1
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Frank HM, Walujkar S, Walsh RM, Laursen WJ, Theobald DL, Garrity PA, Gaudet R. Structural basis of ligand specificity and channel activation in an insect gustatory receptor. Cell Rep 2024; 43:114035. [PMID: 38573859 PMCID: PMC11100771 DOI: 10.1016/j.celrep.2024.114035] [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: 12/10/2023] [Revised: 02/26/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
Gustatory receptors (GRs) are critical for insect chemosensation and are potential targets for controlling pests and disease vectors, making their structural investigation a vital step toward such applications. We present structures of Bombyx mori Gr9 (BmGr9), a fructose-gated cation channel, in agonist-free and fructose-bound states. BmGr9 forms a tetramer similar to distantly related insect odorant receptors (ORs). Upon fructose binding, BmGr9's channel gate opens through helix S7b movements. In contrast to ORs, BmGr9's ligand-binding pocket, shaped by a kinked helix S4 and a shorter extracellular S3-S4 loop, is larger and solvent accessible in both agonist-free and fructose-bound states. Also, unlike ORs, fructose binding by BmGr9 involves helix S5 and a pocket lined with aromatic and polar residues. Structure-based sequence alignments reveal distinct patterns of ligand-binding pocket residue conservation in GR subfamilies associated with different ligand classes. These data provide insight into the molecular basis of GR ligand specificity and function.
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Affiliation(s)
- Heather M Frank
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Sanket Walujkar
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Richard M Walsh
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Willem J Laursen
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | | | - Paul A Garrity
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA.
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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2
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Frank HM, Walujkar S, Walsh RM, Laursen WJ, Theobald DL, Garrity PA, Gaudet R. Structure of an insect gustatory receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572336. [PMID: 38187590 PMCID: PMC10769236 DOI: 10.1101/2023.12.19.572336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Gustatory Receptors (GRs) are critical for insect chemosensation and are potential targets for controlling pests and disease vectors. However, GR structures have not been experimentally determined. We present structures of Bombyx mori Gr9 (BmGr9), a fructose-gated cation channel, in agonist-free and fructose-bound states. BmGr9 forms a tetramer similar to distantly related insect Olfactory Receptors (ORs). Upon fructose binding, BmGr9's ion channel gate opens through helix S7b movements. In contrast to ORs, BmGR9's ligand-binding pocket, shaped by a kinked helix S4 and a shorter extracellular S3-S4 loop, is larger and solvent accessible in both agonist-free and fructose-bound states. Also unlike ORs, fructose binding by BmGr9 involves helix S5 and a binding pocket lined with aromatic and polar residues. Structure-based sequence alignments reveal distinct patterns of ligand-binding pocket residue conservation in GR subfamilies associated with distinct ligand classes. These data provide insight into the molecular basis of GR ligand specificity and function.
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Affiliation(s)
- Heather M. Frank
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
- These authors contributed equally
| | - Sanket Walujkar
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
- These authors contributed equally
| | - Richard M. Walsh
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- These authors contributed equally
| | - Willem J. Laursen
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | | | - Paul A. Garrity
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
- Lead contact
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3
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Himmel NJ, Moi D, Benton R. Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life. Curr Biol 2023; 33:5023-5033.e4. [PMID: 37913770 DOI: 10.1016/j.cub.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/26/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
Many proteins exist in the so-called "twilight zone" of sequence alignment, where low pairwise sequence identity makes it difficult to determine homology and phylogeny.1,2 As protein tertiary structure is often more conserved,3 recent advances in ab initio protein folding have made structure-based identification of putative homologs feasible.4,5,6 We present a pipeline for the identification and characterization of distant homologs and apply it to 7-transmembrane-domain ion channels (7TMICs), a protein group founded by insect odorant and gustatory receptors. Previous sequence and limited structure-based searches identified putatively related proteins, mainly in other animals and plants.7,8,9,10 However, very few 7TMICs have been identified in non-animal, non-plant taxa. Moreover, these proteins' remarkable sequence dissimilarity made it uncertain whether disparate 7TMIC types (Gr/Or, Grl, GRL, DUF3537, PHTF, and GrlHz) are homologous or convergent, leaving their evolutionary history unresolved. Our pipeline identified thousands of new 7TMICs in archaea, bacteria, and unicellular eukaryotes. Using graph-based analyses and protein language models to extract family-wide signatures, we demonstrate that 7TMICs have structure and sequence similarity, supporting homology. Through sequence- and structure-based phylogenetics, we classify eukaryotic 7TMICs into two families (Class-A and Class-B), which are the result of a gene duplication predating the split(s) leading to Amorphea (animals, fungi, and allies) and Diaphoretickes (plants and allies). Our work reveals 7TMICs as a cryptic superfamily, with origins close to the evolution of cellular life. More generally, this study serves as a methodological proof of principle for the identification of extremely distant protein homologs.
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Affiliation(s)
- Nathaniel J Himmel
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.
| | - David Moi
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.
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4
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Kleinheinz D, D’Onofrio C, Carraher C, Bozdogan A, Ramach U, Schuster B, Geiß M, Valtiner M, Knoll W, Andersson J. Activity of Single Insect Olfactory Receptors Triggered by Airborne Compounds Recorded in Self-Assembled Tethered Lipid Bilayer Nanoarchitectures. ACS APPLIED MATERIALS & INTERFACES 2023; 15:46655-46667. [PMID: 37753951 PMCID: PMC10571041 DOI: 10.1021/acsami.3c09304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023]
Abstract
Membrane proteins are among the most difficult to study as they are embedded in the cellular membrane, a complex and fragile environment with limited experimental accessibility. To study membrane proteins outside of these environments, model systems are required that replicate the fundamental properties of the cellular membrane without its complexity. We show here a self-assembled lipid bilayer nanoarchitecture on a solid support that is stable for several days at room temperature and allows the measurement of insect olfactory receptors at the single-channel level. Using an odorant binding protein, we capture airborne ligands and transfer them to an olfactory receptor from Drosophila melanogaster (OR22a) complex embedded in the lipid membrane, reproducing the complete olfaction process in which a ligand is captured from air and transported across an aqueous reservoir by an odorant binding protein and finally triggers a ligand-gated ion channel embedded in a lipid bilayer, providing direct evidence for ligand capture and olfactory receptor triggering facilitated by odorant binding proteins. This model system presents a significantly more user-friendly and robust platform to exploit the extraordinary sensitivity of insect olfaction for biosensing. At the same time, the platform offers a new opportunity for label-free studies of the olfactory signaling pathways of insects, which still have many unanswered questions.
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Affiliation(s)
- David Kleinheinz
- Austrian
Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
| | - Chiara D’Onofrio
- Austrian
Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
| | - Colm Carraher
- The
New Zealand Institute for Plant and Food Research, 120 Mount Albert Road, Sandringham, Auckland 1025, New Zealand
| | - Anil Bozdogan
- Austrian
Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
| | - Ulrich Ramach
- Technische
Universität Wien, Wiedner Hauptstr. 8-10/134, Wien 1040, Austria
- CEST
Kompetenzzentrum für Oberflächentechnologie, Viktor Kaplan-Straße 2, Wiener Neustadt 2700, Austria
| | - Bernhard Schuster
- Department
of Bionanosciences, Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Sciences
(BOKU), Muthgasse 11, Vienna 1190, Austria
| | - Manuela Geiß
- Software
Competence Center Hagenberg GmbH, Softwarepark 32a, Hagenberg 4232, Austria
| | - Markus Valtiner
- Technische
Universität Wien, Wiedner Hauptstr. 8-10/134, Wien 1040, Austria
| | - Wolfgang Knoll
- Austrian
Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
- Danube
Private University, Steiner
Landstraße 124, Krems an der Donau 3500, Austria
| | - Jakob Andersson
- Austrian
Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
- Technische
Universität Wien, Wiedner Hauptstr. 8-10/134, Wien 1040, Austria
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5
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Jin S, Qian K, He L, Zhang Z. iORandLigandDB: A Website for Three-Dimensional Structure Prediction of Insect Odorant Receptors and Docking with Odorants. INSECTS 2023; 14:560. [PMID: 37367376 DOI: 10.3390/insects14060560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/28/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
The use of insect-specific odorants to control the behavior of insects has always been a hot spot in research on "green" control strategies of insects. However, it is generally time-consuming and laborious to explore insect-specific odorants with traditional reverse chemical ecology methods. Here, an insect odorant receptor (OR) and ligand database website (iORandLigandDB) was developed for the specific exploration of insect-specific odorants by using deep learning algorithms. The website provides a range of specific odorants before molecular biology experiments as well as the properties of ORs in closely related insects. At present, the existing three-dimensional structures of ORs in insects and the docking data with related odorants can be retrieved from the database and further analyzed.
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Affiliation(s)
- Shuo Jin
- College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Kun Qian
- College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Lin He
- College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Zan Zhang
- College of Plant Protection, Southwest University, Chongqing 400716, China
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6
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Benton R, Dahanukar A. Chemosensory Coding in Drosophila Single Sensilla. Cold Spring Harb Protoc 2023; 2023:107803-pdb.top. [PMID: 36446528 DOI: 10.1101/pdb.top107803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The chemical senses-smell and taste-detect and discriminate an enormous diversity of environmental stimuli and provide fascinating but challenging models to investigate how sensory cues are represented in the brain. Important stimulus-coding events occur in peripheral sensory neurons, which express specific combinations of chemosensory receptors with defined ligand-response profiles. These receptors convert ligand recognition into spatial and temporal patterns of neural activity that are transmitted to, and interpreted in, central brain regions. Drosophila melanogaster provides an attractive model to study chemosensory coding because it possesses relatively simple peripheral olfactory and gustatory systems that display many organizational parallels to those of vertebrates. Moreover, nearly all peripheral chemosensory neurons have been molecularly characterized and are accessible for physiological analysis, as they are exposed on the surface of sensory organs housed in specialized hairs called sensilla. Here, we briefly review anatomical, molecular, and physiological properties of adult Drosophila olfactory and gustatory systems and provide background to methods for electrophysiological recordings of ligand-evoked activity from different types of chemosensory sensilla.
