OR.git ), and used it to process 1,695 sequenced chordate genomes in the NCBI Assembly database as of January, 2021. In total, 765,248 olfactory receptor genes were annotated, with 404,426 functional genes and 360,822 pseudogenes, which represents a four-fold increase in the number of annotated olfactory receptors. Based on the annotation data, we built a database called Chordata Olfactory Receptor Database (CORD, https://cord.ihuman.shanghaitech.edu.cn ) for archiving, analysing and disseminating the data. Beyond the primary data, we offer derivative information, including pictures of species, cross references to public databases, structural models, sequence similarity networks and sequence profiles in the CORD. Furthermore, we did brief analyses on these receptors, including building a huge protein sequence similarity network covering all receptors in the database, and clustering them into 20 communities, classifying the 20 communities into three categories based on their presences/absences in ray-finned fish and/or lobe-finned fish. We infer that olfactory receptors should have unique activation and desensitization mechanisms by analysing their sequences and structural models. We believe the CORD can benefit the researchers and the general public who are interested in olfaction.

Placing human gene families into their evolutionary context

Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.

Short-Chain Fatty Acid Receptors and Blood Pressure Regulation: Council on Hypertension Mid-Career Award for Research Excellence 2021

The gut microbiome influences host physiology and pathophysiology through several pathways, one of which is microbial production of chemical metabolites which interact with host signaling pathways. Short-chain fatty acids (SCFAs) are a class of gut microbial metabolites known to activate multiple signaling pathways in the host. Growing evidence indicates that the gut microbiome is linked to blood pressure, that SCFAs modulate blood pressure regulation, and that delivery of exogenous SCFAs lowers blood pressure. Given that hypertension is a key risk factor for cardiovascular disease, the examination of novel contributors to blood pressure regulation has the potential to lead to novel approaches or treatments. Thus, this review will discuss SCFAs with a focus on their host G protein-coupled receptors including GPR41 (G protein-coupled receptor 41), GPR43, and GPR109A, as well as OLFR78 (olfactory receptor 78) and OLFR558. This includes a discussion of the ligand profiles, G protein coupling, and tissue distribution of each receptor. We will also review phenotypes relevant to blood pressure regulation which have been reported to date for Gpr41, Gpr43, Gpr109a, and Olfr78 knockout mice. In addition, we will consider how SCFA signaling influences physiology at baseline, and, how SCFA signaling may contribute to blood pressure regulation in settings of hypertension. In sum, this review will integrate current knowledge regarding how SCFAs and their receptors regulate blood pressure.

Emerging roles of olfactory receptors in glucose metabolism

Olfactory receptors (ORs) are widely expressed in extra-nasal tissues, where they participate in the regulation of divergent physiological processes. An increasing body of evidence over the past decade has revealed important regulatory roles for extra-nasal ORs in glucose metabolism. Recently, nonodorant endogenous ligands of ORs with metabolic significance have been identified, implying the therapeutic potential of ORs in the treatment of metabolic diseases, such as diabetes and obesity. In this review, we summarize current understanding of the expression patterns and functions of ORs in key tissues involved in glucose metabolism modulation, describe odorant and endogenous OR ligands, explain the biased signaling downstream of ORs, and outline OR therapeutic potential.

Decoding the olfactory map through targeted transcriptomics links murine olfactory receptors to glomeruli

Sensory processing in 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 in the mouse. Here we combined sequential 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.

The Quest for Orthologs orthology benchmark service in 2022

The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.

Principles of odor coding in vertebrates and artificial chemosensory systems

The biological olfactory system is the sensory system responsible for the detection of the chemical composition of the environment. Several attempts to mimic biological olfactory systems have led to various artificial olfactory systems using different technical approaches. Here we provide a parallel description of biological olfactory systems and their technical counterparts. We start with a presentation of the input to the systems, the stimuli, and treat the interface between the external world and the environment where receptor neurons or artificial chemosensors reside. We then delineate the functions of receptor neurons and chemosensors as well as their overall I-O relationships. Up to this point, our account of the systems goes along similar lines. The next processing steps differ considerably: while in biology the processing step following the receptor neurons is the "integration" and "processing" of receptor neuron outputs in the olfactory bulb, this step has various realizations in electronic noses. For a long period of time, the signal processing stages beyond the olfactory bulb, i.e., the higher olfactory centers were little studied. Only recently there has been a marked growth of studies tackling the information processing in these centers. In electronic noses, a third stage of processing has virtually never been considered. In this review, we provide an up-to-date overview of the current knowledge of both fields and, for the first time, attempt to tie them together. We hope it will be a breeding ground for better information, communication, and data exchange between very related but so far little connected fields.

