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Wang J, Wang D, Huang M, Sun B, Ren F, Wu J, Zhang J, Li H, Sun X. Decoding Molecular Mechanism Underlying Human Olfactory Receptor OR8D1 Activation by Sotolone Enantiomers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5403-5415. [PMID: 38386648 DOI: 10.1021/acs.jafc.3c09142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Sotolone, a chiral compound, plays an important role in the food industry. Herein, (R)-/(S)-sotolone were separated to determine their odor characteristics and thresholds in air (R-form: smoky, burned, herb, and green aroma, 0.0514 μg/m3; S-form: sweet, milk, acid, and nutty aroma, 0.0048 μg/m3). OR8D1 responses to (R)-/(S)-sotolone were detected in a HEK293 cell-based luminescence assay. (S)-Sotolone was a more potent agonist than (R)-sotolone (EC50 values of 84.98 ± 1.05 and 167.20 ± 0.25 μmol/L, respectively). Molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area analyses confirmed that the combination of (S)-sotolone and OR8D1 was more stable than that of (R)-sotolone. Odorant docking, multiple sequence alignments, site-directed mutagenesis, and functional studies with recombinant odorant receptors (ORs) in a cell-based luminescence assay identified 11 amino-acid residues that influence the enantioselectivity of OR8D1 toward sotolone significantly and that N2065.46 was indispensable to the activation of OR8D1 by (S)-sotolone.
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Affiliation(s)
- Juan Wang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Danqing Wang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Mingquan Huang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Baoguo Sun
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Fazheng Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Jihong Wu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Jinglin Zhang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Hehe Li
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Xiaotao Sun
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
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2
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Ferreira JS, Bruschi DP. Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species. J Mol Evol 2023; 91:793-805. [PMID: 37906255 DOI: 10.1007/s00239-023-10135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Olfaction is a crucial capability for most vertebrates and is realized through olfactory receptors in the nasal cavity. The enormous diversity of olfactory receptors has been created by gene duplication, following a birth-and-death model of evolution. The olfactory receptor genes of the amphibians have received relatively little attention up to now, although recent studies have increased the number of species for which data are available. This study analyzed the diversity and chromosomal distribution of the OR genes of three anuran species (Engystomops pustulosus, Bufo bufo and Hymenochirus boettgeri). The OR genes were identified through searches for homologies, and sequence filtering and alignment using bioinformatic tools and scripts. A high diversity of OR genes was found in all three species, ranging from 917 in B. bufo to 1194 in H. boettgeri, and a total of 2076 OR genes in E. pustulosus. Six OR groups were recognized using an evolutionary gene tree analysis. While E. pustulosus has one of the highest numbers of genes of the gamma group (which detect airborne odorants) yet recorded in an anuran, B. bufo presented the smallest number of pseudogene sequences ever identified, with no pseudogenes in either the beta or epsilon groups. Although H. boettgeri shares many morphological adaptations for an aquatic lifestyle with Xenopus, and presented a similar number of genes related to the detection of water-soluble odorants, it had comparatively far fewer genes related to the detection of airborne odorants. This study is the first to describe the complete OR repertoire of the three study species and represents an important contribution to the understanding of the evolution and function of the sense of smell in vertebrates.
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Affiliation(s)
- Johnny Sousa Ferreira
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil
| | - Daniel Pacheco Bruschi
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil.
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3
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Nicoli A, Haag F, Marcinek P, He R, Kreißl J, Stein J, Marchetto A, Dunkel A, Hofmann T, Krautwurst D, Di Pizio A. Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1. J Chem Inf Model 2023; 63:2014-2029. [PMID: 36696962 PMCID: PMC10091413 DOI: 10.1021/acs.jcim.2c00752] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With approximately 400 encoding genes in humans, odorant receptors (ORs) are the largest subfamily of class A G protein-coupled receptors (GPCRs). Despite its high relevance and representation, the odorant-GPCRome is structurally poorly characterized: no experimental structures are available, and the low sequence identity of ORs to experimentally solved GPCRs is a significant challenge for their modeling. Moreover, the receptive range of most ORs is unknown. The odorant receptor OR5K1 was recently and comprehensively characterized in terms of cognate agonists. Here, we report two additional agonists and functional data of the most potent compound on two mutants, L1043.32 and L2556.51. Experimental data was used to guide the investigation of the binding modes of OR5K1 ligands into the orthosteric binding site using structural information from AI-driven modeling, as recently released in the AlphaFold Protein Structure Database, and from homology modeling. Induced-fit docking simulations were used to sample the binding site conformational space for ensemble docking. Mutagenesis data guided side chain residue sampling and model selection. We obtained models that could better rationalize the different activity of active (agonist) versus inactive molecules with respect to starting models and also capture differences in activity related to minor structural differences. Therefore, we provide a model refinement protocol that can be applied to model the orthosteric binding site of ORs as well as that of GPCRs with low sequence identity to available templates.
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Affiliation(s)
- Alessandro Nicoli
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Franziska Haag
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Patrick Marcinek
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Ruiming He
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany.,Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Johanna Kreißl
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Jörg Stein
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Alessandro Marchetto
- Computational Biomedicine, Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.,Department of Biology, Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52074 Aachen, Germany
| | - Andreas Dunkel
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, 85354 Freising, Germany
| | - Dietmar Krautwurst
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
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4
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Lowry TW, Kusi-Appiah AE, Fadool DA, Lenhert S. Odor Discrimination by Lipid Membranes. MEMBRANES 2023; 13:151. [PMID: 36837654 PMCID: PMC9962961 DOI: 10.3390/membranes13020151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Odor detection and discrimination in mammals is known to be initiated by membrane-bound G-protein-coupled receptors (GPCRs). The role that the lipid membrane may play in odor discrimination, however, is less well understood. Here, we used model membrane systems to test the hypothesis that phospholipid bilayer membranes may be capable of odor discrimination. The effect of S-carvone, R-carvone, and racemic lilial on the model membrane systems was investigated. The odorants were found to affect the fluidity of supported lipid bilayers as measured by fluorescence recovery after photobleaching (FRAP). The effect of odorants on surface-supported lipid multilayer microarrays of different dimensions was also investigated. The lipid multilayer micro- and nanostructure was highly sensitive to exposure to these odorants. Fluorescently-labeled lipid multilayer droplets of 5-micron diameter were more responsive to these odorants than ethanol controls. Arrays of lipid multilayer diffraction gratings distinguished S-carvone from R-carvone in an artificial nose assay. Our results suggest that lipid bilayer membranes may play a role in odorant discrimination and molecular recognition in general.
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5
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Cho S, Park TH. Advances in the Production of Olfactory Receptors for Industrial Use. Adv Biol (Weinh) 2023; 7:e2200251. [PMID: 36593488 DOI: 10.1002/adbi.202200251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/11/2022] [Indexed: 01/04/2023]
Abstract
In biological olfactory systems, olfactory receptors (ORs) can recognize and discriminate between thousands of volatile organic compounds with very high sensitivity and specificity. The superior properties of ORs have led to the development of OR-based biosensors that have shown promising potential in many applications over the past two decades. In particular, newly designed technologies in gene synthesis, protein expression, solubilization, purification, and membrane mimetics for membrane proteins have greatly opened up the previously inaccessible industrial potential of ORs. In this review, gene design, expression and solubilization strategies, and purification and reconstitution methods available for modern industrial applications are examined, with a focus on ORs. The limitations of current OR production technology are also estimated, and future directions for further progress are suggested.
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Affiliation(s)
- Seongyeon Cho
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Tai Hyun Park
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
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6
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Cong X, Ren W, Pacalon J, Xu R, Xu L, Li X, de March CA, Matsunami H, Yu H, Yu Y, Golebiowski J. Large-Scale G Protein-Coupled Olfactory Receptor-Ligand Pairing. ACS CENTRAL SCIENCE 2022; 8:379-387. [PMID: 35350604 PMCID: PMC8949627 DOI: 10.1021/acscentsci.1c01495] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 05/22/2023]
Abstract
G protein-coupled receptors (GPCRs) conserve common structural folds and activation mechanisms, yet their ligand spectra and functions are highly diverse. This work investigated how the amino-acid sequences of olfactory receptors (ORs)-the largest GPCR family-encode diversified responses to various ligands. We established a proteochemometric (PCM) model based on OR sequence similarities and ligand physicochemical features to predict OR responses to odorants using supervised machine learning. The PCM model was constructed with the aid of site-directed mutagenesis, in vitro functional assays, and molecular simulations. We found that the ligand selectivity of the ORs is mostly encoded in the residues up to 8 Å around the orthosteric pocket. Subsequent predictions using Random Forest (RF) showed a hit rate of up to 58%, as assessed by in vitro functional assays of 111 ORs and 7 odorants of distinct scaffolds. Sixty-four new OR-odorant pairs were discovered, and 25 ORs were deorphanized here. The best model demonstrated a 56% deorphanization rate. The PCM-RF approach will accelerate OR-odorant mapping and OR deorphanization.