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Affiliation(s)
- Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Anupama Dahanukar
- Department of Molecular, Cell & Systems Biology, University of California, Riverside, California 92521, USA
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Gebremedhin MB, Xu Z, Kuang C, Shumuye NA, Cao J, Zhou Y, Zhang H, Zhou J. Current Knowledge on Chemosensory-Related Candidate Molecules Potentially Involved in Tick Olfaction via Haller's Organ. INSECTS 2023; 14:294. [PMID: 36975979 PMCID: PMC10053194 DOI: 10.3390/insects14030294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/11/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Ticks are obligatory hematophagous ectoparasites and vectors of many animal and human pathogens. Chemosensation plays a significant role in tick communication with their environment, including seeking out blood meal hosts. Studies on the structure and function of Haller's organ and its components have improved our understanding regarding tick olfaction and its chemical ecology. Compared with the knowledge on insect olfaction, less is known about the molecular basis of olfaction in ticks. This review focused on the chemosensory-related candidate molecules likely involved in tick olfaction. Members of the ionotropic receptor family and a new class of odorant-binding proteins are now known to be involved in tick olfaction, which appear to differ from that of insects. These candidate molecules are more closely related to those of mites and spiders than to other arthropods. The amino acid sequences of candidate niemann-pick type C2 and microplusin-like proteins in ticks exhibit features indicating their potential role as binding proteins. In the future, more comprehensive pertinent research considering the existing shortcomings will be required to fully understand the molecular basis of tick olfactory chemoreception. This information may contribute to the development of new molecular-based control mechanisms to reduce tick populations and related disease transmission.
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Affiliation(s)
- Mebrahtu Berhe Gebremedhin
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Zhengmao Xu
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Ceyan Kuang
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Nigus Abebe Shumuye
- State Key Laboratory of Veterinary Etiological Biology, National Animal Echinococcosis Para-Reference Laboratory, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jie Cao
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yongzhi Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Houshuang Zhang
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jinlin Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
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8
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Structure modelling of odorant receptor from Aedes aegypti and identification of potential repellent molecules. Comput Struct Biotechnol J 2023; 21:2204-2214. [PMID: 37013002 PMCID: PMC10066510 DOI: 10.1016/j.csbj.2023.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/05/2023] [Accepted: 03/05/2023] [Indexed: 03/08/2023] Open
Abstract
Odorant receptors (ORs) are important class of proteins involved in olfactory behaviour of insects. These are GPCR-like heptahelical transmembrane proteins with inverted topology compared to GPCR and require a co-receptor (ORco) for their function. OR function can be modulated through small molecules and negative modulation can be beneficial in case of disease vectors like Aedes aegypti. OR4 of A. aegypti is implicated in host recognition through human odour. Aedes aegypti is a vector for viruses that spread diseases like dengue, Zika and Chikungunya. In this study, we have attempted to model the full-length structure of OR4 and the ORco of A. aegypti due to lack of experimental structure. Further, we have screened a library of natural compounds (>0.3 million) along with known repellent molecules against ORco and OR4. Many natural compounds, including those from plants like Ocimum tenuiflorum (Holy Basil) and Piper nigrum (Black pepper), were found to have better binding affinity towards ORco compared to known repellents like DEET providing an alternative to existing repellent molecules. For specific inhibitor of OR4, several natural compounds (including those from plant like Mulberry) were identified. Further, we have utilized multiple docking approaches and conservation analysis to understand the interaction between OR4 and ORco. It was observed that the residues from the seventh transmembrane helix of OR4 and pore forming helix of ORco could play an important role along with known intracellular loop 3 residues in mediating the heteromer formation of OR and ORco.
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9
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Sun J, Kulandaisamy A, Liu J, Hu K, Gromiha MM, Zhang Y. Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications. Comput Struct Biotechnol J 2023; 21:1205-1226. [PMID: 36817959 PMCID: PMC9932300 DOI: 10.1016/j.csbj.2023.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
Membrane proteins mediate a wide spectrum of biological processes, such as signal transduction and cell communication. Due to the arduous and costly nature inherent to the experimental process, membrane proteins have long been devoid of well-resolved atomic-level tertiary structures and, consequently, the understanding of their functional roles underlying a multitude of life activities has been hampered. Currently, computational tools dedicated to furthering the structure-function understanding are primarily focused on utilizing intelligent algorithms to address a variety of site-wise prediction problems (e.g., topology and interaction sites), but are scattered across different computing sources. Moreover, the recent advent of deep learning techniques has immensely expedited the development of computational tools for membrane protein-related prediction problems. Given the growing number of applications optimized particularly by manifold deep neural networks, we herein provide a review on the current status of computational strategies mainly in membrane protein type classification, topology identification, interaction site detection, and pathogenic effect prediction. Meanwhile, we provide an overview of how the entire prediction process proceeds, including database collection, data pre-processing, feature extraction, and method selection. This review is expected to be useful for developing more extendable computational tools specific to membrane proteins.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Headington, Oxford OX3 7LD, UK
| | - Arulsamy Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Kai Hu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India,Corresponding authors.
| | - Yuan Zhang
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China,Corresponding authors.
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10
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Sun H, Bu LA, Su SC, Guo D, Gao CF, Wu SF. Knockout of the odorant receptor co-receptor, orco, impairs feeding, mating and egg-laying behavior in the fall armyworm Spodoptera frugiperda. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 152:103889. [PMID: 36493964 DOI: 10.1016/j.ibmb.2022.103889] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The olfactory transduction system of insects is involved in multiple behavioral processes such as foraging, mating, and egg-laying behavior. In the insect olfactory receptor neurons (ORNs), the odorant receptor co-receptor (Orco) is an obligatory component that is required for dimerization with odorant receptors (ORs) to form a ligand-gated ion channel complex. The ORs/Orco heteromeric complex plays a crucial role in insect olfaction. To explore the function of OR-mediated olfaction in the physiological behavior of the fall armyworm, Spodoptera frugiperda, we applied CRISPR/Cas9 genome editing to mutate its Orco gene and constructed a homozygous mutant strain of Orco (Orco-/-) by genetic crosses. Electroantennogram (EAG) analysis showed that the responses of Orco-/- male moths to two universal sex pheromones, Z9-14: Ac and Z7-12: Ac, were abolished. We found that Orco-/- males cannot successfully mate with female moths. An oviposition preference assay confirmed that Orco-/- female moths had a reduced preference for the optimal host plant maize. A larval feeding assay revealed that the time for Orco-/- larvae to locate the food source was significantly longer than in the wild-type. Overall, in the absence of Orco, the OR-dependent olfactory behavior was impaired in both larval and adult stages. Our results confirm that Orco is essential for multiple behavioral processes related to olfaction in the fall armyworm.
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Affiliation(s)
- Hao Sun
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Ling-Ao Bu
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Shao-Cong Su
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Di Guo
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Cong-Fen Gao
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China
| | - Shun-Fan Wu
- College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Weigang Road 1, Nanjing, 210095, Jiangsu, China.
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11
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Abstract
Among the many wonders of nature, the sense of smell of the fly Drosophila melanogaster might seem, at first glance, of esoteric interest. Nevertheless, for over a century, the 'nose' of this insect has been an extraordinary system to explore questions in animal behaviour, ecology and evolution, neuroscience, physiology and molecular genetics. The insights gained are relevant for our understanding of the sensory biology of vertebrates, including humans, and other insect species, encompassing those detrimental to human health. Here, I present an overview of our current knowledge of D. melanogaster olfaction, from molecules to behaviours, with an emphasis on the historical motivations of studies and illustration of how technical innovations have enabled advances. I also highlight some of the pressing and long-term questions.
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Affiliation(s)
- Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
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12
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Aruçi E, Saliou JM, Ferveur JF, Briand L. Proteomic Characterization of Drosophila melanogaster Proboscis. BIOLOGY 2022; 11:1687. [PMID: 36421401 PMCID: PMC9687345 DOI: 10.3390/biology11111687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/07/2022] [Accepted: 11/17/2022] [Indexed: 09/02/2023]
Abstract
Drosophila melanogaster flies use their proboscis to taste and distinguish edible compounds from toxic compounds. With their proboscis, flies can detect sex pheromones at a close distance or by contact. Most of the known proteins associated with probosci's detection belong to gustatory receptor families. To extend our knowledge of the proboscis-taste proteins involved in chemo-detection, we used a proteomic approach to identify soluble proteins from Drosophila females and males. This investigation, performed with hundreds of dissected proboscises, was initiated by the chromatographic separation of tryptic peptides, followed by tandem mass spectrometry, allowing for femtomole detection sensitivity. We found 586 proteins, including enzymes, that are involved in intermediary metabolism and proteins dedicated to various functions, such as nucleic acid metabolism, ion transport, immunity, digestion, and organ development. Among 60 proteins potentially involved in chemosensory detection, we identified two odorant-binding proteins (OBPs), i.e., OBP56d (which showed much higher expression in females than in males) and OBP19d. Because OBP56d was also reported to be more highly expressed in the antennae of females, this protein can be involved in the detection of both volatile and contact male pheromone(s). Our proteomic study paves the way to better understand the complex role of Drosophila proboscis in the chemical detection of food and pheromonal compounds.
