iORbase:A database for the prediction of the structures andfunctions of insect olfactory receptors

Insect olfactory receptors(iORs)with atypical 7-transmembrane domains,unlike Chordata olfactory receptors,are not in the GPCR protein family.iORs selectively bind to volatile ligands in the environment and affect essential insect behaviors.In this study,we constructed a new platform(iORbase,https://www.iorbase.com)for the structural and functional analysis of iORs based on a combined algorithm for gene annotation and protein structure prediction.Moreover,it provides the option to calculate the binding affinities and binding residues between iORs and pheromone molecules by virtual screening of docking.Furthermore,iORbase supports the automatic structural and functional prediction of user-submitted iORs or pheromones.iORbase contains the well-analyzed results of approximately 6000 iORs and their 3D protein structures identified from 59 insect species and 2077 insect pheromones from the literature,as well as approximately 12 million pairs of simulated interactions between functional iORs and pheromones.We also built 4 online modules,iORPDB,iInteraction,iModelTM,and iOdorTool to easily retrieve and visualize the 3D structures and interactions.iORbase can help greatly improve the experimental efficiency and success rate,identify new insecticide targets,or develop electronic nose technology.This study will shed light on the olfactory recognition mechanism and evolutionary characteristics from the perspectives of omics and macroevolution.

Progress in Research on Insect Olfactory Perception of Habitat Odor Molecules

A highly sensitive olfactory system allows insects to precisely identify and position volatile compounds from different sources in their habitats,and plays a crucial role in their foraging,mating,and oviposition activities.During evolution,insects have successfully developed a large and complex olfactory system to adapt to heterogeneous environments,enabling the maintenance of inset population.A comprehensive examination of the olfactory system of insects may therefore yield novel insights into the development of innovative pest control and prevention strategies,as well as the study of olfactory mechanisms in vertebrates and even humans.This paper outlines the current state of research into the signal transduction mechanism by which insects perceive the olfactory molecules of their habitats.The aim of this review is to provide a reference point for future studies into the olfactory perception mechanism and its potential applications in pest management.

The olfactory system of Pieris brassicae caterpllars:from receptors to glomeruli

Tolfactory system of adult lepidopterans is among the best described neuronal circuits.However,comparatively little is known about the organization of the olfactory system in the larval stage of these insects.Here,we explore the expression of olfactory receptors and the organization of olfactory sensory neurons in caterpillars of Pieris brassicae,a significant pest species in Europe and a well-studied species for its chemical ecology.To describe the larval olfactory system in this species,we first analyzed the head transcriptome of third-instar larvae(L3)and identified 16 odorant receptors(ORs)including the OR coreceptor(Orco),13 ionotropic receptors(IRs),and 8 gustatory receptors(GRs).We then quantified the expression of these 16 ORs in different life stages,using qPCR,and found that the majority of ORs had significantly higher expression in the L4 stage than in the L3 and L5 stages,indicating that the larval olfactory system is not static throughout caterpillar development.Using an Orco-specific antibody,we identified all olfactory receptor neurons(ORNs)expressing the Orco protein in L3,L4,and L5 caterpillars and found a total of 34 Orco-positive ORNs,distributed among three sensilla on the antenna.The number of Orco-positive ORNs did not differ among the three larval instars.Finally,we used retrograde axon tracing of the antennal nerve and identified a mean of 15 glomeruli in the larval antennal center(LAC),suggesting that the caterpillar olfactory system follows a similar design as the adult olfactory system,although with a lower numerical redundancy.Taken together,our results provide a detailed analysis of the larval olfactory neurons in P brassicae,highlighting both the differences as well as the commonalities with the adult olfactory system.These findings contribute to a better understanding of the development of the olfactory system in insects and its life-stage-specific adaptations.