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Affiliation(s)
- Xiaojing Cong
- Université
Côte d’Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice 06108, France
- E-mail:
| | - Wenwen Ren
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200031, People’s Republic of China
| | - Jody Pacalon
- Université
Côte d’Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice 06108, France
| | - Rui Xu
- School
of Life Sciences, Shanghai University, Shanghai 200444, People’s Republic of China
| | - Lun Xu
- Ear,
Nose & Throat Institute, Department of Otolaryngology, Eye, Ear,
Nose & Throat Hospital, Fudan University, Shanghai 200031, People’s Republic of China
| | - Xuewen Li
- School
of Life Sciences, Shanghai University, Shanghai 200444, People’s Republic of China
| | - Claire A. de March
- Department
of Molecular Genetics and Microbiology, and Department of Neurobiology,
and Duke Institute for Brain Sciences, Duke
University Medical Center, Research Drive, Durham, North Carolina 27710, United States
| | - Hiroaki Matsunami
- Department
of Molecular Genetics and Microbiology, and Department of Neurobiology,
and Duke Institute for Brain Sciences, Duke
University Medical Center, Research Drive, Durham, North Carolina 27710, United States
| | - Hongmeng Yu
- Ear,
Nose & Throat Institute, Department of Otolaryngology, Eye, Ear,
Nose & Throat Hospital, Fudan University, Shanghai 200031, People’s Republic of China
- Clinical
and Research Center for Olfactory Disorders, Eye, Ear, Nose &
Throat Hospital, Fudan University, Shanghai 200031, People’s Republic of China
- Research
Units of New Technologies of Endoscopic Surgery in Skull Base Tumor,
Chinese Academy of Medical Sciences, Beijing 100730, People’s
Republic of China
| | - Yiqun Yu
- Ear,
Nose & Throat Institute, Department of Otolaryngology, Eye, Ear,
Nose & Throat Hospital, Fudan University, Shanghai 200031, People’s Republic of China
- Clinical
and Research Center for Olfactory Disorders, Eye, Ear, Nose &
Throat Hospital, Fudan University, Shanghai 200031, People’s Republic of China
- E-mail:
| | - Jérôme Golebiowski
- Université
Côte d’Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice 06108, France
- Department
of Brain and Cognitive Sciences, Daegu Gyeongbuk
Institute of Science and Technology, Daegu 711-873, South Korea
- E-mail:
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7
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Xu Z, Guo L, Qian X, Yu C, Li S, Zhu C, Ma X, Li H, Zhu G, Zhou H, Dai W, Li Q, Gao X. Two entry tunnels in mouse TAAR9 suggest the possibility of multi-entry tunnels in olfactory receptors. Sci Rep 2022; 12:2691. [PMID: 35177711 PMCID: PMC8854740 DOI: 10.1038/s41598-022-06591-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022] Open
Abstract
Orthosteric binding sites of olfactory receptors have been well understood for ligand-receptor interactions. However, a lack of explanation for subtle differences in ligand profile of olfactory receptors even with similar orthosteric binding sites promotes more exploration into the entry tunnels of the receptors. An important question regarding entry tunnels is the number of entry tunnels, which was previously believed to be one. Here, we used TAAR9 that recognizes important biogenic amines such as cadaverine, spermine, and spermidine as a model for entry tunnel study. We identified two entry tunnels in TAAR9 and described the residues that form the tunnels. In addition, we found two vestibular binding pockets, each located in one tunnel. We further confirmed the function of two tunnels through site-directed mutagenesis. Our study challenged the existing views regarding the number of entry tunnels in the subfamily of olfactory receptors and demonstrated the possible mechanism how the entry tunnels function in odorant recognition.
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Affiliation(s)
- ZhengRong Xu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - LingNa Guo
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Institute of Life Sciences, Southeast University, Nanjing, 210096, China
| | - XiaoYun Qian
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - ChenJie Yu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - ShengJu Li
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - ChengWen Zhu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - XiaoFeng Ma
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Hui Li
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - GuangJie Zhu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Han Zhou
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - WenXuan Dai
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Qian Li
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, 201210, China.
| | - Xia Gao
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China. .,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.
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8
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Marcinek P, Haag F, Geithe C, Krautwurst D. An evolutionary conserved olfactory receptor for foodborne and semiochemical alkylpyrazines. FASEB J 2021; 35:e21638. [PMID: 34047404 DOI: 10.1096/fj.202100224r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022]
Abstract
Molecular recognition is a fundamental principle in biological systems. The olfactory detection of both food and predators via ecological relevant odorant cues are abilities of eminent evolutionary significance for many species. Pyrazines are such volatile cues, some of which act as both human-centered key food odorants (KFOs) and semiochemicals. A pyrazine-selective odorant receptor has been elusive. Here we screened 2,3,5-trimethylpyrazine, a KFO and semiochemical, and 2,5-dihydro-2,4,5-trimethylthiazoline, an innate fear-associated non-KFO, against 616 human odorant receptor variants, in a cell-based luminescence assay. OR5K1 emerged as sole responding receptor. Tested against a comprehensive collection of 178 KFOs, we newly identified 18 pyrazines and (2R/2S)-4-methoxy-2,5-dimethylfuran-3(2H)-one as agonists. Notably, OR5K1 orthologs in mouse and domesticated species displayed a human-like, potency-ranked activation pattern of pyrazines, suggesting a domestication-led co-evolution of OR5K1 and its orthologs. In summary, OR5K1 is a specialized olfactory receptor across mammals for the detection of pyrazine-based key food odors and semiochemicals.
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Affiliation(s)
- Patrick Marcinek
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.,Hamilton Germany GmbH, Gräfelfing, Germany
| | - Franziska Haag
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Christiane Geithe
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.,Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Dietmar Krautwurst
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
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9
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Fry E, Kim SK, Chigurapti S, Mika KM, Ratan A, Dammermann A, Mitchell BJ, Miller W, Lynch VJ. Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth. Genome Biol Evol 2021; 12:48-58. [PMID: 32031213 PMCID: PMC7094797 DOI: 10.1093/gbe/evz279] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2019] [Indexed: 12/21/2022] Open
Abstract
Woolly mammoths were among the most abundant cold-adapted species during the Pleistocene. Their once-large populations went extinct in two waves, an end-Pleistocene extinction of continental populations followed by the mid-Holocene extinction of relict populations on St. Paul Island ∼5,600 years ago and Wrangel Island ∼4,000 years ago. Wrangel Island mammoths experienced an episode of rapid demographic decline coincident with their isolation, leading to a small population, reduced genetic diversity, and the fixation of putatively deleterious alleles, but the functional consequences of these processes are unclear. Here, we show that a Wrangel Island mammoth genome had many putative deleterious mutations that are predicted to cause diverse behavioral and developmental defects. Resurrection and functional characterization of several genes from the Wrangel Island mammoth carrying putatively deleterious substitutions identified both loss and gain of function mutations in genes associated with developmental defects (HYLS1), oligozoospermia and reduced male fertility (NKD1), diabetes (NEUROG3), and the ability to detect floral scents (OR5A1). These data suggest that at least one Wrangel Island mammoth may have suffered adverse consequences from reduced population size and isolation.
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Affiliation(s)
- Erin Fry
- Department of Human Genetics, The University of Chicago
| | - Sun K Kim
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University
| | | | | | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia
| | | | - Brian J Mitchell
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University
| | - Webb Miller
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University
| | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo, SUNY
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10
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Wu W, Li S, Yang M, Lin Y, Zheng K, Akutse KS. Citronellal perception and transmission by Anopheles gambiae s.s. (Diptera: Culicidae) females. Sci Rep 2020; 10:18615. [PMID: 33122679 PMCID: PMC7596511 DOI: 10.1038/s41598-020-75782-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/14/2020] [Indexed: 11/08/2022] Open
Abstract
Anopheles gambiae s.s. is a key vector of Plasmodium parasites. Repellents, which may be a promising alternative to pesticides used to control malaria mosquitoes. Although citronellal is a known mosquito repellent, its repellency characteristics are largely unknown. Determining the specific odorant-binding proteins (OBPs) and odorant receptors (ORs) that detect and transfer the citronellal molecule in A. gambiae s.s. will help to define the mode of action of this compound. In this research, we assessed the repellent activity of citronellal in A. gambiae s.s. using a Y-tube olfactory meter, screened candidate citronellal-binding OBPs and ORs using reverse molecular docking, clarified the binding properties of predicted proteins for citronellal using fluorescence competition binding assay. Results showed that citronellal had a dosage effect on repelling A. gambiae s.s.. The 50% repellent rate was determined to be 4.02 nmol. Results of simulated molecular docking showed that the only proteins that bound tightly with citronellal were AgamOBP4 and AgamORC7. Fluorescence competitive binding assays confirmed the simulations. This research determined that citronellal was captured by AgamOBP4 and transmitted to AgamORC7 in A. gambiae s.s.. Our study will be beneficial in the further understanding the repellent mechanism of citronellal against A. gambiae s.s..
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Affiliation(s)
- Weijian Wu
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China
| | - Shanshan Li
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China
| | - Min Yang
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China
| | - Yongwen Lin
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China.
| | - Kaibin Zheng
- Institute of Subtropical Agriculture, Fujian Academy of Agriculture Sciences & Zhangzhou Institute of Technology, Zhangzhou, 363001, China
| | - Komivi Senyo Akutse
- International Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya
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11
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Pfister P, Smith BC, Evans BJ, Brann JH, Trimmer C, Sheikh M, Arroyave R, Reddy G, Jeong HY, Raps DA, Peterlin Z, Vergassola M, Rogers ME. Odorant Receptor Inhibition Is Fundamental to Odor Encoding. Curr Biol 2020; 30:2574-2587.e6. [PMID: 32470365 DOI: 10.1016/j.cub.2020.04.086] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 03/31/2020] [Accepted: 04/28/2020] [Indexed: 11/18/2022]
Abstract
Most natural odors are complex mixtures of volatile components, competing to bind odorant receptors (ORs) expressed in olfactory sensory neurons (OSNs) of the nose. To date, surprisingly little is known about how OR antagonism shapes neuronal representations in the detection layer of the olfactory system. Here, we investigated its prevalence, the degree to which it disrupts OR ensemble activity, and its conservation across phylogenetically related ORs. Calcium imaging microscopy of dissociated OSNs revealed significant inhibition, often complete attenuation, of responses to indole-a commonly occurring volatile associated with both floral and fecal odors-by a set of 36 tested odorants. To confirm an OR mechanism for the observed inhibition, we performed single-cell transcriptomics on OSNs exhibiting specific response profiles to a diagnostic panel of odorants and identified three paralogous receptors-Olfr740, Olfr741, and Olfr743-which, when tested in vitro, recapitulated OSN responses. We screened ten ORs from the Olfr740 gene family with ∼800 perfumery-related odorants spanning a range of chemical scaffolds and functional groups. Over half of these compounds (430) antagonized at least one of the ten ORs. OR activity fitted a mathematical model of competitive receptor binding and suggests normalization of OSN ensemble responses to odorant mixtures is the rule rather than the exception. In summary, we observed OR antagonism occurred frequently and in a combinatorial manner. Thus, extensive receptor-mediated computation of mixture information appears to occur in the olfactory epithelium prior to transmission of odor information to the olfactory bulb.