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Affiliation(s)
- Enisa Aruçi
- Centre des Sciences du Goût et de l’Alimentation, CNRS, INRAE, Institut Agro, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Jean-Michel Saliou
- CNRS, INSERM CHU Lille, Institut Pasteur de Lille, UAR CNRS 2014–US Inserm 41–PLBS, University of Lille, 59000 Lille, France
| | - Jean-François Ferveur
- Centre des Sciences du Goût et de l’Alimentation, CNRS, INRAE, Institut Agro, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Loïc Briand
- Centre des Sciences du Goût et de l’Alimentation, CNRS, INRAE, Institut Agro, Université Bourgogne Franche-Comté, 21000 Dijon, France
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13
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Wittmund M, Cadet F, Davari MD. Learning Epistasis and Residue Coevolution Patterns: Current Trends and Future Perspectives for Advancing Enzyme Engineering. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marcel Wittmund
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Frederic Cadet
- Laboratory of Excellence LABEX GR, DSIMB, Inserm UMR S1134, University of Paris city & University of Reunion, Paris 75014, France
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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14
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Nucleotide-based genetic networks: Methods and applications. J Biosci 2022. [PMID: 36226367 PMCID: PMC9554864 DOI: 10.1007/s12038-022-00290-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genomic variations have been acclaimed as among the key players in understanding the biological mechanisms behind migration, evolution, and adaptation to extreme conditions. Due to stochastic evolutionary forces, the frequency of polymorphisms is affected by changes in the frequency of nearby polymorphisms in the same DNA sample, making them connected in terms of evolution. This article presents all the ingredients to understand the cumulative effects and complex behaviors of genetic variations in the human mitochondrial genome by analyzing co-occurrence networks of nucleotides, and shows key results obtained from such analyses. The article emphasizes recent investigations of these co-occurrence networks, describing the role of interactions between nucleotides in fundamental processes of human migration and viral evolution. The corresponding co-mutation-based genetic networks revealed genetic signatures of human adaptation in extreme environments. This article provides the methods of constructing such networks in detail, along with their graph-theoretical properties, and applications of the genomic networks in understanding the role of nucleotide co-evolution in evolution of the whole genome.
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15
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Lee MS, Tuohy PJ, Kim CY, Lichauco K, Parrish HL, Van Doorslaer K, Kuhns MS. Enhancing and inhibitory motifs regulate CD4 activity. eLife 2022; 11:79508. [PMID: 35861317 PMCID: PMC9333989 DOI: 10.7554/elife.79508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/20/2022] [Indexed: 11/15/2022] Open
Abstract
CD4+ T cells use T cell receptor (TCR)–CD3 complexes, and CD4, to respond to peptide antigens within MHCII molecules (pMHCII). We report here that, through ~435 million years of evolution in jawed vertebrates, purifying selection has shaped motifs in the extracellular, transmembrane, and intracellular domains of eutherian CD4 that enhance pMHCII responses, and covary with residues in an intracellular motif that inhibits responses. Importantly, while CD4 interactions with the Src kinase, Lck, are viewed as key to pMHCII responses, our data indicate that CD4–Lck interactions derive their importance from the counterbalancing activity of the inhibitory motif, as well as motifs that direct CD4–Lck pairs to specific membrane compartments. These results have implications for the evolution and function of complex transmembrane receptors and for biomimetic engineering.
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Affiliation(s)
- Mark S Lee
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, United States
| | - Peter J Tuohy
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, United States
| | - Caleb Y Kim
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, United States
| | - Katrina Lichauco
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, United States
| | - Heather L Parrish
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, United States
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, United States
| | - Michael S Kuhns
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, United States
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16
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Sims C, Birkett MA, Withall DM. Enantiomeric Discrimination in Insects: The Role of OBPs and ORs. INSECTS 2022; 13:insects13040368. [PMID: 35447810 PMCID: PMC9030700 DOI: 10.3390/insects13040368] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/27/2023]
Abstract
Olfaction is a complex recognition process that is critical for chemical communication in insects. Though some insect species are capable of discrimination between compounds that are structurally similar, little is understood about how this high level of discrimination arises. Some insects rely on discriminating between enantiomers of a compound, demonstrating an ability for highly selective recognition. The role of two major peripheral olfactory proteins in insect olfaction, i.e., odorant-binding proteins (OBPs) and odorant receptors (ORs) has been extensively studied. OBPs and ORs have variable discrimination capabilities, with some found to display highly specialized binding capability, whilst others exhibit promiscuous binding activity. A deeper understanding of how odorant-protein interactions induce a response in an insect relies on further analysis such as structural studies. In this review, we explore the potential role of OBPs and ORs in highly specific recognition, specifically enantiomeric discrimination. We summarize the state of research into OBP and OR function and focus on reported examples in the literature of clear enantiomeric discrimination by these proteins.
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Affiliation(s)
- Cassie Sims
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; (C.S.); (M.A.B.)
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Michael A. Birkett
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; (C.S.); (M.A.B.)
| | - David M. Withall
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; (C.S.); (M.A.B.)
- Correspondence: ; Tel.: +44-(0)-1582-938201
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17
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Huff RM, Pitts RJ. Functional conservation of Anopheline linalool receptors through 100 million years of evolution. Chem Senses 2022; 47:bjac032. [PMID: 36458901 PMCID: PMC9717389 DOI: 10.1093/chemse/bjac032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Insects rely on olfactory receptors to detect and respond to diverse environmental chemical cues. Detection of semiochemicals by these receptors modulates insect behavior and has a direct impact on species fitness. Volatile organic compounds (VOCs) are released by animals and plants and can provide contextual cues that a blood meal host or nectar source is present. One such VOC is linalool, an enantiomeric monoterpene, that is emitted from plants and bacteria species. This compound exists in nature as one of two possible stereoisomers, (R)-(-)-linalool or (S)-(+)-linalool. In this study, we use a heterologous expression system to demonstrate differential responsiveness of a pair of Anopheline odorant receptors (Ors) to enantiomers of linalool. The mosquitoes Anopheles gambiae and Anopheles stephensi encode single copies of Or29 and Or53, which are expressed in the labella of An. gambiae. (S)-(+)-linalool activates Or29 orthologs with a higher potency than (R)-(-)-linalool, while the converse is observed for Or53 orthologs. The conservation of these receptors across a broad range of Anopheline species suggests they may function in the discrimination of linalool stereoisomers, thereby influencing the chemical ecology of mosquitoes. One potential application of this knowledge would be in the design of novel attractants or repellents to be used in integrated pest management practices.
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Affiliation(s)
- Robert M Huff
- Department of Biology, Baylor University, Waco, TX 76706, USA
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18
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Functional incorporation of the insect odorant receptor coreceptor in tethered lipid bilayer nanoarchitectures. Biosens Bioelectron 2022; 203:114024. [DOI: 10.1016/j.bios.2022.114024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/06/2022] [Accepted: 01/18/2022] [Indexed: 11/02/2022]
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19
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Hou XQ, Yuvaraj JK, Roberts RE, Zhang DD, Unelius CR, Löfstedt C, Andersson MN. Functional Evolution of a Bark Beetle Odorant Receptor Clade Detecting Monoterpenoids of Different Ecological Origins. Mol Biol Evol 2021; 38:4934-4947. [PMID: 34293158 PMCID: PMC8557457 DOI: 10.1093/molbev/msab218] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Insects detect odors using an array of odorant receptors (ORs), which may expand through gene duplication. How and which new functions may evolve among related ORs within a species remain poorly investigated. We addressed this question by functionally characterizing ORs from the Eurasian spruce bark beetle Ips typographus, in which physiological and behavioral responses to pheromones, volatiles from host and nonhost trees, and fungal symbionts are well described. In contrast, knowledge of OR function is restricted to two receptors detecting the pheromone compounds (S)-(-)-ipsenol (ItypOR46) and (R)-(-)-ipsdienol (ItypOR49). These receptors belong to an Ips-specific OR-lineage comprising seven ItypORs. To gain insight into the functional evolution of related ORs, we characterized the five remaining ORs in this clade using Xenopus oocytes. Two receptors responded primarily to the host tree monoterpenes (+)-3-carene (ItypOR25) and p-cymene (ItypOR27). Two receptors responded to oxygenated monoterpenoids produced in larger relative amounts by the beetle-associated fungi, with ItypOR23 specific for (+)-trans-(1R, 4S)-4-thujanol, and ItypOR29 responding to (+)-isopinocamphone and similar ketones. ItypOR28 responded to the pheromone E-myrcenol from the competitor Ips duplicatus. Overall, the OR responses match well with those of previously characterized olfactory sensory neuron classes except that neurons detecting E-myrcenol have not been identified. The characterized ORs are under strong purifying selection and demonstrate a shared functional property in that they all primarily respond to monoterpenoids. The variation in functional groups among OR ligands and their diverse ecological origins suggest that neofunctionalization has occurred early in the evolution of this OR-lineage following gene duplication.
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Affiliation(s)
- Xiao-Qing Hou
- Department of Biology, Lund University, Lund, Sweden
| | | | | | - Dan-Dan Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - C Rikard Unelius
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
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20
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Lin JY, Yang Z, Yang C, Du JX, Yang F, Cheng J, Pan W, Zhang SJ, Yan X, Wang J, Wang J, Tie L, Yu X, Chen X, Sun JP. An ionic lock and a hydrophobic zipper mediate the coupling between an insect pheromone receptor BmOR3 and downstream effectors. J Biol Chem 2021; 297:101160. [PMID: 34480896 PMCID: PMC8477192 DOI: 10.1016/j.jbc.2021.101160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 01/14/2023] Open
Abstract
Pheromone receptors (PRs) recognize specific pheromone compounds to guide the behavioral outputs of insects, which are the most diverse group of animals on earth. The activation of PRs is known to couple to the calcium permeability of their coreceptor (Orco) or putatively with G proteins; however, the underlying mechanisms of this process are not yet fully understood. Moreover, whether this transverse seven transmembrane domain (7TM)-containing receptor is able to couple to arrestin, a common effector for many conventional 7TM receptors, is unknown. Herein, using the PR BmOR3 from the silk moth Bombyx mori and its coreceptor BmOrco as a template, we revealed that an agonist-induced conformational change of BmOR3 was transmitted to BmOrco through transmembrane segment 7 from both receptors, resulting in the activation of BmOrco. Key interactions, including an ionic lock and a hydrophobic zipper, are essential in mediating the functional coupling between BmOR3 and BmOrco. BmOR3 also selectively coupled with Gi proteins, which was dispensable for BmOrco coupling. Moreover, we demonstrated that trans-7TM BmOR3 recruited arrestin in an agonist-dependent manner, which indicates an important role for BmOR3–BmOrco complex formation in ionotropic functions. Collectively, our study identified the coupling of G protein and arrestin to a prototype trans-7TM PR, BmOR3, and provided important mechanistic insights into the coupling of active PRs to their downstream effectors, including coreceptors, G proteins, and arrestin.