Molecular Cloning and cDNA Sequence Analysis of Two New Lepidopteran OR83b Orthologue Chemoreceptors

The aim of this study was to isolate the full-length cDNA sequences of an unusually highly conserved olfactory receptor （orthologue to the Drosophila melanogaster DOR83b） from the antennae of Spodoptera exigua and S. litura by using reverse transcription-polymerase chain reaction （RT-PCR） and rapid amplification of cDNA ends （RACE） methods. Bioinformatics methods were used to further analyze the cDNA sequences and putative amino acid sequences. The two full-length cDNA sequences from olfactory receptor （OR） of male S. exigua and S. litura were named as SexiOR2 and SlitOR2, respectively. SexiOR2 and SlitOR2 consisted of nucleotide sequence of 1 906 and 2 483 bp, respectively, and both with deduced amino acid sequences of 473 residues. The sequence analysis indicated that the deduced amino acid sequences of the cDNA shared the high homologies with OR83b orthologue chemoreceptor sequences from previously reported moths, implying that the cDNA sequences were of OR83b orthologue chemoreceptor genes.

The Olfactory Receptor Pseudo-pseudogene: A Potential Therapeutic Target in Human Diseases

Recently, Prieto-Godino et al.[1] found that the olfactory receptor 75a （Ir75a） gene is a functional pseudo-pseudogene in Drosophila sechellia. For a long time, Ir75a has been regarded as an acetic acid receptor that detects acetic acid and induces obvious olfactory responses in olfactory sensory neurons （OSNs）f2J. Nonetheless, Prieto-Godino et al. confirmed that Ir75a lost its sensitivity to acetic acid in D. sechellia. Thus, the D. sechelfia Ir75a gene is generally recognized as a pseudogene in OSNs.

Comparison of the fraction of olfactory receptor pseudogenes in wolf (Canis lupus) with domestic dog (Canis familiaris)

Olfactory receptors（ORs）,the first dedicated molecules with which odorants physically interact to arouse an olfactory sensation,constitute the largest gene family in vertebrates.Dogs and wolves,like many other mammals,have a highly developed capability to detect and identify odorant molecules,even at minimum concentrations.In this study,the olfactory receptor repertoire from domestic dog and its closest relative,the wolf,were sequenced to estimate the fraction of pseudogenes in each subspecies.The fraction of disrupted olfactory receptor genes in dog was 17.78%,whereas,that in wolf was 12.08%.As expected the dog was less dependent on olfaction than the wolf,and the dog had more olfactory receptor pseudogenes.However,the observed difference between the two subspecies was not at the significant level（χ2 = 1.388,p = 0.239 0.05）.The values indicated that although domestication might play a role in the reduction of OR genes,it could not be concluded that the living environment provided by domestication lead to a significant reduction of the functional olfactory receptor repertoire.Furthermore,the purpose of domestication may also have influence on the ratio of functional olfactory receptor genes reduction.

Microencapsulation improves inhibitory effects of transplanted olfactory ensheathing cells on pain after sciatic nerve injury

Olfactory bulb tissue transplantation inhibits P2X2/3 receptor-mediated neuropathic pain. However, the olfactory bulb has a complex cellular composition, and the mechanism underlying the action of purified transplanted olfactory ensheathing cells（OECs） remains unclear. In the present study, we microencapsulated OECs in alginic acid, and transplanted free and microencapsulated OECs into the region surrounding the injured sciatic nerve in rat models of chronic constriction injury. We assessed mechanical nociception in the rat models 7 and 14 days after surgery by measuring paw withdrawal threshold, and examined P2X2/3 receptor expression in L4–5 dorsal root ganglia using immunohistochemistry. Rats that received free and microencapsulated OEC transplants showed greater withdrawal thresholds than untreated model rats, and weaker P2X2/3 receptor immunoreactivity in dorsal root ganglia. At 14 days, paw withdrawal threshold was much higher in the microencapsulated OEC-treated animals. Our results confirm that microencapsulated OEC transplantation suppresses P2X2/3 receptor expression in L4–5 dorsal root ganglia in rat models of neuropathic pain and reduces allodynia, and also suggest that transplantation of microencapsulated OECs is more effective than transplantation of free OECs for the treatment of neuropathic pain.