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Affiliation(s)
- Patrick Pfister
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Benjamin C Smith
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Barry J Evans
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Jessica H Brann
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Casey Trimmer
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Mushhood Sheikh
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Randy Arroyave
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Gautam Reddy
- Department of Physics, UC San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Hyo-Young Jeong
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Daniel A Raps
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Zita Peterlin
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA
| | - Massimo Vergassola
- Department of Physics, UC San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Matthew E Rogers
- Firmenich Incorporated, 250 Plainsboro Road, Plainsboro, NJ 08536, USA.
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12
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Haag F, Ahmed L, Reiss K, Block E, Batista VS, Krautwurst D. Copper-mediated thiol potentiation and mutagenesis-guided modeling suggest a highly conserved copper-binding motif in human OR2M3. Cell Mol Life Sci 2020; 77:2157-2179. [PMID: 31435697 PMCID: PMC7256108 DOI: 10.1007/s00018-019-03279-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
Sulfur-containing compounds within a physiological relevant, natural odor space, such as the key food odorants, typically constitute the group of volatiles with the lowest odor thresholds. The observation that certain metals, such as copper, potentiate the smell of sulfur-containing, metal-coordinating odorants led to the hypothesis that their cognate receptors are metalloproteins. However, experimental evidence is sparse-so far, only one human odorant receptor, OR2T11, and a few mouse receptors, have been reported to be activated by sulfur-containing odorants in a copper-dependent way, while the activation of other receptors by sulfur-containing odorants did not depend on the presence of metals. Here we identified an evolutionary conserved putative copper interaction motif CC/CSSH, comprising two copper-binding sites in TMH5 and TMH6, together with the binding pocket for 3-mercapto-2-methylpentan-1-ol in the narrowly tuned human receptor OR2M3. To characterize the copper-binding motif, we combined homology modeling, docking studies, site-directed mutagenesis, and functional expression of recombinant ORs in a cell-based, real-time luminescence assay. Ligand activation of OR2M3 was potentiated in the presence of copper. This effect of copper was mimicked by ionic and colloidal silver. In two broadly tuned receptors, OR1A1 and OR2W1, which did not reveal a putative copper interaction motif, activation by their most potent, sulfur-containing key food odorants did not depend on the presence of copper. Our results suggest a highly conserved putative copper-binding motif to be necessary for a copper-modulated and thiol-specific function of members from three subfamilies of family 2 ORs.
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Affiliation(s)
- Franziska Haag
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany
| | - Lucky Ahmed
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Eric Block
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Dietmar Krautwurst
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany.
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13
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Hu XS, Ikegami K, Vihani A, Zhu KW, Zapata M, de March CA, Do M, Vaidya N, Kucera G, Bock C, Jiang Y, Yohda M, Matsunami H. Concentration-Dependent Recruitment of Mammalian Odorant Receptors. eNeuro 2020; 7:ENEURO.0103-19.2019. [PMID: 32015097 PMCID: PMC7189481 DOI: 10.1523/eneuro.0103-19.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
A fundamental challenge in studying principles of organization used by the olfactory system to encode odor concentration information has been identifying comprehensive sets of activated odorant receptors (ORs) across a broad concentration range inside freely behaving animals. In mammals, this has recently become feasible with high-throughput sequencing-based methods that identify populations of activated ORs in vivo In this study, we characterized the mouse OR repertoires activated by the two odorants, acetophenone (ACT) and 2,5-dihydro-2,4,5-trimethylthiazoline (TMT), from 0.01% to 100% (v/v) as starting concentrations using phosphorylated ribosomal protein S6 capture followed by RNA-Seq. We found Olfr923 to be one of the most sensitive ORs that is enriched by ACT. Using a mouse line that genetically labels Olfr923-positive axons, we provided evidence that ACT activates the Olfr923 glomeruli in the olfactory bulb. Through molecular dynamics stimulations, we identified amino acid residues in the Olfr923 binding cavity that facilitate ACT binding. This study sheds light on the active process by which unique OR repertoires may collectively facilitate the discrimination of odorant concentrations.
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Affiliation(s)
- Xiaoyang Serene Hu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Kentaro Ikegami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
- Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan
| | - Aashutosh Vihani
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC 27710
| | - Kevin W Zhu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Marcelo Zapata
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Claire A de March
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Matthew Do
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Natasha Vaidya
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
- North Carolina School of Science and Mathematics, Durham, NC 27705
| | - Gary Kucera
- DCI Rodent Cancer Models Shared Resource, Duke University Medical Center, Durham, NC 27710
| | - Cheryl Bock
- DCI Rodent Cancer Models Shared Resource, Duke University Medical Center, Durham, NC 27710
| | - Yue Jiang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Masafumi Yohda
- Tokyo University of Agriculture and Technology, Tokyo 183-8538, Japan
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC 27710
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14
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C Silva M, Chibucos M, Munro JB, Daugherty S, Coelho MM, C Silva J. Signature of adaptive evolution in olfactory receptor genes in Cory's Shearwater supports molecular basis for smell in procellariiform seabirds. Sci Rep 2020; 10:543. [PMID: 31953474 PMCID: PMC6969042 DOI: 10.1038/s41598-019-56950-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/12/2019] [Indexed: 11/17/2022] Open
Abstract
Olfactory receptors (ORs), encoded by the largest vertebrate multigene family, enable the detection of thousands of unique odorants in the environment and consequently play a critical role in species survival. Here, we advance our knowledge of OR gene evolution in procellariiform seabirds, an avian group which relies on the sense of olfaction for critical ecological functions. We built a cosmid library of Cory's Shearwater (Calonectris borealis) genomic DNA, a model species for the study of olfaction-based navigation, and sequence OR gene-positive cosmid clones with a combination of sequencing technologies. We identified 220 OR open reading frames, 20 of which are full length, intact OR genes, and found a large ratio of partial and pseudogenes to intact OR genes (2:1), suggestive of a dynamic mode of evolution. Phylogenetic analyses revealed that while a few genes cluster with those of other sauropsid species in a γ (gamma) clade that predates the divergence of different avian lineages, most genes belong to an avian-specific γ-c clade, within which sequences cluster by species, suggesting frequent duplication and/or gene conversion events. We identified evidence of positive selection on full length γ-c clade genes. These patterns are consistent with a key role of adaptation in the functional diversification of olfactory receptor genes in a bird lineage that relies extensively on olfaction.
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Affiliation(s)
- Mónica C Silva
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
| | - Marcus Chibucos
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - Sean Daugherty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - M Manuela Coelho
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
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15
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Liu A, He F, Shen L, Liu R, Wang Z, Zhou J. Convergent degeneration of olfactory receptor gene repertoires in marine mammals. BMC Genomics 2019; 20:977. [PMID: 31842731 PMCID: PMC6916060 DOI: 10.1186/s12864-019-6290-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 11/14/2019] [Indexed: 11/10/2022] Open
Abstract
Background Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified, and the factors that might underlie these variations are unknown. Results To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had fewer OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions Marine mammals have experienced large numbers of OR gene losses compared with their related terrestrial lineages, which may result from the frequent birth-and-death evolution under varied functional constrains. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.
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Affiliation(s)
- Ake Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, Shanxi, 046011, People's Republic of China.,School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Funan He
- School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Libing Shen
- Institute of Neuroscience, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Ruixiang Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, Shanxi, 046011, People's Republic of China
| | - Zhijun Wang
- Department of Chemistry, Changzhi University, Changzhi, Shanxi, 046011, People's Republic of China.
| | - Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
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16
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Milanetti E, Gosti G, De Flaviis L, Olimpieri PP, Schwartz S, Caprini D, Ruocco G, Folli V. Investigation of the binding between olfactory receptors and odorant molecules in C. elegans organism. Biophys Chem 2019; 255:106264. [DOI: 10.1016/j.bpc.2019.106264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 01/27/2023]
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17
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Wasilewski T, Szulczyński B, Wojciechowski M, Kamysz W, Gębicki J. A Highly Selective Biosensor Based on Peptide Directly Derived from the HarmOBP7 Aldehyde Binding Site. SENSORS 2019; 19:s19194284. [PMID: 31623308 PMCID: PMC6806164 DOI: 10.3390/s19194284] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 01/15/2023]
Abstract
This paper presents the results of research on determining the optimal length of a peptide chain to effectively bind octanal molecules. Peptides that map the aldehyde binding site in HarmOBP7 were immobilized on piezoelectric transducers. Based on computational studies, four Odorant Binding Protein-derived Peptides (OBPPs) with different sequences were selected. Molecular modelling results of ligand docking with selected peptides were correlated with experimental results. The use of low-molecular synthetic peptides, instead of the whole protein, enabled the construction OBPPs-based biosensors. This work aims at developing a biomimetic piezoelectric OBPPs sensor for selective detection of octanal. Moreover, the research is concerned with the ligand binding affinity depending on different peptides’ chain lengths. The authors believe that the chain length can have a substantial influence on the type and effectiveness of peptide–ligand interaction. A confirmation of in silico investigation results is the correlation with the experimental results, which shows that the highest affinity to octanal is exhibited by the longest peptide (OBPP4 – KLLFDSLTDLKKKMSEC-NH2). We hypothesized that the binding of long chain aldehydes to the peptide, mimicking the binding site of HarmOBP7, induced a conformational change in the peptide deposited on a selected transducer. The constructed OBPP4-based biosensors were able to selectively bind octanal in the gas phase. It was also shown that the sensors were characterized by high selectivity with respect to octanal, as well as to acetaldehyde and benzaldehyde. The results indicate that the OBPP4 peptide, mimicking the binding domain in the Odorant Binding Protein, can provide new opportunities for the development of biomimicking materials in the field of odor biosensors.