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Affiliation(s)
- Jing-Yu Lin
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Zhao Yang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Chan Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Ji-Xiang Du
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Fan Yang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Jie Cheng
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Wei Pan
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Shi-Jie Zhang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Xu Yan
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Jia Wang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Jin Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Lu Tie
- Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, China.
| | - Xin Chen
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, China.
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan, China; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.
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21
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Del Mármol J, Yedlin MA, Ruta V. The structural basis of odorant recognition in insect olfactory receptors. Nature 2021; 597:126-131. [PMID: 34349260 PMCID: PMC8410599 DOI: 10.1038/s41586-021-03794-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Olfactory systems must detect and discriminate amongst an enormous variety of odorants1. To contend with this challenge, diverse species have converged on a common strategy in which odorant identity is encoded through the combinatorial activation of large families of olfactory receptors1-3, thus allowing a finite number of receptors to detect a vast chemical world. Here we offer structural and mechanistic insight into how an individual olfactory receptor can flexibly recognize diverse odorants. We show that the olfactory receptor MhOR5 from the jumping bristletail4 Machilis hrabei assembles as a homotetrameric odorant-gated ion channel with broad chemical tuning. Using cryo-electron microscopy, we elucidated the structure of MhOR5 in multiple gating states, alone and in complex with two of its agonists-the odorant eugenol and the insect repellent DEET. Both ligands are recognized through distributed hydrophobic interactions within the same geometrically simple binding pocket located in the transmembrane region of each subunit, suggesting a structural logic for the promiscuous chemical sensitivity of this receptor. Mutation of individual residues lining the binding pocket predictably altered the sensitivity of MhOR5 to eugenol and DEET and broadly reconfigured the receptor's tuning. Together, our data support a model in which diverse odorants share the same structural determinants for binding, shedding light on the molecular recognition mechanisms that ultimately endow the olfactory system with its immense discriminatory capacity.
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Affiliation(s)
- Josefina Del Mármol
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY, USA
| | - Mackenzie A Yedlin
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY, USA
| | - Vanessa Ruta
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY, USA.
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22
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Legan AW, Jernigan CM, Miller SE, Fuchs MF, Sheehan MJ. Expansion and Accelerated Evolution of 9-Exon Odorant Receptors in Polistes Paper Wasps. Mol Biol Evol 2021; 38:3832-3846. [PMID: 34151983 PMCID: PMC8383895 DOI: 10.1093/molbev/msab023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Independent origins of sociality in bees and ants are associated with independent expansions of particular odorant receptor (OR) gene subfamilies. In ants, one clade within the OR gene family, the 9-exon subfamily, has dramatically expanded. These receptors detect cuticular hydrocarbons (CHCs), key social signaling molecules in insects. It is unclear to what extent 9-exon OR subfamily expansion is associated with the independent evolution of sociality across Hymenoptera, warranting studies of taxa with independently derived social behavior. Here, we describe OR gene family evolution in the northern paper wasp, Polistes fuscatus, and compare it to four additional paper wasp species spanning ∼40 million years of evolutionary divergence. We find 200 putatively functional OR genes in P. fuscatus, matching predictions from neuroanatomy, and more than half of these are in the 9-exon subfamily. Most OR gene expansions are tandemly arrayed at orthologous loci in Polistes genomes, and microsynteny analysis shows species-specific gain and loss of 9-exon ORs within tandem arrays. There is evidence of episodic positive diversifying selection shaping ORs in expanded subfamilies. Values of omega (dN/dS) are higher among 9-exon ORs compared to other OR subfamilies. Within the Polistes OR gene tree, branches in the 9-exon OR clade experience relaxed negative (relaxed purifying) selection relative to other branches in the tree. Patterns of OR evolution within Polistes are consistent with 9-exon OR function in CHC perception by combinatorial coding, with both natural selection and neutral drift contributing to interspecies differences in gene copy number and sequence.
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Affiliation(s)
- Andrew W Legan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Christopher M Jernigan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Sara E Miller
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Matthieu F Fuchs
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
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23
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Li LL, Xu JW, Yao WC, Yang HH, Dewer Y, Zhang F, Zhu XY, Zhang YN. Chemosensory genes in the head of Spodoptera litura larvae. BULLETIN OF ENTOMOLOGICAL RESEARCH 2021; 111:454-463. [PMID: 33632348 DOI: 10.1017/s0007485321000109] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The tobacco cutworm Spodoptera litura (Lepidoptera: Noctuidae) is a polyphagous pest with a highly selective and sensitive chemosensory system involved in complex physiological behaviors such as searching for food sources, feeding, courtship, and oviposition. However, effective management strategies for controlling the insect pest populations under threshold levels are lacking. Therefore, there is an urgent need to formulate eco-friendly pest control strategies based on the disruption of the insect chemosensory system. In this study, we identified 158 putative chemosensory genes based on transcriptomic and genomic data for S. litura, including 45 odorant-binding proteins (OBPs, nine were new), 23 chemosensory proteins (CSPs), 60 odorant receptors (ORs, three were new), and 30 gustatory receptors (GRs, three were new), a number higher than those reported by previous transcriptome studies. Subsequently, we constructed phylogenetic trees based on these genes in moths and analyzed the dynamic expression of various genes in head capsules across larval instars using quantitative real-time polymerase chain reaction. Nine genes-SlitOBP8, SlitOBP9, SlitOBP25, SlitCSP1, SlitCSP7, SlitCSP18, SlitOR34, SlitGR240, and SlitGR242-were highly expressed in the heads of 3- to 5-day-old S. litura larvae. The genes differentially expressed in olfactory organs during larval development might play crucial roles in the chemosensory system of S. litura larvae. Our findings substantially expand the gene inventory for S. litura and present potential target genes for further studies on larval feeding in S. litura.
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Affiliation(s)
- Lu-Lu Li
- College of Life Sciences, Huaibei Normal University, 100 Dongshan Road, Huaibei235000, China
| | - Ji-Wei Xu
- College of Life Sciences, Huaibei Normal University, 100 Dongshan Road, Huaibei235000, China
| | - Wei-Chen Yao
- College of Life Sciences, Huaibei Normal University, 100 Dongshan Road, Huaibei235000, China
| | - Hui-Hui Yang
- College of Life Sciences, Huaibei Normal University, 100 Dongshan Road, Huaibei235000, China
| | - Youssef Dewer
- Bioassay Research Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, 7 Nadi El-Seid Street, Dokki 12618Giza, Egypt
| | - Fan Zhang
- Key Laboratory of Animal Resistance Research, College of Life Science, Shandong Normal University, 88 East Wenhua Road, Jinan250014, China
| | - Xiu-Yun Zhu
- College of Life Sciences, Huaibei Normal University, 100 Dongshan Road, Huaibei235000, China
| | - Ya-Nan Zhang
- College of Life Sciences, Huaibei Normal University, 100 Dongshan Road, Huaibei235000, China
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24
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Graphene Bioelectronic Nose for the Detection of Odorants with Human Olfactory Receptor 2AG1. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9070174] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A real-time sensor for the detection of amyl butyrate (AB) utilising human olfactory receptor 2AG1 (OR2AG1), a G-protein coupled receptor (GPCR) consisting of seven transmembrane domains, immobilized onto a graphene resistor is demonstrated. Using CVD graphene as the sensor platform, allows greater potential for more sensitive detection than similar sensors based on carbon nanotubes, gold or graphene oxide platforms. A specific graphene resistor sensor was fabricated and modified via non-covalent π–π stacking of 1,5 diaminonaphthalene (DAN) onto the graphene channel, and subsequent anchoring of the OR2AG1 receptor to the DAN molecule using glutaraldehyde coupling. Binding between the target odorant, amyl butyrate, and the OR2AG1 receptor protein generated a change in resistance of the graphene resistor sensor. The functionalized graphene resistor sensors exhibited a linear sensor response between 0.1–500 pM and high selectively towards amyl butyrate, with a sensitivity as low as 500 fM, whilst control measurements using non-specific esters, produced a negligible sensor response. The approach described here provides an alternative sensing platform that can be used in bioelectronic nose applications.
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25
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Genome-Wide Identification of the Gustatory Receptor Gene Family of the Invasive Pest, Red Palm Weevil, Rhynchophorus ferrugineus (Olivier, 1790). INSECTS 2021; 12:insects12070611. [PMID: 34357271 PMCID: PMC8308034 DOI: 10.3390/insects12070611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/03/2021] [Indexed: 11/17/2022]
Abstract
The red palm weevil (Rhynchophorus ferrugineus) is a highly destructive pest of oil palm, date, and coconut in many parts of Asia, Europe, and Africa. The Food and Agriculture Organization of the United Nations has called for international collaboration to develop a multidisciplinary strategy to control this invasive pest. Previous research focused on the molecular basis of chemoreception in this species, particularly olfaction, to develop biosensors for early detection and more effective bait traps for mass trapping. However, the molecular basis of gustation, which plays an essential role in discriminating food and egg-laying sites and chemical communication in this species, is limited because its complete gustatory receptor gene family still has not been characterized. We manually annotated the gene family from the recently available genome and transcriptome data and reported 50 gustatory receptor genes encoding 65 gustatory receptors, including 7 carbon dioxide, 9 sugar, and 49 bitter receptors. This study provides a platform for future functional analysis and comparative chemosensory study. A better understanding of gustation will improve our understanding of this species' complex chemoreception, which is an important step toward developing more effective control methods.