Related Factors Affecting Olfactory Ability of Dogs

Dog has a very sensitive olfactory sensory system. Observation showed that there were great differences in olfactory ability of different breeds of dogs, and even the same dog presented different olfactory abilities under different physiological conditions. Thus, the author discussed several factors influencing olfaction of dog from the aspects of gene, environment, anatomy and physiology.

Prediction of Tumor Microenvironment Characteristics and Treatment Response in Lung Squamous Cell Carcinoma by Pseudogene OR7E47P-related Immune Genes

Objective Pseudogenes are initially regarded as nonfunctional genomic sequences,but some pseudogenes regulate tumor initiation and progression by interacting with other genes to modulate their transcriptional activities.Olfactory receptor family 7 subfamily E member 47 pseudogene(OR7E47P)is expressed broadly in lung tissues and has been identified as a positive regulator in the tumor microenvironment(TME)of lung adenocarcinoma(LUAD).This study aimed to elucidate the correlation between OR7E47P and tumor immunity in lung squamous cell carcinoma(LUSC).Methods Clinical and molecular information from The Cancer Genome Atlas(TCGA)LUSC cohort was used to identify OR7E47P-related immune genes(ORIGs)by weighted gene correlation network analysis(WGCNA).Based on the ORIGs,2 OR7E47P clusters were identified using non-negative matrix factorization(NMF)clustering,and the stability of the clustering was tested by an extreme gradient boosting classifier(XGBoost).LASSO-Cox and stepwise regressions were applied to further select prognostic ORIGs and to construct a predictive model(ORPScore)for immunotherapy.The Botling cohorts and 8 immunotherapy cohorts(the Samstein,Braun,Jung,Gide,IMvigor210,Lauss,Van Allen,and Cho cohorts)were included as independent validation cohorts.Results OR7E47P expression was positively correlated with immune cell infiltration and enrichment of immune-related pathways in LUSC.A total of 57 ORIGs were identified to classify the patients into 2 OR7E47P clusters(Cluster 1 and Cluster 2)with distinct immune,mutation,and stromal programs.Compared to Cluster 1,Cluster 2 had more infiltration by immune and stromal cells,lower mutation rates of driver genes,and higher expression of immune-related proteins.The clustering performed well in the internal and 5 external validation cohorts.Based on the 7 ORIGs(HOPX,STX2,WFS,DUSP22,SLFN13,GGCT,and CCSER2),the ORPScore was constructed to predict the prognosis and the treatment response.In addition,the ORPScore was a better prognostic factor and correlated positively with the immunotherapeutic response in cancer patients.The area under the curve values ranged from 0.584 to 0.805 in the 6 independent immunotherapy cohorts.Conclusion Our study suggests a significant correlation between OR7E47P and TME modulation in LUSC.ORIGs can be applied to molecularly stratify patients,and the ORPScore may serve as a biomarker for clinical decision-making regarding individualized prognostication and immunotherapy.

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/To Hanwei/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.

Olfactory receptor gene evolution is unusually rapid across Tetrapoda and outpaces chemosensory phenotypic change