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Affiliation(s)
- Tomasz Wasilewski
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdansk, Poland.
| | - Bartosz Szulczyński
- Department of Process Engineering and Chemical Technology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
| | - Marek Wojciechowski
- Department of Pharmaceutical Technology and Biochemistry, Chemical Faculty, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdansk, Poland.
| | - Jacek Gębicki
- Department of Process Engineering and Chemical Technology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
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18
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Genva M, Kenne Kemene T, Deleu M, Lins L, Fauconnier ML. Is It Possible to Predict the Odor of a Molecule on the Basis of its Structure? Int J Mol Sci 2019; 20:ijms20123018. [PMID: 31226833 PMCID: PMC6627536 DOI: 10.3390/ijms20123018] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
The olfactory sense is the dominant sensory perception for many animals. When Richard Axel and Linda B. Buck received the Nobel Prize in 2004 for discovering the G protein-coupled receptors’ role in olfactory cells, they highlighted the importance of olfaction to the scientific community. Several theories have tried to explain how cells are able to distinguish such a wide variety of odorant molecules in a complex context in which enantiomers can result in completely different perceptions and structurally different molecules. Moreover, sex, age, cultural origin, and individual differences contribute to odor perception variations that complicate the picture. In this article, recent advances in olfaction theory are presented, and future trends in human olfaction such as structure-based odor prediction and artificial sniffing are discussed at the frontiers of chemistry, physiology, neurobiology, and machine learning.
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Affiliation(s)
- Manon Genva
- Laboratory of Chemistry of Natural Molecules, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Tierry Kenne Kemene
- Laboratory of Chemistry of Natural Molecules, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Magali Deleu
- Laboratory of Molecular Biophysics at Interfaces, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Laurence Lins
- Laboratory of Molecular Biophysics at Interfaces, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Marie-Laure Fauconnier
- Laboratory of Chemistry of Natural Molecules, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
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19
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Liu MT, Ho J, Liu JK, Purakait R, Morzan UN, Ahmed L, Batista VS, Matsunami H, Ryan K. Carbon chain shape selectivity by the mouse olfactory receptor OR-I7. Org Biomol Chem 2019; 16:2541-2548. [PMID: 29569669 DOI: 10.1039/c8ob00205c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rodent OR-I7 is an olfactory receptor exemplar activated by aliphatic aldehydes such as octanal. Normal alkanals shorter than heptanal bind OR-I7 without activating it and hence function as antagonists in vitro. We report a series of aldehydes designed to probe the structural requirements for aliphatic ligand chains too short to meet the minimum approximate 6.9 Å length requirement for receptor activation. Experiments using recombinant mouse OR-I7 expressed in heterologous cells show that in the context of short aldehyde antagonists, OR-I7 prefers binding aliphatic chains without branches, though a single methyl on carbon-3 is permitted. The receptor can accommodate a surprisingly large number of carbons (e.g. ten in adamantyl) as long as the carbons are part of a conformationally constrained ring system. A rhodopsin-based homology model of mouse OR-I7 docked with the new antagonists suggests that small alkyl branches on the alkyl chain sterically interfere with the hydrophobic residues lining the binding site, but branch carbons can be accommodated when tied back into a compact ring system like the adamantyl and bicyclo[2.2.2]octyl systems.
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Affiliation(s)
- Min Ting Liu
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA. and Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Jianghai Ho
- Department of Molecular Genetics and Microbiology, and Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC 27710, USA.
| | - Jason Karl Liu
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Radhanath Purakait
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA.
| | - Uriel N Morzan
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Lucky Ahmed
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, and Neurobiology, Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC 27710, USA.
| | - Kevin Ryan
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA. and Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA and Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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20
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Wu C, Thach TT, Kim YJ, Lee SJ. Olfactory receptor 43 reduces hepatic lipid accumulation and adiposity in mice. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:489-499. [PMID: 30639733 DOI: 10.1016/j.bbalip.2019.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 12/30/2018] [Accepted: 01/05/2019] [Indexed: 12/14/2022]
Abstract
Olfactory receptors are primarily expressed in nasal olfactory epithelium, but these receptors are also ectopically expressed in diverse tissues. In this study, we investigated the biological functions of Olfr43, a mouse homolog of human OR1A1, in cultured hepatocytes and mice to assess its functionality in lipid metabolism. Olfr43 was expressed in mouse hepatocytes, and Olfr43 activation by a known ligand, (-)-carvone, stimulated cAMP response element-binding protein (CREB) activity. In ligand-receptor binding studies using site-directed mutagenesis, (-)-carvone binding required two residues, M257 and Y258, in Olfr43. In the mouse study, oral administration of (-)-carvone for 5 weeks in high-fat diet-fed mice improved energy metabolism, including reductions in hepatic steatosis and adiposity, and improved glucose and insulin tolerance. In mouse livers and cultured mouse hepatocytes, Olfr43 activation simulated the CREB-hairy and enhancer of split 1 (HES1)-peroxisome proliferator-activated receptor (PPAR)-γ signaling axis, leading to a reduction in hepatic triglyceride accumulation in the mouse liver. Thus, long-term administration of (-)-carvone reduces hepatic steatosis. The knockdown of Olfr43 gene expression in cultured hepatocytes negated these effects of (-)-carvone. In conclusion, an ectopic olfactory receptor, hepatic Olfr43, regulates energy metabolism via the CREB-HES1-PPARγ signaling axis.
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Affiliation(s)
- Chunyan Wu
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Korea University, Seoul 02841, Republic of Korea
| | - Trung Thanh Thach
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Korea University, Seoul 02841, Republic of Korea
| | - Yeon-Ji Kim
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Korea University, Seoul 02841, Republic of Korea
| | - Sung-Joon Lee
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Korea University, Seoul 02841, Republic of Korea.
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21
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Bushdid C, de March CA, Fiorucci S, Matsunami H, Golebiowski J. Agonists of G-Protein-Coupled Odorant Receptors Are Predicted from Chemical Features. J Phys Chem Lett 2018; 9:2235-2240. [PMID: 29648835 PMCID: PMC7294703 DOI: 10.1021/acs.jpclett.8b00633] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Predicting the activity of chemicals for a given odorant receptor is a longstanding challenge. Here the activity of 258 chemicals on the human G-protein-coupled odorant receptor (OR)51E1, also known as prostate-specific G-protein-coupled receptor 2 (PSGR2), was virtually screened by machine learning using 4884 chemical descriptors as input. A systematic control by functional in vitro assays revealed that a support vector machine algorithm accurately predicted the activity of a screened library. It allowed us to identify two novel agonists in vitro for OR51E1. The transferability of the protocol was assessed on OR1A1, OR2W1, and MOR256-3 odorant receptors, and, in each case, novel agonists were identified with a hit rate of 39-50%. We further show how ligands' efficacy is encoded into residues within OR51E1 cavity using a molecular modeling protocol. Our approach allows widening the chemical spaces associated with odorant receptors. This machine-learning protocol based on chemical features thus represents an efficient tool for screening ligands for G-protein-coupled odorant receptors that modulate non-olfactory functions or, upon combinatorial activation, give rise to our sense of smell.
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Affiliation(s)
- C. Bushdid
- Institute of Chemistry of Nice, UMR CNRS 7272, Université Côte d’Azur, Nice, France
| | - C. A. de March
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - S. Fiorucci
- Institute of Chemistry of Nice, UMR CNRS 7272, Université Côte d’Azur, Nice, France
| | - H. Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Neurobiology and Duke Institute for Brain Sciences, Duke University, Durham, North Carolina 27710, United States
- Corresponding Authors: (J.G.)., (H.M.)
| | - J. Golebiowski
- Institute of Chemistry of Nice, UMR CNRS 7272, Université Côte d’Azur, Nice, France
- Department of Brain & Cognitive Sciences, DGIST, Daegu, Republic of Korea
- Corresponding Authors: (J.G.)., (H.M.)