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26
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Liu N, Wang Y, Li T, Feng X. G-Protein Coupled Receptors (GPCRs): Signaling Pathways, Characterization, and Functions in Insect Physiology and Toxicology. Int J Mol Sci 2021; 22:ijms22105260. [PMID: 34067660 PMCID: PMC8156084 DOI: 10.3390/ijms22105260] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are known to play central roles in the physiology of many organisms. Members of this seven α-helical transmembrane protein family transduce the extracellular signals and regulate intracellular second messengers through coupling to heterotrimeric G-proteins, adenylate cyclase, cAMPs, and protein kinases. As a result of the critical function of GPCRs in cell physiology and biochemistry, they not only play important roles in cell biology and the medicines used to treat a wide range of human diseases but also in insects’ physiological functions. Recent studies have revealed the expression and function of GPCRs in insecticide resistance, improving our understanding of the molecular complexes governing the development of insecticide resistance. This article focuses on the review of G-protein coupled receptor (GPCR) signaling pathways in insect physiology, including insects’ reproduction, growth and development, stress responses, feeding, behaviors, and other physiological processes. Hormones and polypeptides that are involved in insect GPCR regulatory pathways are reviewed. The review also gives a brief introduction of GPCR pathways in organisms in general. At the end of the review, it provides the recent studies on the function of GPCRs in the development of insecticide resistance, focusing in particular on our current knowledge of the expression and function of GPCRs and their downstream regulation pathways and their roles in insecticide resistance and the regulation of resistance P450 gene expression. The latest insights into the exciting technological advances and new techniques for gene expression and functional characterization of the GPCRs in insects are provided.
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Affiliation(s)
- Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (Y.W.); (T.L.)
- Correspondence: ; Tel.: +1-334-844-5076
| | - Yifan Wang
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (Y.W.); (T.L.)
| | - Ting Li
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (Y.W.); (T.L.)
| | - Xuechun Feng
- Department of Biology Sciences, University of California, San Diego, CA 92093, USA;
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27
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Zhang X, Liu P, Qin Q, Li M, Meng R, Zhang T. Characterizing the Role of Orco Gene in Detecting Aggregation Pheromone and Food Resources in Protaetia brevitarsis Leiws (Coleoptera: Scarabaeidae). Front Physiol 2021; 12:649590. [PMID: 33927641 PMCID: PMC8076894 DOI: 10.3389/fphys.2021.649590] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/17/2021] [Indexed: 11/20/2022] Open
Abstract
An accurate olfactory system for recognizing semiochemicals and environmental chemical signals plays crucial roles in survival and reproduction of insects. Among all olfaction-related proteins, olfactory receptors (ORs) contribute to the conversion of chemical stimuli to electric signals and thereby are vital in odorant recognition. Olfactory receptor co-receptor (Orco), one of the most conserved ORs, is extremely essential in recognizing odorants through forming a ligand-gated ion channel complex with conventional ligand-binding odorant receptors. We have previously identified aggregation pheromone in Protaetia brevitarsis (Coleoptera: Scarabaeidae), a native agricultural and horticultural pest in East-Asia. However, to our best knowledge, its olfaction recognition mechanisms are still veiled. To illustrate how P. brevitarsis recognize aggregation pheromone and host plants, in the present study we cloned and sequenced the full-length Orco gene from P. brevitarsis antennae (named PbreOrco) and found that PbreOrco is highly conserved and similar to Orcos from other Coleoptera insects. Our real-time quantitative PCR (qRT-PCR) results showed that PbreOrco is mainly expressed in antenna. We also demonstrated that silencing PbreOrco using RNA interference through injecting dsOrco fragment significantly inhibited PbreOrco expression in comparison with injecting control dsGFP and subsequently revealed using electroantennogram and behavioral bioassays that decreasing PbreOrco transcript abundance significantly impaired the responses of P. brevitarsis to intraspecific aggregation pheromone and prolonged the time of P. brevitarsis spending on food seeking. Overall, our results demonstrated that PbreOrco is crucial in mediating odorant perception in P. brevitarsis.
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Affiliation(s)
- Xiaofang Zhang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Baoding, China.,Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, China
| | - Panjing Liu
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Baoding, China.,Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, China
| | - Qiuju Qin
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Min Li
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Baoding, China.,Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, China
| | - Runjie Meng
- Baoding Vocational and Technical College, Baoding, China
| | - Tao Zhang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Baoding, China.,Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding, China
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28
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The 40-Year Mystery of Insect Odorant-Binding Proteins. Biomolecules 2021; 11:biom11040509. [PMID: 33808208 PMCID: PMC8067015 DOI: 10.3390/biom11040509] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022] Open
Abstract
The survival of insects depends on their ability to detect molecules present in their environment. Odorant-binding proteins (OBPs) form a family of proteins involved in chemoreception. While OBPs were initially found in olfactory appendages, recently these proteins were discovered in other chemosensory and non-chemosensory organs. OBPs can bind, solubilize and transport hydrophobic stimuli to chemoreceptors across the aqueous sensilla lymph. In addition to this broadly accepted "transporter role", OBPs can also buffer sudden changes in odorant levels and are involved in hygro-reception. The physiological roles of OBPs expressed in other body tissues, such as mouthparts, pheromone glands, reproductive organs, digestive tract and venom glands, remain to be investigated. This review provides an updated panorama on the varied structural aspects, binding properties, tissue expression and functional roles of insect OBPs.
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29
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Zou T, Woodrum BW, Halloran N, Campitelli P, Bobkov AA, Ghirlanda G, Ozkan SB. Local Interactions That Contribute Minimal Frustration Determine Foldability. J Phys Chem B 2021; 125:2617-2626. [PMID: 33687216 DOI: 10.1021/acs.jpcb.1c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Earlier experiments suggest that the evolutionary information (conservation and coevolution) encoded in protein sequences is necessary and sufficient to specify the fold of a protein family. However, there is no computational work to quantify the effect of such evolutionary information on the folding process. Here we explore the role of early folding steps for sequences designed using coevolution and conservation through a combination of computational and experimental methods. We simulated a repertoire of native and designed WW domain sequences to analyze early local contact formation and found that the N-terminal β-hairpin turn would not form correctly due to strong non-native local contacts in unfoldable sequences. Through a maximum likelihood approach, we identified five local contacts that play a critical role in folding, suggesting that a small subset of amino acid pairs can be used to solve the "needle in the haystack" problem to design foldable sequences. Thus, using the contact probability of those five local contacts that form during the early stage of folding, we built a classification model that predicts the foldability of a WW sequence with 81% accuracy. This classification model was used to redesign WW domain sequences that could not fold due to frustration and make them foldable by introducing a few mutations that led to the stabilization of these critical local contacts. The experimental analysis shows that a redesigned sequence folds and binds to polyproline peptides with a similar affinity as those observed for native WW domains. Overall, our analysis shows that evolutionary-designed sequences should not only satisfy the folding stability but also ensure a minimally frustrated folding landscape.
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Affiliation(s)
- Taisong Zou
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Brian W Woodrum
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Halloran
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Andrey A Bobkov
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States
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30
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Bobkov YV, Walker Iii WB, Cattaneo AM. Altered functional properties of the codling moth Orco mutagenized in the intracellular loop-3. Sci Rep 2021; 11:3893. [PMID: 33594162 PMCID: PMC7887336 DOI: 10.1038/s41598-021-83024-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/27/2021] [Indexed: 12/04/2022] Open
Abstract
Amino acid substitutions within the conserved polypeptide sequence of the insect olfactory receptor co-receptor (Orco) have been demonstrated to influence its pharmacological properties. By sequence analysis and phylogenetic investigation, in the Lepidopteran subgroup Ditrysia we identified a fixed substitution in the intracellular loop-3 (ICL-3) of a conserved histidine to glutamine. By means of HEK293 cells as a heterologous system, we functionally expressed Orco from the Ditrysian model Cydia pomonella (CpomOrco) and compared its functional properties with a site-directed mutagenized version where this ICL-3-glutamine was reverted to histidine (CpomOrcoQ417H). The mutagenized CpomOrcoQ417H displayed decreased responsiveness to VUAA1 and reduced response efficacy to an odorant agonist was observed, when co-transfected with the respective OR subunit. Evidence of reduced responsiveness and sensitivity to ligands for the mutagenized Orco suggest the fixed glutamine substitution to be optimized for functionality of the cation channel within Ditrysia. In addition, contrary to the wild type, the mutagenized CpomOrcoQ417H preserved characteristics of VUAA-binding when physiologic conditions turned to acidic. Taken together, our findings provide further evidence of the importance of ICL-3 in forming basic functional properties of insect Orco- and Orco/OR-channels, and suggest involvement of ICL-3 in the potential functional adaptation of Ditrysian Orcos to acidified extra-/intracellular environment.
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Affiliation(s)
- Yuriy V Bobkov
- Whitney Laboratory, Center for Smell and Taste, and McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - William B Walker Iii
- Department of Plant Protection Biology, Chemical Ecology Unit, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Alberto Maria Cattaneo
- Whitney Laboratory, Center for Smell and Taste, and McKnight Brain Institute, University of Florida, Gainesville, FL, USA. .,Department of Plant Protection Biology, Chemical Ecology Unit, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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31
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Millan CR, Francis M, Khandelwal NK, Thompson VF, Thaker TM, Tomasiak TM. A Conserved Motif in Intracellular Loop 1 Stabilizes the Outward-Facing Conformation of TmrAB. J Mol Biol 2021; 433:166834. [PMID: 33524413 DOI: 10.1016/j.jmb.2021.166834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/05/2023]
Abstract
The ATP binding cassette (ABC) family of transporters moves small molecules (lipids, sugars, peptides, drugs, nutrients) across membranes in nearly all organisms. Transport activity requires conformational switching between inward-facing and outward-facing states driven by ATP-dependent dimerization of two nucleotide binding domains (NBDs). The mechanism that connects ATP binding and hydrolysis in the NBDs to conformational changes in a substrate binding site in the transmembrane domains (TMDs) is currently an outstanding question. Here we use sequence coevolution analyses together with biochemical characterization to investigate the role of a highly conserved region in intracellular loop 1 we define as the GRD motif in coordinating domain rearrangements in the heterodimeric peptide exporter from Thermus thermophilus, TmrAB. Mutations in the GRD motif alter ATPase activity as well as transport. Disulfide crosslinking, evolutionary trace, and evolutionary coupling analysis reveal that these effects are likely due to the destabilization of a network in which the GRD motif in TmrA bridges residues of the Q-loop, X-loop, and ABC motif in the NBDs to residues in the TmrAB peptide substrate binding site, thus providing an avenue for conformational coupling. We further find that disruption of this network in TmrA versus TmrB has different functional consequences, hinting at an intrinsic asymmetry in heterodimeric ABC transporters extending beyond that of the NBDs. These results support a mechanism in which the GRD motifs help coordinate a transition to an outward open conformation, and each half of the transporter likely plays a different role in the conformational cycle of TmrAB.