Chemosensation is the most ubiquitous sense in animals,enacted by the products of complex gene families that detect environmental chemical cues and larger-scale sensory structures that process these cues.While there is a general conception that olfactory receptor(OR)genes evolve rapidly,the universality of this phenomenon across vertebrates,and its magnitude,are unclear.The supposed correlation between molecular rates of chemosensory evolution and phenotypic diversity of chemosensory systems is largely untested.We combine comparative genomics and sensory morphology to test whether OR genes and olfactory phenotypic traits evolve at faster rates than other genes or traits.Using published genomes,we identified ORs in 21 tetrapods,including amphibia ns,reptiles,birds,and mammals and compared their rates of evolution to those of orthologous non-OR protein-coding genes.We found that,for all clades investigated,most OR genes evolve nearly an order of magnitude faster than other protein-coding genes,with many OR genes showing signatures of diversifying selection across nearly all taxa in this study.This rapid rate of evolution suggests that chemoreceptor genes are in "evolutionary overdrive,"perhaps evolving in response to the ever-changing chemical space of the environment.To obtain complementary morphological data,we stained whole fixed specimens with iodine,μCT-scanned the specimens,and digitally segmented chemosensory and nonchemosensory brain regions.We then estimated phenotypic variation within traits and among tetrapods.While we found considerable variation in chemosensory structures,they were no more diverse than nonchemosensory regions.We suggest chemoreceptor genes evolve quickly in reflection of an ever-changing chemical space,whereas chemosensory phe no types and processing regions are more conserved because they use a standardized or constrained architecture to receive and process a range of chemical cues.

The genetic basis of the leafy seadragon's unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling

The leafy seadragon certainly is among evolution’s most“beautiful and wonderful”species aptly named for its extraordinary camouflage mimicking its coastal seaweed habitat.However,limited information is known about the genetic basis of its phenotypes and conspicuous camouflage.Here,we revealed genomic signatures of rapid evolution and positive selection in core genes related to its camouflage,which allowed us to predict population dynamics for this species.Comparative genomic analysis revealed that seadragons have the smallest olfactory repertoires among all ray-finned fishes,suggesting adaptations to the highly specialized habitat.Other positively selected and rapidly evolving genes that serve in bone development and coloration are highly expressed in the leaf-like appendages,supporting a recent adaptive shift in camouflage appendage formation.Knock-out of bmp6 results in dysplastic intermuscular bones with a significantly reduced number in zebrafish,implying its important function in bone formation.Global climate change-induced loss of seagrass beds now severely threatens the continued existence of this enigmatic species.The leafy seadragon has a historically small population size likely due to its specific habitat requirements that further exacerbate its vulnerability to climate change.Therefore,taking climate change-induced range shifts into account while developing future protection strategies.

Molecular identification and characterization of the Orco orthologue of Spodoptera litura

A highly conserved and broadly expressed receptor protein Orco （olfactory coreceptor） is crucial for insect olfaction, and an orthologue of Orco has been identified in several insect species. Here we report the identification and characterization of Orco from Spodoptera litura. The protein displays high primary amino acid sequence conservation with other previously identified Orco orthologues. Bioinformatic analysis revealed that it has common features with other members of the Orco subfamily： seven-transmembrane domains with intracellular N-terminus and extracellular C-terminus. The transcript was detected in abundance in the chemosensory organs of the antennae of both male and female adults by real-time polymerase chain reaction analysis, and was localized at the bases of all categories of olfactory sensilla through in situ hybridization.

FET-based nanobiosensors for the detection of smell and taste

Various nanobiosensors composed of biomaterials and nanomaterials have been developed,due to their demonstrated advantage of showing high performance.Among various biomaterials for biological recognition elements of the nanobiosensor,sensory receptors,such as olfactory and taste receptors,are promising biomaterials for developing nanobiosensors,because of their high selectivity to target molecules.Field-effect transistors(FET)with nanomaterials such as carbon nanotube(CNT),graphene,and conducting polymer nanotube(CPNT),can be combined with the biomaterials to enhance the sensitivity of nanobiosensors.Recently,many efforts have been made to develop nanobiosensors using biomaterials,such as olfactory receptors and taste receptors for detecting various smells and tastes.This review focuses on the biomaterials and nanomaterials used in nanobiosensor systems and studies of various types of nanobiosensor platforms that utilize olfactory receptors and taste receptors which could be applied to a wide range of industrial fields,including the food and beverage industry,environmental monitoring,the biomedical field,and anti-terrorism.