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22
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Wolf S, Jovancevic N, Gelis L, Pietsch S, Hatt H, Gerwert K. Dynamical Binding Modes Determine Agonistic and Antagonistic Ligand Effects in the Prostate-Specific G-Protein Coupled Receptor (PSGR). Sci Rep 2017; 7:16007. [PMID: 29167480 PMCID: PMC5700038 DOI: 10.1038/s41598-017-16001-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 11/03/2017] [Indexed: 01/14/2023] Open
Abstract
We analysed the ligand-based activation mechanism of the prostate-specific G-protein coupled receptor (PSGR), which is an olfactory receptor that mediates cellular growth in prostate cancer cells. Furthermore, it is an olfactory receptor with a known chemically near identic antagonist/agonist pair, α- and β-ionone. Using a combined theoretical and experimental approach, we propose that this receptor is activated by a ligand-induced rearrangement of a protein-internal hydrogen bond network. Surprisingly, this rearrangement is not induced by interaction of the ligand with the network, but by dynamic van der Waals contacts of the ligand with the involved amino acid side chains, altering their conformations and intraprotein connectivity. Ligand recognition in this GPCR is therefore highly stereo selective, but seemingly lacks any ligand recognition via polar contacts. A putative olfactory receptor-based drug design scheme will have to take this unique mode of protein/ligand action into account.
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Affiliation(s)
- Steffen Wolf
- Department of Biophysics, ND 04 North, Ruhr-University Bochum, 44780, Bochum, Germany.
- Department of Biophysics, CAS-MPG Partner Institute for Computational Biology, Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P.R. China.
| | - Nikolina Jovancevic
- Department of Cellphysiology, ND 4, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Lian Gelis
- Department of Cellphysiology, ND 4, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Sebastian Pietsch
- Department of Biophysics, ND 04 North, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Hanns Hatt
- Department of Cellphysiology, ND 4, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Klaus Gerwert
- Department of Biophysics, ND 04 North, Ruhr-University Bochum, 44780, Bochum, Germany
- Department of Biophysics, CAS-MPG Partner Institute for Computational Biology, Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P.R. China
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23
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Geithe C, Protze J, Kreuchwig F, Krause G, Krautwurst D. Structural determinants of a conserved enantiomer-selective carvone binding pocket in the human odorant receptor OR1A1. Cell Mol Life Sci 2017; 74:4209-4229. [PMID: 28656349 PMCID: PMC11107518 DOI: 10.1007/s00018-017-2576-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/29/2017] [Accepted: 06/16/2017] [Indexed: 12/17/2022]
Abstract
Chirality is a common phenomenon within odorants. Most pairs of enantiomers show only moderate differences in odor quality. One example for enantiomers that are easily discriminated by their odor quality is the carvones: humans significantly distinguish between the spearmint-like (R)-(-)-carvone and caraway-like (S)-(+)-carvone enantiomers. Moreover, for the (R)-(-)-carvone, an anosmia is observed in about 8% of the population, suggesting enantioselective odorant receptors (ORs). With only about 15% de-orphaned human ORs, the lack of OR crystal structures, and few comprehensive studies combining in silico and experimental approaches to elucidate structure-function relations of ORs, knowledge on cognate odorant/OR interactions is still sparse. An adjusted homology modeling approach considering OR-specific proline-caused conformations, odorant docking studies, single-nucleotide polymorphism (SNP) analysis, site-directed mutagenesis, and subsequent functional studies with recombinant ORs in a cell-based, real-time luminescence assay revealed 11 amino acid positions to constitute an enantioselective binding pocket necessary for a carvone function in human OR1A1 and murine Olfr43, respectively. Here, we identified enantioselective molecular determinants in both ORs that discriminate between minty and caraway odor. Comparison with orthologs from 36 mammalian species demonstrated a hominid-specific carvone binding pocket with about 100% conservation. Moreover, we identified loss-of-function SNPs associated with the carvone binding pocket of OR1A1. Given carvone enantiomer-specific receptor activation patterns including OR1A1, our data suggest OR1A1 as a candidate receptor for constituting a carvone enantioselective phenotype, which may help to explain mechanisms underlying a (R)-(-)-carvone-specific anosmia in humans.
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Affiliation(s)
- Christiane Geithe
- Deutsche Forschungsanstalt für Lebensmittelchemie Leibniz Institut (DFA), Freising, Germany
| | - Jonas Protze
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Franziska Kreuchwig
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Gerd Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| | - Dietmar Krautwurst
- Deutsche Forschungsanstalt für Lebensmittelchemie Leibniz Institut (DFA), Freising, Germany.
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24
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McDougal RA, Morse TM, Carnevale T, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hines ML. Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. J Comput Neurosci 2017; 42:1-10. [PMID: 27629590 PMCID: PMC5279891 DOI: 10.1007/s10827-016-0623-7] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/17/2016] [Accepted: 08/30/2016] [Indexed: 11/29/2022]
Abstract
Neuron modeling may be said to have originated with the Hodgkin and Huxley action potential model in 1952 and Rall's models of integrative activity of dendrites in 1964. Over the ensuing decades, these approaches have led to a massive development of increasingly accurate and complex data-based models of neurons and neuronal circuits. ModelDB was founded in 1996 to support this new field and enhance the scientific credibility and utility of computational neuroscience models by providing a convenient venue for sharing them. It has grown to include over 1100 published models covering more than 130 research topics. It is actively curated and developed to help researchers discover and understand models of interest. ModelDB also provides mechanisms to assist running models both locally and remotely, and has a graphical tool that enables users to explore the anatomical and biophysical properties that are represented in a model. Each of its capabilities is undergoing continued refinement and improvement in response to user experience. Large research groups (Allen Brain Institute, EU Human Brain Project, etc.) are emerging that collect data across multiple scales and integrate that data into many complex models, presenting new challenges of scale. We end by predicting a future for neuroscience increasingly fueled by new technology and high performance computation, and increasingly in need of comprehensive user-friendly databases such as ModelDB to provide the means to integrate the data for deeper insights into brain function in health and disease.
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Affiliation(s)
- Robert A McDougal
- Department of Neuroscience, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA.
| | - Thomas M Morse
- Department of Neuroscience, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA
| | - Ted Carnevale
- Department of Neuroscience, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA
| | - Luis Marenco
- Department of Neuroscience, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
- Center for Medical Informatics, Yale University, New Haven, CT, 06520, USA
| | - Rixin Wang
- Center for Medical Informatics, Yale University, New Haven, CT, 06520, USA
- Department of Anesthesiology, Yale University, New Haven, CT, 06520, USA
| | - Michele Migliore
- Department of Neuroscience, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Perry L Miller
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
- Center for Medical Informatics, Yale University, New Haven, CT, 06520, USA
- Department of Anesthesiology, Yale University, New Haven, CT, 06520, USA
| | - Gordon M Shepherd
- Department of Neuroscience, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA
| | - Michael L Hines
- Department of Neuroscience, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA
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25
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Noe F, Polster J, Geithe C, Kotthoff M, Schieberle P, Krautwurst D. OR2M3: A Highly Specific and Narrowly Tuned Human Odorant Receptor for the Sensitive Detection of Onion Key Food Odorant 3-Mercapto-2-methylpentan-1-ol. Chem Senses 2016; 42:195-210. [DOI: 10.1093/chemse/bjw118] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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26
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Gao S, Liu S, Yao J, Li N, Yuan Z, Zhou T, Li Q, Liu Z. Genomic organization and evolution of olfactory receptors and trace amine-associated receptors in channel catfish, Ictalurus punctatus. Biochim Biophys Acta Gen Subj 2016; 1861:644-651. [PMID: 27773705 DOI: 10.1016/j.bbagen.2016.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/05/2016] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Channel catfish (Ictalurus punctatus) live in turbid waters with limited visibility to chase prey within a certain distance. This can be compensated through detecting specific water-soluble substances by the olfactory receptors (ORs) and trace amine associated receptors (TAARs) expressed on the olfactory epithelium. METHODS We identified the OR and TAAR repertoires in channel catfish, and characterized the genomic organizations of these two gene families by data mining available genomic resources. RESULTS A total of 47 putative OR genes and 36 putative TAAR genes were identified in the channel catfish genome, including 27 functional OR genes and 28 functional TAAR genes. Phylogenetic and orthogroup analyses were conducted to illustrate the evolutionary dynamics of the vertebrate ORs and TAARs. Collinear analysis revealed the presence of two conserved orthologous blocks that contain OR genes between the catfish genome and zebrafish genome. The complete loss of a conserved motif in fish OR family H may contribute to the divergence of family H from other families. The dN/dS analysis indicated that the highest degree of selection pressure was imposed on TAAR subfamily 14 among all fish ORs and TAARs. CONCLUSIONS The present study provides understanding of the evolutionary dynamics of the two gene families (OR and TAAR) associated with olfaction in channel catfish. GENERAL SIGNIFICANCE This is the first systematic study of ORs and TAARs in catfish, which could provide valuable genomic resources for further investigation of olfactory mechanisms in teleost fish.
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Affiliation(s)
- Sen Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jun Yao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Qi Li
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
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27
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Greer PL, Bear DM, Lassance JM, Bloom ML, Tsukahara T, Pashkovski SL, Masuda FK, Nowlan AC, Kirchner R, Hoekstra HE, Datta SR. A Family of non-GPCR Chemosensors Defines an Alternative Logic for Mammalian Olfaction. Cell 2016; 165:1734-1748. [PMID: 27238024 DOI: 10.1016/j.cell.2016.05.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/14/2016] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
Odor perception in mammals is mediated by parallel sensory pathways that convey distinct information about the olfactory world. Multiple olfactory subsystems express characteristic seven-transmembrane G-protein-coupled receptors (GPCRs) in a one-receptor-per-neuron pattern that facilitates odor discrimination. Sensory neurons of the "necklace" subsystem are nestled within the recesses of the olfactory epithelium and detect diverse odorants; however, they do not express known GPCR odor receptors. Here, we report that members of the four-pass transmembrane MS4A protein family are chemosensors expressed within necklace sensory neurons. These receptors localize to sensory endings and confer responses to ethologically relevant ligands, including pheromones and fatty acids, in vitro and in vivo. Individual necklace neurons co-express many MS4A proteins and are activated by multiple MS4A ligands; this pooling of information suggests that the necklace is organized more like subsystems for taste than for smell. The MS4As therefore define a distinct mechanism and functional logic for mammalian olfaction.