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Affiliation(s)
- Cinthia R Millan
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | - Martina Francis
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | | | - Valery F Thompson
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | - Tarjani M Thaker
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
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32
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Yuvaraj JK, Roberts RE, Sonntag Y, Hou XQ, Grosse-Wilde E, Machara A, Zhang DD, Hansson BS, Johanson U, Löfstedt C, Andersson MN. Putative ligand binding sites of two functionally characterized bark beetle odorant receptors. BMC Biol 2021; 19:16. [PMID: 33499862 PMCID: PMC7836466 DOI: 10.1186/s12915-020-00946-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/22/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Bark beetles are major pests of conifer forests, and their behavior is primarily mediated via olfaction. Targeting the odorant receptors (ORs) may thus provide avenues towards improved pest control. Such an approach requires information on the function of ORs and their interactions with ligands, which is also essential for understanding the functional evolution of these receptors. Hence, we aimed to identify a high-quality complement of ORs from the destructive spruce bark beetle Ips typographus (Coleoptera, Curculionidae, Scolytinae) and analyze their antennal expression and phylogenetic relationships with ORs from other beetles. Using 68 biologically relevant test compounds, we next aimed to functionally characterize ecologically important ORs, using two systems for heterologous expression. Our final aim was to gain insight into the ligand-OR interaction of the functionally characterized ORs, using a combination of computational and experimental methods. RESULTS We annotated 73 ORs from an antennal transcriptome of I. typographus and report the functional characterization of two ORs (ItypOR46 and ItypOR49), which are responsive to single enantiomers of the common bark beetle pheromone compounds ipsenol and ipsdienol, respectively. Their responses and antennal expression correlate with the specificities, localizations, and/or abundances of olfactory sensory neurons detecting these enantiomers. We use homology modeling and molecular docking to predict their binding sites. Our models reveal a likely binding cleft lined with residues that previously have been shown to affect the responses of insect ORs. Within this cleft, the active ligands are predicted to specifically interact with residues Tyr84 and Thr205 in ItypOR46. The suggested importance of these residues in the activation by ipsenol is experimentally supported through site-directed mutagenesis and functional testing, and hydrogen bonding appears key in pheromone binding. CONCLUSIONS The emerging insight into ligand binding in the two characterized ItypORs has a general importance for our understanding of the molecular and functional evolution of the insect OR gene family. Due to the ecological importance of the characterized receptors and widespread use of ipsenol and ipsdienol in bark beetle chemical communication, these ORs should be evaluated for their potential use in pest control and biosensors to detect bark beetle infestations.
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Affiliation(s)
- Jothi K Yuvaraj
- Department of Biology, Lund University, SE-223 62, Lund, Sweden
| | | | - Yonathan Sonntag
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-223 62, Lund, Sweden
| | - Xiao-Qing Hou
- Department of Biology, Lund University, SE-223 62, Lund, Sweden
| | - Ewald Grosse-Wilde
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
- Present address: Faculty of Forestry & Wood Sci, Excellent Team for Mitigation, Czech University Life Sci Prague, Kamycka 129, Prague 6, 16521, Suchdol, Czech Republic
| | - Aleš Machara
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Dan-Dan Zhang
- Department of Biology, Lund University, SE-223 62, Lund, Sweden
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
| | - Urban Johanson
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-223 62, Lund, Sweden
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33
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Yuvaraj JK, Roberts RE, Sonntag Y, Hou XQ, Grosse-Wilde E, Machara A, Zhang DD, Hansson BS, Johanson U, Löfstedt C, Andersson MN. Putative ligand binding sites of two functionally characterized bark beetle odorant receptors. BMC Biol 2021. [PMID: 33499862 DOI: 10.1101/2020.03.07.980797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
BACKGROUND Bark beetles are major pests of conifer forests, and their behavior is primarily mediated via olfaction. Targeting the odorant receptors (ORs) may thus provide avenues towards improved pest control. Such an approach requires information on the function of ORs and their interactions with ligands, which is also essential for understanding the functional evolution of these receptors. Hence, we aimed to identify a high-quality complement of ORs from the destructive spruce bark beetle Ips typographus (Coleoptera, Curculionidae, Scolytinae) and analyze their antennal expression and phylogenetic relationships with ORs from other beetles. Using 68 biologically relevant test compounds, we next aimed to functionally characterize ecologically important ORs, using two systems for heterologous expression. Our final aim was to gain insight into the ligand-OR interaction of the functionally characterized ORs, using a combination of computational and experimental methods. RESULTS We annotated 73 ORs from an antennal transcriptome of I. typographus and report the functional characterization of two ORs (ItypOR46 and ItypOR49), which are responsive to single enantiomers of the common bark beetle pheromone compounds ipsenol and ipsdienol, respectively. Their responses and antennal expression correlate with the specificities, localizations, and/or abundances of olfactory sensory neurons detecting these enantiomers. We use homology modeling and molecular docking to predict their binding sites. Our models reveal a likely binding cleft lined with residues that previously have been shown to affect the responses of insect ORs. Within this cleft, the active ligands are predicted to specifically interact with residues Tyr84 and Thr205 in ItypOR46. The suggested importance of these residues in the activation by ipsenol is experimentally supported through site-directed mutagenesis and functional testing, and hydrogen bonding appears key in pheromone binding. CONCLUSIONS The emerging insight into ligand binding in the two characterized ItypORs has a general importance for our understanding of the molecular and functional evolution of the insect OR gene family. Due to the ecological importance of the characterized receptors and widespread use of ipsenol and ipsdienol in bark beetle chemical communication, these ORs should be evaluated for their potential use in pest control and biosensors to detect bark beetle infestations.
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Affiliation(s)
- Jothi K Yuvaraj
- Department of Biology, Lund University, SE-223 62, Lund, Sweden
| | | | - Yonathan Sonntag
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-223 62, Lund, Sweden
| | - Xiao-Qing Hou
- Department of Biology, Lund University, SE-223 62, Lund, Sweden
| | - Ewald Grosse-Wilde
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
- Present address: Faculty of Forestry & Wood Sci, Excellent Team for Mitigation, Czech University Life Sci Prague, Kamycka 129, Prague 6, 16521, Suchdol, Czech Republic
| | - Aleš Machara
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Dan-Dan Zhang
- Department of Biology, Lund University, SE-223 62, Lund, Sweden
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
| | - Urban Johanson
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-223 62, Lund, Sweden
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34
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Wicher D, Miazzi F. Functional properties of insect olfactory receptors: ionotropic receptors and odorant receptors. Cell Tissue Res 2021; 383:7-19. [PMID: 33502604 PMCID: PMC7873100 DOI: 10.1007/s00441-020-03363-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/19/2020] [Indexed: 10/27/2022]
Abstract
The majority of insect olfactory receptors belong to two distinct protein families, the ionotropic receptors (IRs), which are related to the ionotropic glutamate receptor family, and the odorant receptors (ORs), which evolved from the gustatory receptor family. Both receptor types assemble to heteromeric ligand-gated cation channels composed of odor-specific receptor proteins and co-receptor proteins. We here present in short the current view on evolution, function, and regulation of IRs and ORs. Special attention is given on how their functional properties can meet the environmental and ecological challenges an insect has to face.
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Affiliation(s)
- Dieter Wicher
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany.
| | - Fabio Miazzi
- Research Group Predators and Toxic Prey, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
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35
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Abstract
The sense of smell enables insects to recognize olfactory signals crucial for survival and reproduction. In insects, odorant detection highly depends on the interplay of distinct proteins expressed by specialized olfactory sensory neurons (OSNs) and associated support cells which are housed together in chemosensory units, named sensilla, mainly located on the antenna. Besides odorant-binding proteins (OBPs) and olfactory receptors, so-called sensory neuron membrane proteins (SNMPs) are indicated to play a critical role in the detection of certain odorants. SNMPs are insect-specific membrane proteins initially identified in pheromone-sensitive OSNs of Lepidoptera and are indispensable for a proper detection of pheromones. In the last decades, genome and transcriptome analyses have revealed a wide distribution of SNMP-encoding genes in holometabolous and hemimetabolous insects, with a given species expressing multiple subtypes in distinct cells of the olfactory system. Besides SNMPs having a neuronal expression in subpopulations of OSNs, certain SNMP types were found expressed in OSN-associated support cells suggesting different decisive roles of SNMPs in the peripheral olfactory system. In this review, we will report the state of knowledge of neuronal and non-neuronal members of the SNMP family and discuss their possible functions in insect olfaction.
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Affiliation(s)
- Sina Cassau
- Institute of Biology/Zoology, Department of Animal Physiology, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jürgen Krieger
- Institute of Biology/Zoology, Department of Animal Physiology, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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36
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Benton R, Dessimoz C, Moi D. A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor. eLife 2020; 9:62507. [PMID: 33274716 PMCID: PMC7746228 DOI: 10.7554/elife.62507] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/03/2020] [Indexed: 01/26/2023] Open
Abstract
The insect chemosensory repertoires of Odorant Receptors (ORs) and Gustatory Receptors (GRs) together represent one of the largest families of ligand-gated ion channels. Previous analyses have identified homologous 'Gustatory Receptor-Like' (GRL) proteins across Animalia, but the evolutionary origin of this novel class of ion channels is unknown. We describe a survey of unicellular eukaryotic genomes for GRLs, identifying several candidates in fungi, protists and algae that contain many structural features characteristic of animal GRLs. The existence of these proteins in unicellular eukaryotes, together with ab initio protein structure predictions, provide evidence for homology between GRLs and a family of uncharacterized plant proteins containing the DUF3537 domain. Together, our analyses suggest an origin of this protein superfamily in the last common eukaryotic ancestor.