The Olfactory System as Marker of Neurodegeneration in Aging, Neurological and Neuropsychiatric Disorders

Research studies that focus on understanding the onset of neurodegenerative pathology and therapeutic interventions to inhibit its causative factors, have shown a crucial role of olfactory bulb neurons as they transmit and propagate nerve impulses to higher cortical and limbic structures. In rodent models, removal of the olfactory bulb results in pathology of the frontal cortex that shows striking similarity with frontal cortex features of patients diagnosed with neurodegenerative disorders. Widely different approaches involving behavioral symptom analysis, histopathological and molecular alterations, genetic and environmental influences, along with age-related alterations in cellular pathways, indicate a strong correlation of olfactory dysfunction and neurodegeneration. Indeed, declining olfactory acuity and olfactory deficits emerge either as the very first symptoms or as prodromal symptoms of progressing neurodegeneration of classical conditions. Olfactory dysfunction has been associated with most neurodegenerative, neuropsychiatric, and communication disorders. Evidence revealing the dual molecular function of the olfactory receptor neurons at dendritic and axonal ends indicates the significance of olfactory processing pathways that come under environmental pressure right from the onset. Here, we review findings that olfactory bulb neuronal processing serves as a marker of neuropsychiatric and neurodegenerative disorders.

Characterization of Four Orphan Receptors (GPR3, GPR6, GPR12 and GPR12L) in Chickens and Ducks and Regulation of GPR12 Expression in Ovarian Granulosa Cells by Progesterone

The three structurally related orphan G protein-coupled receptors, GRP3, GPR6, and GPR12, are reported to be constitutively active and likely involved in the regulation of many physiological/pathological processes, such as neuronal outgrowth and oocyte meiotic arrest in mammals. However, the information regarding these orphan receptors in nonmammalian vertebrates is extremely limited. Here, we reported the structure, constitutive activity, and tissue expression of these receptors in two representative avian models: chickens and ducks. The cloned duck GPR3 and duck/chicken GPR6 and GPR12 are intron-less and encode receptors that show high amino acid (a.a.) sequence identities (66–88%) with their respective mammalian orthologs. Interestingly, a novel GPR12-like receptor (named GPR12L) sharing 66% a.a. identity to that in vertebrates was reported in the present study. Using dual-luciferase reporter assay and Western blot, we demonstrated that GPR3, GPR6, GPR12, and GPR12L are constitutively active and capable of stimulating the cAMP/PKA signaling pathway without ligand stimulation in birds (and zebrafish), indicating their conserved signaling property across vertebrates. RNA-seq data/qRT-PCR assays revealed that GPR6 and GPR12L expression is mainly restricted to the chicken brain, while GPR12 is highly expressed in chicken ovarian granulosa cells (GCs) and oocytes of 6 mm growing follicles and its expression in cultured GCs is upregulated by progesterone. Taken together, our data reveal the structure, function, and expression of GPR3, GPR6, GPR12, and GPR12L in birds, thus providing the first piece of evidence that GPR12 expression is upregulated by gonadal steroid (i.e., progesterone) in vertebrates.

Genenames.org: the HGNC and VGNC resources in 2021

The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problematic symbols, we are working towards stabilizing symbols where possible; over 2000 symbols for disease associated genes are now marked as stable in our symbol reports. All of our data is available at the HGNC website https://www.genenames.org. The Vertebrate Gene Nomenclature Committee (VGNC) was established to assign standardized nomenclature in line with human for vertebrate species lacking their own nomenclature committee. In addition to the previous VGNC core species of chimpanzee, cow, horse and dog, we now name genes in cat, macaque and pig. Gene groups have been added to VGNC and currently include two complex families: olfactory receptors (ORs) and cytochrome P450s (CYPs). In collaboration with specialists we have also named CYPs in species beyond our core set. All VGNC data is available at https://vertebrate.genenames.org/. This article provides an overview of our online data and resources, focusing on updates over the last two years.

The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution

Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T), and loss (L). These processes are usually modeled independently, but in reality, ILS can affect gene copy number polymorphism, that is, interfere with DTL. This has been previously recognized, but not treated in a satisfactory way, mainly because DTL events are naturally modeled forward-in-time, while ILS is naturally modeled backward-in-time with the coalescent. Here, we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realized rate of D, T, and L becomes nonhomogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent, which also accounts for any level of linkage between loci, generalizes the multispecies coalescent (MSC) model and offers a versatile, powerful framework for proper simulation, and inference of gene family evolution. [Gene duplication; gene loss; horizontal gene transfer; incomplete lineage sorting; multispecies coalescent; hemiplasy; recombination.].