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Affiliation(s)
- Paul L Greer
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel M Bear
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jean-Marc Lassance
- Departments of Molecular and Cellular Biology and Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | | | - Tatsuya Tsukahara
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Stan L Pashkovski
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Francis Kei Masuda
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexandra C Nowlan
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Rory Kirchner
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Hopi E Hoekstra
- Departments of Molecular and Cellular Biology and Organismic and Evolutionary Biology, Center for Brain Science, Harvard University, Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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28
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Odorant receptors of Drosophila are sensitive to the molecular volume of odorants. Sci Rep 2016; 6:25103. [PMID: 27112241 PMCID: PMC4844992 DOI: 10.1038/srep25103] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 04/08/2016] [Indexed: 01/08/2023] Open
Abstract
Which properties of a molecule define its odor? This is a basic yet unanswered question regarding the olfactory system. The olfactory system of Drosophila has a repertoire of approximately 60 odorant receptors. Molecules bind to odorant receptors with different affinities and activate them with different efficacies, thus providing a combinatorial code that identifies odorants. We hypothesized that the binding affinity of an odorant-receptor pair is affected by their relative sizes. The maximum affinity can be attained when the molecular volume of an odorant matches the volume of the binding pocket. The affinity drops to zero when the sizes are too different, thus obscuring the effects of other molecular properties. We developed a mathematical formulation of this hypothesis and verified it using Drosophila data. We also predicted the volume and structural flexibility of the binding site of each odorant receptor; these features significantly differ between odorant receptors. The differences in the volumes and structural flexibilities of different odorant receptor binding sites may explain the difference in the scents of similar molecules with different sizes.
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29
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Zhao W, Ho L, Wang J, Bi W, Yemul S, Ward L, Freire D, Mazzola P, Brathwaite J, Mezei M, Sanchez R, Elder GA, Pasinetti GM. In Silico Modeling of Novel Drug Ligands for Treatment of Concussion Associated Tauopathy. J Cell Biochem 2016; 117:2241-8. [PMID: 26910498 DOI: 10.1002/jcb.25521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/19/2016] [Indexed: 11/07/2022]
Abstract
The objective of this study was to develop an in silico screening model for characterization of potential novel ligands from commercial drug libraries able to functionally activate certain olfactory receptors (ORs), which are members of the class A rhodopsin-like family of G protein couple receptors (GPCRs), in the brain of murine models of concussion. We previously found that concussions may significantly influence expression of certain ORs, for example, OR4M1 in subjects with a history of concussion/traumatic brain injury (TBI). In this study, we built a 3-D OR4M1 model and used it in in silico screening of potential novel ligands from commercial drug libraries. We report that in vitro activation of OR4M1 with the commercially available ZINC library compound 10915775 led to a significant attenuation of abnormal tau phosphorylation in embryonic cortico-hippocampal neuronal cultures derived from NSE-OR4M1 transgenic mice, possibly through modulation of the JNK signaling pathway. The attenuation of abnormal tau phosphorylation was rather selective since ZINC10915775 significantly decreased tau phosphorylation on tau Ser202/T205 (AT8 epitope) and tau Thr212/Ser214 (AT100 epitope), but not on tau Ser396/404 (PHF-1 epitope). Moreover, no response of ZINC10915775 was found in control hippocampal neuronal cultures derived from wild type littermates. Our in silico model provides novel means to pharmacologically modulate select ubiquitously expressed ORs in the brain through high affinity ligand activation to prevent and eventually to treat concussion induced down regulation of ORs and subsequent cascade of tau pathology. J. Cell. Biochem. 117: 2241-2248, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Wei Zhao
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York.,Geriatric Research Education Clinical Center at James J. Peters VA Medical Center, Bronx, New York
| | - Lap Ho
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York
| | - Jun Wang
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York.,Geriatric Research Education Clinical Center at James J. Peters VA Medical Center, Bronx, New York
| | - Weina Bi
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York
| | - Shrishailam Yemul
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York
| | - Libby Ward
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York
| | - Daniel Freire
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York
| | - Paolo Mazzola
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York.,School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Justin Brathwaite
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York
| | - Mihaly Mezei
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York.,Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York
| | - Roberto Sanchez
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York.,Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York
| | - Gregory A Elder
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York
| | - Giulio Maria Pasinetti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York.,Geriatric Research Education Clinical Center at James J. Peters VA Medical Center, Bronx, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York
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30
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Baud O, Yuan S, Veya L, Filipek S, Vogel H, Pick H. Exchanging ligand-binding specificity between a pair of mouse olfactory receptor paralogs reveals odorant recognition principles. Sci Rep 2015; 5:14948. [PMID: 26449412 PMCID: PMC4598832 DOI: 10.1038/srep14948] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/07/2015] [Indexed: 12/20/2022] Open
Abstract
A multi-gene family of ~1000 G protein-coupled olfactory receptors (ORs) constitutes the molecular basis of mammalian olfaction. Due to the lack of structural data its remarkable capacity to detect and discriminate thousands of odorants remains poorly understood on the structural level of the receptor. Using site-directed mutagenesis we transferred ligand specificity between two functionally related ORs and thereby revealed amino acid residues of central importance for odorant recognition and discrimination of the two receptors. By exchanging two of three residues, differing at equivalent positions of the putative odorant binding site between the mouse OR paralogs Olfr73 (mOR-EG) and Olfr74 (mOR-EV), we selectively changed ligand preference but remarkably also signaling activation strength in both ORs. Computer modeling proposed structural details at atomic resolution how the very same odorant molecule might interact with different contact residues to induce different functional responses in two related receptors. Our findings provide a mechanistic explanation of how the olfactory system distinguishes different molecular aspects of a given odorant molecule, and unravel important molecular details of the combinatorial encoding of odorant identity at the OR level.
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Affiliation(s)
- Olivia Baud
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne Switzerland
| | - Shuguang Yuan
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne Switzerland
| | - Luc Veya
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne Switzerland
| | - Slawomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Poland
| | - Horst Vogel
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne Switzerland
| | - Horst Pick
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne Switzerland
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31
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de March CA, Kim SK, Antonczak S, Goddard WA, Golebiowski J. G protein-coupled odorant receptors: From sequence to structure. Protein Sci 2015; 24:1543-8. [PMID: 26044705 PMCID: PMC4570547 DOI: 10.1002/pro.2717] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/25/2015] [Indexed: 12/14/2022]
Abstract
Odorant receptors (ORs) are the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date and atomic-level insights are likely to be obtained by means of molecular modeling. In this article, we critically align sequences of ORs with those GPCRs for which a structure is available. Here, an alignment consistent with available site-directed mutagenesis data on various ORs is proposed. Using this alignment, the choice of the template is deemed rather minor for identifying residues that constitute the wall of the binding cavity or those involved in G protein recognition.
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Affiliation(s)
- Claire A de March
- Institute of Chemistry—Nice, UMR 7272 CNRS—University Nice—Sophia AntipolisNice Cedex 2, 06108, France
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (MC139-74), California Institute of TechnologyPasadena, California, 91125
| | - Serge Antonczak
- Institute of Chemistry—Nice, UMR 7272 CNRS—University Nice—Sophia AntipolisNice Cedex 2, 06108, France
| | - William A Goddard
- Materials and Process Simulation Center (MC139-74), California Institute of TechnologyPasadena, California, 91125
| | - Jérôme Golebiowski
- Institute of Chemistry—Nice, UMR 7272 CNRS—University Nice—Sophia AntipolisNice Cedex 2, 06108, France
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32
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Harini K, Sowdhamini R. Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening. PLoS One 2015. [PMID: 26221959 PMCID: PMC4519343 DOI: 10.1371/journal.pone.0131077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Olfactory receptors (ORs) belong to the class A G-Protein Coupled Receptor superfamily of proteins. Unlike G-Protein Coupled Receptors, ORs exhibit a combinatorial response to odors/ligands. ORs display an affinity towards a range of odor molecules rather than binding to a specific set of ligands and conversely a single odorant molecule may bind to a number of olfactory receptors with varying affinities. The diversity in odor recognition is linked to the highly variable transmembrane domains of these receptors. The purpose of this study is to decode the odor-olfactory receptor interactions using in silico docking studies. In this study, a ligand (odor molecules) dataset of 125 molecules was used to carry out in silico docking using the GLIDE docking tool (SCHRODINGER Inc Pvt LTD). Previous studies, with smaller datasets of ligands, have shown that orthologous olfactory receptors respond to similarly-tuned ligands, but are dramatically different in their efficacy and potency. Ligand docking results were applied on homologous pairs (with varying sequence identity) of ORs from human and mouse genomes and ligand binding residues and the ligand profile differed among such related olfactory receptor sequences. This study revealed that homologous sequences with high sequence identity need not bind to the same/ similar ligand with a given affinity. A ligand profile has been obtained for each of the 20 receptors in this analysis which will be useful for expression and mutation studies on these receptors.