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Affiliation(s)
- Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.,Department of Computer Science, University College London, London, United Kingdom
| | - David Moi
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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37
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Khadka R, Carraher C, Hamiaux C, Travas-Sejdic J, Kralicek A. Synergistic improvement in the performance of insect odorant receptor based biosensors in the presence of Orco. Biosens Bioelectron 2020; 153:112040. [DOI: 10.1016/j.bios.2020.112040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/23/2019] [Accepted: 01/20/2020] [Indexed: 11/30/2022]
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38
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Jian Y, Wang X, Qiu J, Wang H, Liu Z, Zhao Y, Zeng C. DIRECT: RNA contact predictions by integrating structural patterns. BMC Bioinformatics 2019; 20:497. [PMID: 31615418 PMCID: PMC6794908 DOI: 10.1186/s12859-019-3099-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 09/13/2019] [Indexed: 01/25/2023] Open
Abstract
Background It is widely believed that tertiary nucleotide-nucleotide interactions are essential in determining RNA structure and function. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequence from its homologous sequence alignment across different species. DCA and similar approaches that use sequence information alone typically yield a low accuracy, especially when the available homologous sequences are limited. Therefore, new methods for RNA structural contact inference are desirable because even a single correctly predicted tertiary contact can potentially make the difference between a correct and incorrectly predicted structure. Here we present a new method DIRECT (Direct Information REweighted by Contact Templates) that incorporates a Restricted Boltzmann Machine (RBM) to augment the information on sequence co-variations with structural features in contact inference. Results Benchmark tests demonstrate that DIRECT achieves better overall performance than DCA approaches. Compared to mfDCA and plmDCA, DIRECT produces a substantial increase of 41 and 18%, respectively, in accuracy on average for contact prediction. DIRECT improves predictions for long-range contacts and captures more tertiary structural features. Conclusions We developed a hybrid approach that incorporates a Restricted Boltzmann Machine (RBM) to augment the information on sequence co-variations with structural templates in contact inference. Our results demonstrate that DIRECT is able to improve the RNA contact prediction.
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Affiliation(s)
- Yiren Jian
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China.,Department of Physics, The George Washington University, Washington DC, 20052, USA
| | - Xiaonan Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Jaidi Qiu
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Huiwen Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Zhichao Liu
- Department of Physics, The George Washington University, Washington DC, 20052, USA
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China.
| | - Chen Zeng
- Department of Physics, The George Washington University, Washington DC, 20052, USA.
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39
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Thoma M, Missbach C, Jordan MD, Grosse-Wilde E, Newcomb RD, Hansson BS. Transcriptome Surveys in Silverfish Suggest a Multistep Origin of the Insect Odorant Receptor Gene Family. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00281] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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40
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Tiwari V, Karpe SD, Sowdhamini R. Topology prediction of insect olfactory receptors. Curr Opin Struct Biol 2019; 55:194-203. [PMID: 31233963 DOI: 10.1016/j.sbi.2019.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
Abstract
Olfactory receptors are important transmembrane proteins that enable organisms to perceive odours and react to them. Structural understanding of insect olfactory receptors is scarce. In this review, we discuss different transmembrane helix prediction methods, consensus methods, topology prediction methods which can enable topology prediction of these proteins. We discuss the current success rates by applying the algorithms on few G-protein coupled receptors of known structure and olfactory receptor sequences and outstanding challenges. Finally, we discuss the impact of topology prediction on biology and modeling of ORs.
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Affiliation(s)
- Vikas Tiwari
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Snehal D Karpe
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India.
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41
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Xu JW, Zhu XY, Chao QJ, Zhang YJ, Yang YX, Wang RR, Zhang Y, Xie MZ, Ge YT, Wu XL, Zhang F, Zhang YN, Ji L, Xu L. Chemosensory Gene Families in the Oligophagous Pear Pest Cacopsylla chinensis (Hemiptera: Psyllidae). INSECTS 2019; 10:insects10060175. [PMID: 31212973 PMCID: PMC6628306 DOI: 10.3390/insects10060175] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 01/28/2023]
Abstract
Chemosensory systems play an important role in insect behavior, and some key associated genes have potential as novel targets for pest control. Cacopsylla chinensis is an oligophagous pest and has become one of the main pests of pear trees, but little is known about the molecular-level means by which it locates its hosts. In this study, we assembled the head transcriptome of C. chinensis using Illumina sequencing, and 63,052 Unigenes were identified. A total of 36 candidate chemosensory genes were identified, including five different families: 12 odorant binding proteins (OBPs), 11 chemosensory proteins (CSPs), 7 odorant receptors (ORs), 4 ionotropic receptors (IRs), and 2 gustatory receptors (GRs). The number of chemosensory gene families is consistent with that found in other Hemipteran species, indicating that our approach successfully obtained the chemosensory genes of C. chinensis. The tissue expression of all genes using quantitative real-time PCR (qRT-PCR) found that some genes displayed male head, female head, or nymph-biased specific/expression. Our results enrich the gene inventory of C. chinensis and provide valuable resources for the analysis of the functions of some key genes. This will help in developing molecular targets for disrupting feeding behavior in C. chinensis.
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Affiliation(s)
- Ji-Wei Xu
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Xiu-Yun Zhu
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Qiu-Jie Chao
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Yong-Jie Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Yu-Xia Yang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Ran-Ran Wang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Yu Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Meng-Zhen Xie
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Ya-Ting Ge
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Xin-Lai Wu
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Fan Zhang
- Key Laboratory of Animal Resistance Research, College of Life Science, Shandong Normal University, Jinan 250000, China.
| | - Ya-Nan Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Lei Ji
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Lu Xu
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
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42
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Garczynski SF, Cattaneo AM, Walker WB. Alternative Splicing of the CpomOR53 Gene Produces Three Transcripts Expressed in Codling Moth (Lepidoptera: Tortricidae) Antennae. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:991-996. [PMID: 30535047 DOI: 10.1093/jee/toy370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Indexed: 06/09/2023]
Abstract
Incorporation of semiochemicals into codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), IPM programs has drastically reduced the amount of chemical insecticides needed to control this orchard pest. Odorant receptors are key sensors in the detection of semiochemicals and trigger downstream signaling events leading to behavioral responses. For codling moth, 58 odorant receptors have been identified in antennal transcriptomes, a few of which have been characterized for ligand activation. From the codling moth antennal transcriptome, a single transcript encoding CpomOR53 was annotated but re-evaluation suggests two or more variants of this receptor may be present and it is hypothesized that they are produced by alternative splicing. In this study, the complete open reading frame of CpomOR53 was amplified from codling moth male and female antennal RNAs, with three distinct transcripts detected. Characterization of these transcripts indicate that they are produced by alternative splicing of the CpomOR53 gene. The membrane topology for each of the CpomOR53 variants shows that alternative spliced products altered the length of intracellular loop two of the predicted proteins. The effects of these alterations were not determined but will be addressed in future studies determining the ligand(s) that activate each CpomOR53 transcript variant.
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Affiliation(s)
| | - Alberto M Cattaneo
- Swedish University of Agricultural Sciences, Department of Plant Protection Biology, Chemical Ecology Horticulture Research Unit, Alnarp, Sweden
| | - William B Walker
- Swedish University of Agricultural Sciences, Department of Plant Protection Biology, Chemical Ecology Horticulture Research Unit, Alnarp, Sweden
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43
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Li J, Liu X, Man Y, Chen Q, Pei D, Wu W. Cell-free expression, purification and characterization of Drosophila melanogaster odorant receptor OR42a and its co-receptor. Protein Expr Purif 2019; 159:27-33. [PMID: 30872132 DOI: 10.1016/j.pep.2019.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 01/06/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
Abstract
Olfactory receptors (OR), a group of classic membrane proteins, plays a vital role in insect reproduction and acclimatization. Deciphering the molecular mechanism of insect olfaction could enhance pest control and environmental protection. Studies on ORs have faced a major bottleneck due to the notoriously strong hydrophobicity of ORs, which results in difficult expression in heterologous cell systems. Here, we demonstrated that insect ORs could be functionally produced using the E. coli cell-free protein synthesis system (CFPS), in which the highest yield of total ORs is 350 μg per 1 ml reaction. We tested the effects of detergent types and concentrations on soluble expression of ORs. The ORs showed a classic α-helical infrared spectrum. Quartz crystal microbalance (QCM) was used to demonstrate that ORs fold correctly and respond to their ligands. This is the first report that insect OR42a could be functionally produced in vitro. This approach may facilitate the development of biomimetic olfactory biosensors and may also be utilized for drug positioning and development, environmental protection and agriculture.
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Affiliation(s)
- Jianyong Li
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Xingping Liu
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Yahui Man
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Qian Chen
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Di Pei
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China
| | - Wenjian Wu
- Department of Biology and Chemistry, National University of Defense Technology, Changsha, 410000, Hunan, China.
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44
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Robertson HM. Molecular Evolution of the Major Arthropod Chemoreceptor Gene Families. ANNUAL REVIEW OF ENTOMOLOGY 2019; 64:227-242. [PMID: 30312552 DOI: 10.1146/annurev-ento-020117-043322] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The evolutionary origins of the three major families of chemoreceptors in arthropods-the odorant receptor (OR), gustatory receptor (GR), and ionotropic receptor (IR) families-occurred at the base of the Insecta, Animalia, and Protostomia, respectively. Comparison of receptor family sizes across arthropods reveals a generally positive correlation with their widely disparate complexity of chemical ecology. Closely related species reveal the ongoing processes of gene family evolution, including gene duplication, divergence, pseudogenization, and loss, that mediate these larger patterns. Sets of paralogous receptors within species reveal positive selection on amino acids in regions likely to contribute to ligand binding and specificity. Ligands of many ORs and some GRs and IRs have been identified; however, ligand identification for many more chemoreceptors is needed, as are structures for the OR/GR superfamily, to improve our understanding of the molecular evolution of these ecologically important receptors in arthropods.