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Affiliation(s)
- K. Harini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, India
- * E-mail:
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Khan I, Yang Z, Maldonado E, Li C, Zhang G, Gilbert MTP, Jarvis ED, O’Brien SJ, Johnson WE, Antunes A. Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida. Mol Biol Evol 2015. [DOI: 10.1093/molbev/msv155] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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de March CA, Yu Y, Ni MJ, Adipietro KA, Matsunami H, Ma M, Golebiowski J. Conserved Residues Control Activation of Mammalian G Protein-Coupled Odorant Receptors. J Am Chem Soc 2015; 137:8611-8616. [PMID: 26090619 PMCID: PMC4497840 DOI: 10.1021/jacs.5b04659] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Odorant receptor (OR) genes and proteins represent more than 2% of our genome and 4% of our proteome and constitute the largest subgroup of G protein-coupled receptors (GPCRs). The mechanism underlying OR activation remains poorly understood, as they do not share some of the highly conserved motifs critical for activation of non-olfactory GPCRs. By combining site-directed mutagenesis, heterologous expression, and molecular dynamics simulations that capture the conformational change of constitutively active mutants, we tentatively identified crucial residues for the function of these receptors using the mouse MOR256-3 (Olfr124) as a model. The toggle switch for sensing agonists involves a highly conserved tyrosine residue in helix VI. The ionic lock is located between the "DRY" motif in helix III and a positively charged "R/K" residue in helix VI. This study provides an unprecedented model that captures the main mechanisms of odorant receptor activation.
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Affiliation(s)
- Claire A. de March
- Institute of Chemistry - Nice, UMR 7272 CNRS - University Nice - Sophia Antipolis, 06108 Nice cedex 2, France
| | - Yiqun Yu
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mengjue J. Ni
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kaylin A. Adipietro
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Minghong Ma
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jérôme Golebiowski
- Institute of Chemistry - Nice, UMR 7272 CNRS - University Nice - Sophia Antipolis, 06108 Nice cedex 2, France
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Hayden S, Teeling EC. The molecular biology of vertebrate olfaction. Anat Rec (Hoboken) 2015; 297:2216-26. [PMID: 25312375 DOI: 10.1002/ar.23031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 06/25/2014] [Indexed: 01/16/2023]
Abstract
The importance of chemosensation for vertebrates is reflected in the vast and variable nature of their chemosensory tissues, neurons, and genes, which we explore in this review. Immense progress has been made in elucidating the molecular biology of olfaction since the discovery of the olfactory receptor genes by Buck and Axel, which eventually won the authors the Nobel Prize. In particular, research linking odor ligands to olfactory receptors (ORs) is truly revolutionizing our understanding of how a large but limited number of chemosensory receptors can allow us to perceive the massive diversity of odors in our habitat. This research is providing insight into the evolution of genomes and providing the raw data needed to explore links between genotype and phenotype, still a grand challenge in biology. Research into olfaction is still developing and will no doubt continue until we have a clear understanding of how all odors are detected and the evolutionary forces that have molded the chemosensory subgenome in vertebrates. This knowledge will not only be a huge step in elucidating olfactory function, advancing scientific knowledge and techniques, but there are also commercial applications for this research. This review focuses on the molecular basis of chemosensation, particularly olfaction, its evolution across vertebrates and the recent molecular advances linking odors to their cognate receptors.
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Affiliation(s)
- Sara Hayden
- Department of Biochemistry, University of Washington, Seattle, Washington
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de March CA, Ryu S, Sicard G, Moon C, Golebiowski J. Structure-odour relationships reviewed in the postgenomic era. FLAVOUR FRAG J 2015. [DOI: 10.1002/ffj.3249] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Claire A. de March
- Institut de Chimie de Nice; Université Nice Sophia Antipolis; UMR CNRS 7272, parc Valrose 06108 Nice cedex 02 France
| | - SangEun Ryu
- Laboratory of Chemical Senses, Department of Brain and Cognitive Science; DGIST (Daegu Gyeongbuk Institute of Science & Technology); 50-1 Sang-Ri, Hyeonpung-Myeon, Dalseong-Gun Daegu 711-873 Korea
| | - Gilles Sicard
- Neurobiology of Cellular Interactions and Neurophysiopathology; Aix-Marseille Université; UMR CNRS 7259 13331 Marseille cedex 03 France
| | - Cheil Moon
- Laboratory of Chemical Senses, Department of Brain and Cognitive Science; DGIST (Daegu Gyeongbuk Institute of Science & Technology); 50-1 Sang-Ri, Hyeonpung-Myeon, Dalseong-Gun Daegu 711-873 Korea
| | - Jérôme Golebiowski
- Institut de Chimie de Nice; Université Nice Sophia Antipolis; UMR CNRS 7272, parc Valrose 06108 Nice cedex 02 France
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Ho J, Perez-Aguilar JM, Gao L, Saven JG, Matsunami H, Eckenhoff RG. Molecular recognition of ketamine by a subset of olfactory G protein-coupled receptors. Sci Signal 2015; 8:ra33. [PMID: 25829447 DOI: 10.1126/scisignal.2005912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ketamine elicits various neuropharmacological effects, including sedation, analgesia, general anesthesia, and antidepressant activity. Through an in vitro screen, we identified four mouse olfactory receptors (ORs) that responded to ketamine. In addition to their presence in the olfactory epithelium, these G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors (GPCRs) are distributed throughout the central nervous system. To better understand the molecular basis of the interactions between ketamine and ORs, we used sequence comparison and molecular modeling to design mutations that (i) increased, reduced, or abolished ketamine responsiveness in responding receptors, and (ii) rendered nonresponding receptors responsive to ketamine. We showed that olfactory sensory neurons (OSNs) that expressed distinct ORs responded to ketamine in vivo, suggesting that ORs may serve as functional targets for ketamine. The ability to both abolish and introduce responsiveness to ketamine in GPCRs enabled us to identify and confirm distinct interaction loci in the binding site, which suggested a signature ketamine-binding pocket that may guide exploration of additional receptors for this general anesthetic drug.
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Affiliation(s)
- Jianghai Ho
- Department of Molecular Genetics and Microbiology, and Department of Neurobiology, Duke University, Durham, NC 27710, USA
| | | | - Lu Gao
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, and Department of Neurobiology, Duke University, Durham, NC 27710, USA.,Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA
| | - Roderic G Eckenhoff
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Li J, Haddad R, Santos V, Bavan S, Luetje CW. Receptive range analysis of a mouse odorant receptor subfamily. J Neurochem 2015; 134:47-55. [PMID: 25772782 DOI: 10.1111/jnc.13095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 02/09/2015] [Accepted: 03/03/2015] [Indexed: 11/30/2022]
Abstract
Mammals deploy a large array of odorant receptors (ORs) to detect and distinguish a vast number of odorant molecules. ORs vary widely in the type of odorant structures recognized and in the breadth of molecular receptive range (MRR), with some ORs recognizing a small group of closely related molecules and other ORs recognizing a wide range of structures. While closely related ORs have been shown to have similar MRRs, the functional relationships among less closely related ORs are unclear. We screened a small group of ORs with a diverse odorant panel to identify a new odorant-OR pairing (unsaturated aldehydes and MOR263-3). We then extensively screened MOR263-3 and a series of additional MORs related to MOR263-3 in various ways. MORs related by phylogenetic analysis (several other members of the MOR263 subfamily) had MRRs that overlapped with the MRR of MOR263-3, even with amino acid identity as low as 48% (MOR263-2). MOR171-17, predicted to be functionally related to MOR263-3 by an alternative bioinformatic analysis, but with only 39% amino acid identity, had a distinct odorant specificity. Our results support the use of phylogenetic analysis to predict functional relationships among ORs with relatively low amino acid identity. We screened a small group of mouse odorant receptors (MORs) with a diverse odorant panel to identify a new odorant-OR pairing (unsaturated aldehydes and MOR263-3), then extensively screened a series of additional MORs related to MOR263-3 in various ways. MORs related by phylogenetic analysis had odorant specificities that overlapped with that of MOR263-3, but MOR171-17, predicted to be functionally related to MOR263-3 by an alternative bioinformatic analysis, had a distinct odorant specificity.
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Affiliation(s)
- Jingyi Li
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Rafi Haddad
- Gonda Brain Research Center, Bar Ilan University, Ramat Gan, Israel
| | - Vanessa Santos
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Selvan Bavan
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Charles W Luetje
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, USA
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Persuy MA, Sanz G, Tromelin A, Thomas-Danguin T, Gibrat JF, Pajot-Augy E. Mammalian olfactory receptors: molecular mechanisms of odorant detection, 3D-modeling, and structure-activity relationships. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 130:1-36. [PMID: 25623335 DOI: 10.1016/bs.pmbts.2014.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This chapter describes the main characteristics of olfactory receptor (OR) genes of vertebrates, including generation of this large multigenic family and pseudogenization. OR genes are compared in relation to evolution and among species. OR gene structure and selection of a given gene for expression in an olfactory sensory neuron (OSN) are tackled. The specificities of OR proteins, their expression, and their function are presented. The expression of OR proteins in locations other than the nasal cavity is regulated by different mechanisms, and ORs display various additional functions. A conventional olfactory signal transduction cascade is observed in OSNs, but individual ORs can also mediate different signaling pathways, through the involvement of other molecular partners and depending on the odorant ligand encountered. ORs are engaged in constitutive dimers. Ligand binding induces conformational changes in the ORs that regulate their level of activity depending on odorant dose. When present, odorant binding proteins induce an allosteric modulation of OR activity. Since no 3D structure of an OR has been yet resolved, modeling has to be performed using the closest G-protein-coupled receptor 3D structures available, to facilitate virtual ligand screening using the models. The study of odorant binding modes and affinities may infer best-bet OR ligands, to be subsequently checked experimentally. The relationship between spatial and steric features of odorants and their activity in terms of perceived odor quality are also fields of research that development of computing tools may enhance.
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Affiliation(s)
- Marie-Annick Persuy
- INRA UR 1197 NeuroBiologie de l'Olfaction, Domaine de Vilvert, Jouy-en-Josas, France
| | - Guenhaël Sanz
- INRA UR 1197 NeuroBiologie de l'Olfaction, Domaine de Vilvert, Jouy-en-Josas, France
| | - Anne Tromelin
- INRA UMR 1129 Flaveur, Vision et Comportement du Consommateur, Dijon, France
| | | | - Jean-François Gibrat
- INRA UR1077 Mathématique Informatique et Génome, Domaine de Vilvert, Jouy-en-Josas, France
| | - Edith Pajot-Augy
- INRA UR 1197 NeuroBiologie de l'Olfaction, Domaine de Vilvert, Jouy-en-Josas, France.
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40
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Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history. Nat Genet 2014; 46:1303-10. [DOI: 10.1038/ng.3137] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 10/09/2014] [Indexed: 11/08/2022]
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41
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Don CG, Riniker S. Scents and sense:In silicoperspectives on olfactory receptors. J Comput Chem 2014; 35:2279-87. [DOI: 10.1002/jcc.23757] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/23/2014] [Accepted: 09/27/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Charleen G. Don
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich; 8093 Zurich Switzerland
| | - Sereina Riniker
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich; 8093 Zurich Switzerland
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Topin J, de March CA, Charlier L, Ronin C, Antonczak S, Golebiowski J. Discrimination between olfactory receptor agonists and non-agonists. Chemistry 2014; 20:10227-30. [PMID: 25043138 DOI: 10.1002/chem.201402486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Indexed: 01/27/2023]
Abstract
A joint approach combining free-energy calculations and calcium-imaging assays on the broadly tuned human 1G1 olfactory receptor is reported. The free energy of binding of ten odorants was computed by means of molecular-dynamics simulations. This state function allows separating the experimentally determined eight agonists from the two non-agonists. This study constitutes a proof-of-principle for the computational deorphanization of olfactory receptors.
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Affiliation(s)
- Jérémie Topin
- Université de Nice - Sophia Antipolis, Institut de Chimie de Nice UMR 7272, Parc Valrose 28, Avenue Valrose 06108, Nice, Cedex 2 (France)
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A computational microscope focused on the sense of smell. Biochimie 2014; 107 Pt A:3-10. [PMID: 24952349 DOI: 10.1016/j.biochi.2014.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/07/2014] [Indexed: 11/24/2022]
Abstract
In this article, we review studies of the protagonists of the perception of smell focusing on Odorant-Binding Proteins and Olfactory Receptors. We notably put forward studies performed by means of molecular modeling, generally combined with experimental data. Those works clearly emphasize that computational approaches are now a force to reckon with. In the future, they will certainly be more and more used, notably in the framework of a computational microscope meant to observe how the laws of physics govern the biomolecular systems originating our sense of smell.
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Peterlin Z, Firestein S, Rogers ME. The state of the art of odorant receptor deorphanization: a report from the orphanage. ACTA ACUST UNITED AC 2014; 143:527-42. [PMID: 24733839 PMCID: PMC4003190 DOI: 10.1085/jgp.201311151] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The odorant receptors (ORs) provide our main gateway to sensing the world of volatile chemicals. This involves a complex encoding process in which multiple ORs, each of which detects its own set of odorants, work as an ensemble to produce a distributed activation code that is presumably unique to each odorant. One marked challenge to decoding the olfactory code is OR deorphanization, the identification of a set of activating odorants for a particular receptor. Here, we survey various methods used to try to express defined ORs of interest. We also suggest strategies for selecting odorants for test panels to evaluate the functional expression of an OR. Integrating these tools, while retaining awareness of their idiosyncratic limitations, can provide a multi-tiered approach to OR deorphanization, spanning the initial discovery of a ligand to vetting that ligand in a physiologically relevant setting.
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Affiliation(s)
- Zita Peterlin
- Corporate Research and Development, Firmenich Incorporated, Plainsboro, NJ 08536
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46
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Stathopoulos S, Bishop JM, O’Ryan C. Genetic signatures for enhanced olfaction in the African mole-rats. PLoS One 2014; 9:e93336. [PMID: 24699281 PMCID: PMC3974769 DOI: 10.1371/journal.pone.0093336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 03/03/2014] [Indexed: 01/06/2023] Open
Abstract
The Olfactory Receptor (OR) superfamily, the largest in the vertebrate genome, is responsible for vertebrate olfaction and is traditionally subdivided into 17 OR families. Recent studies characterising whole-OR subgenomes revealed a 'birth and death' model of evolution for a range of species, however little is known about fine-scale evolutionary dynamics within single-OR families. This study reports the first assessment of fine-scale OR evolution and variation in African mole-rats (Bathyergidae), a family of subterranean rodents endemic to sub-Saharan Africa. Because of the selective pressures of life underground, enhanced olfaction is proposed to be fundamental to the evolutionary success of the Bathyergidae, resulting in a highly diversified OR gene-repertoire. Using a PCR-sequencing approach, we analysed variation in the OR7 family across 14 extant bathyergid species, which revealed enhanced levels of functional polymorphisms concentrated across the receptors' ligand-binding region. We propose that mole-rats are able to recognise a broad range of odorants and that this diversity is reflected throughout their OR7 gene repertoire. Using both classic tests and tree-based methods to test for signals of selection, we investigate evolutionary forces across the mole-rat OR7 gene tree. Four well-supported clades emerged in the OR phylogeny, with varying signals of selection; from neutrality to positive and purifying selection. Bathyergid life-history traits and environmental niche-specialisation are explored as possible drivers of adaptive OR evolution, emerging as non-exclusive contributors to the positive selection observed at OR7 genes. Our results reveal unexpected complexity of evolutionary mechanisms acting within a single OR family, providing insightful perspectives into OR evolutionary dynamics.
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Affiliation(s)
- Sofia Stathopoulos
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, Western Cape, South Africa
- * E-mail:
| | - Jacqueline M. Bishop
- Department of Biological Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Colleen O’Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, Western Cape, South Africa
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Lai PC, Guida B, Shi J, Crasto CJ. Preferential binding of an odor within olfactory receptors: a precursor to receptor activation. Chem Senses 2014; 39:107-23. [PMID: 24398973 PMCID: PMC3894857 DOI: 10.1093/chemse/bjt060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Using computational methods, which allow mechanistic insights at a molecular level, we explored the olfactory receptor (OR)-odor interactions for 2 mouse ORs, S79 and S86. Both ORs have been previously experimentally, functionally characterized. The odors used were mostly carboxylic acids, which differed in chain length, substituents on the primary carbon atom-chain and degree of unsaturation. These odors elicited varied activation responses from both ORs. Our studies revealed that both receptors have 2 distinct binding sites. Preferential binding in 1 of the 2 sites is correlated with OR activation. The activating odorants: nonanedioic acid, heptanoic acid, and octanoic acid for OR S79 and nonanoic acid for OR S86 preferentially bind in the region bound by transmembranes (TMs [helical domains]) III, IV, V, and VI. The non excitatory odorants heptanol for S79 and heptanoic acid for S86 showed a greater likelihood of binding in the region bound by TMs I, II, III, and VII. Nanosecond-scale molecular dynamics simulations of the physiologically relevant conditions of docked OR-odorant complexes enabled us to quantitatively assess the roles of individual OR amino acids in odor binding. Amino acid-odorant contact maps and distance determinations over the course of the simulations lend support to our conclusions.
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Affiliation(s)
- Peter C Lai
- Department of Genetics, Division of Research, University of Alabama at Birmingham, 720 20th Street S., Birmingham, AL 35294, USA.
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Abstract
Providing a rationale that associates a chemical structure of an odorant to its induced perception has been sought for a long time. To achieve this, a detailed atomic structure of both the odorant and the olfactory receptor must be known. State-of-the-art techniques to model the 3D structure of an olfactory receptor in complex with various odorants are presented here. These range from sequence alignment with known structures to molecular dynamics simulations in a realistic environment.
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Olender T, Safran M, Edgar R, Stelzer G, Nativ N, Rosen N, Shtrichman R, Mazor Y, West MD, Keydar I, Rappaport N, Belinky F, Warshawsky D, Lancet D. An Overview of Synergistic Data Tools for Biological Scrutiny. Isr J Chem 2013. [DOI: 10.1002/ijch.201200094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
Olfactory receptors (ORs) constitute the largest gene family in the mammalian genome. The existence of these proteins underlies the nature of, and variability in, odorant perception. The Human Olfactory Receptor Data Explorer (HORDE, http://genome.weizmann.ac.il/horde/ ) is a free online resource, which presents a complete compendium of all OR genes and pseudogenes in the genome of human and four other vertebrates. HORDE includes three parts: (1) an automated pipeline, which mines OR gene and pseudogene sequences out of complete genomes, and generates gene symbols based on sequence similarity; (2) a card generator that obtains and displays annotative information on individual ORs retrieved from external databases and relevant studies; and (3) a search engine that allows user retrieval of OR information. For human ORs, HORDE specifically addresses the universe of interindividual variation, as obtained from several sources, including whole genome sequences made possible by next-generation sequencing. This encompasses single nucleotide polymorphisms (SNP) and copy number variation (CNV), including deleterious mutational events. HORDE also hosts a number of tools designed specifically to assist in the study of OR evolution and function. In this chapter, we describe the status of HORDE (build #43). We also discuss plans for future enhancements and a road map for HORDE to become a better community-based bioinformatics tool. We highlight HORDE's role as a major research tool in the study of an expanding cohort of OR repertoires.
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Affiliation(s)
- Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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