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Affiliation(s)
- Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
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Abstract
Thanks to the explosion of genomic sequencing, coevolutionary analysis of protein sequences has gained great and ever-increasing popularity in the last decade, and it is currently an important and well-established tool in structural bioinformatics and computational biology. This chapter concisely introduces the theoretical foundation and the practical aspects of coevolutionary analysis, as well as discusses the molecular modeling strategies to exploit its results in the study of protein structure, dynamics, and interactions. We present here a complete pipeline from sequence extraction to contact prediction through two examples, focusing on the predictions of inter-residue contacts in a single protein domain and on the analysis of a multi-domain protein that undergoes functional, large-scale conformational transitions.
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Affiliation(s)
- Duccio Malinverni
- Laboratory of Statistical Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Alessandro Barducci
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, France.
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46
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Coevolutionary Signals and Structure-Based Models for the Prediction of Protein Native Conformations. Methods Mol Biol 2019; 1851:83-103. [PMID: 30298393 DOI: 10.1007/978-1-4939-8736-8_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The analysis of coevolutionary signals from families of evolutionarily related sequences is a recent conceptual framework that provides valuable information about unique intramolecular interactions and, therefore, can assist in the elucidation of biomolecular conformations. It is based on the idea that compensatory mutations at specific residue positions in a sequence help preserve stability of protein architecture and function and leave a statistical signature related to residue-residue interactions in the 3D structure of the protein. Consequently, statistical analysis of these correlated mutations in subsets of protein sequence alignments can be used to predict which residue pairs should be in spatial proximity in the native functional protein fold. These predicted signals can be then used to guide molecular dynamics (MD) simulations to predict the three-dimensional coordinates of a functional amino acid chain. In this chapter, we introduce a general and efficient methodology to perform coevolutionary analysis on protein sequences and to use this information in combination with computational physical models to predict the native 3D conformation of functional polypeptides. We present a step-by-step methodology that includes the description and application of software tools and databases required to infer tertiary structures of a protein fold. The general pipeline includes instructions on (1) how to obtain direct amino acid couplings from protein sequences using direct coupling analysis (DCA), (2) how to incorporate such signals as interaction potentials in Cα structure-based models (SBMs) to drive protein-folding MD simulations, (3) a procedure to estimate secondary structure and how to include such estimates in the topology files required in the MD simulations, and (4) how to build full atomic models based on the top Cα candidates selected in the pipeline. The information presented in this chapter is self-contained and sufficient to allow a computational scientist to predict structures of proteins using publicly available algorithms and databases.
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47
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Identification of candidate olfactory genes in cicada Subpsaltria yangi by antennal transcriptome analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:122-133. [DOI: 10.1016/j.cbd.2018.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/04/2018] [Accepted: 08/17/2018] [Indexed: 11/22/2022]
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48
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Vorberg S, Seemayer S, Söding J. Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. PLoS Comput Biol 2018; 14:e1006526. [PMID: 30395601 PMCID: PMC6237422 DOI: 10.1371/journal.pcbi.1006526] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/15/2018] [Accepted: 09/24/2018] [Indexed: 12/01/2022] Open
Abstract
Compensatory mutations between protein residues in physical contact can manifest themselves as statistical couplings between the corresponding columns in a multiple sequence alignment (MSA) of the protein family. Conversely, large coupling coefficients predict residue contacts. Methods for de-novo protein structure prediction based on this approach are becoming increasingly reliable. Their main limitation is the strong systematic and statistical noise in the estimation of coupling coefficients, which has so far limited their application to very large protein families. While most research has focused on improving predictions by adding external information, little progress has been made to improve the statistical procedure at the core, because our lack of understanding of the sources of noise poses a major obstacle. First, we show theoretically that the expectation value of the coupling score assuming no coupling is proportional to the product of the square roots of the column entropies, and we propose a simple entropy bias correction (EntC) that subtracts out this expectation value. Second, we show that the average product correction (APC) includes the correction of the entropy bias, partly explaining its success. Third, we have developed CCMgen, the first method for simulating protein evolution and generating realistic synthetic MSAs with pairwise statistical residue couplings. Fourth, to learn exact statistical models that reliably reproduce observed alignment statistics, we developed CCMpredPy, an implementation of the persistent contrastive divergence (PCD) method for exact inference. Fifth, we demonstrate how CCMgen and CCMpredPy can facilitate the development of contact prediction methods by analysing the systematic noise contributions from phylogeny and entropy. Using the entropy bias correction, we can disentangle both sources of noise and find that entropy contributes roughly twice as much noise as phylogeny. Knowledge about the three-dimensional structure of proteins is key to understanding their function and role in biological processes and diseases. The experimental structure determination techniques, such as X-ray crystallography or electron cryo-microscopy, are labour intensive, time-consuming and expensive. Therefore, complementary computational methods to predict a protein’s structure have become indispensable. Over the last years, immense progress has been made in predicting protein structures from their amino acid sequence by utilizing highly accurate predictions of spatial contacts between amino acid residues as constraints in folding simulations. However, contact prediction methods require large numbers of homologous protein sequences in order to discriminate between signal and noise. A major obstacle preventing progress on the statistical methodology is our limited understanding of the different components of noise that are known to affect the predictions. We provide two tools, CCMpredPy and CCMgen, that can be used to learn highly accurate statistical models for contact prediction and to simulate protein evolution according to the statistical constraints between positions of residues as specified by these models, respectively. We showcase their usefulness by quantifying the relative contribution of noise arising from entropy and phylogeny on the predicted contacts, which will facilitate the improvement of the statistical methodology.
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Affiliation(s)
- Susann Vorberg
- Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Seemayer
- Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Johannes Söding
- Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
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49
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Qiu CZ, Zhou QZ, Liu TT, Fang SM, Wang YW, Fang X, Huang CL, Yu QY, Chen CH, Zhang Z. Evidence of peripheral olfactory impairment in the domestic silkworms: insight from the comparative transcriptome and population genetics. BMC Genomics 2018; 19:788. [PMID: 30382813 PMCID: PMC6211594 DOI: 10.1186/s12864-018-5172-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/15/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The insect olfactory system is a highly specific and sensitive chemical detector, which plays important roles in feeding, mating and finding an appropriate oviposition site. The ecological niche of Bombyx mori has changed greatly since domestication from B. mandarina, and its olfactory response to environmental odorants clearly decreased. However, the mechanisms that result in the olfactory impairment are largely unknown. RESULTS The antennal transcriptomes were compared between the domestic and wild silkworms. Comparison of the same sex between the domestic and wild silkworms revealed 1410 and 1173 differentially expressed genes (DEGs) in males and females, respectively. To understand the olfactory impairment, we mainly focused on the olfactory-related genes. In total, 30 olfactory genes and 19 odorant-degrading enzymes (ODEs) showed differential expression in the two comparisons, in which 19 and 14 were down-regulated in the domestic silkworm, respectively. Based on population genomic data, the down-regulated odorant receptors (ORs) showed a higher ratio of unique non-synonymous polymorphisms to synonymous polymorphisms (N/S ratio) in the domestic populations than that in the wild silkworms. Furthermore, one deleterious mutation was found in OR30 of the domestic population, which was located in transmembrane helix 6 (TM6). CONCLUSIONS Our results suggested that down-regulation of the olfactory-related genes and relaxed selection might be the major reasons for olfactory impairment of the domestic silkworm reared completely indoor environment. Reversely, wild silkworm may increase expression and remove deleterious polymorphisms of olfactory-related genes to retain sensitive olfaction.
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Affiliation(s)
- Chuan-Zhen Qiu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Qiu-Zhong Zhou
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Ting-Ting Liu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shou-Min Fang
- College of Life Science, China West Normal University, Nanchang, 637002, China
| | - Ya-Wang Wang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xin Fang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Chun-Li Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Quan-You Yu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| | | | - Ze Zhang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
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50
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Cohanim AB, Amsalem E, Saad R, Shoemaker D, Privman E. Evolution of Olfactory Functions on the Fire Ant Social Chromosome. Genome Biol Evol 2018; 10:2947-2960. [PMID: 30239696 PMCID: PMC6279166 DOI: 10.1093/gbe/evy204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 12/16/2022] Open
Abstract
Understanding the molecular evolutionary basis of social behavior is a major challenge in evolutionary biology. Social insects evolved a complex language of chemical signals to coordinate thousands of individuals. In the fire ant Solenopsis invicta, chemical signals are involved in the determination of a polymorphic social organization. Single-queen (monogyne) or multiqueen (polygyne) social structure is determined by the "social chromosome," a nonrecombining region containing ∼504 genes with two distinct haplotypes, SB and Sb. Monogyne queens are always SBB, while polygyne queens are always SBb. Workers discriminate monogyne from polygyne queens based on olfactory cues. Here, we took an evolutionary genomics approach to search for candidate genes in the social chromosome that could be responsible for this discrimination. We compared the SB and Sb haplotypes and analyzed the evolutionary rates since their divergence. Notably, we identified a cluster of 23 odorant receptors in the nonrecombining region of the social chromosome that stands out in terms of nonsynonymous changes in both haplotypes. The cluster includes twelve genes formed by recent Solenopsis-specific duplications. We found evidence for positive selection on several tree branches and significant differences between the SB and Sb haplotypes of these genes. The most dramatic difference is the complete deletion of two of these genes in Sb. These results suggest that the evolution of polygyne social organization involved adaptations in olfactory genes and opens the way for functional studies of the molecular mechanisms underlying social behavior.
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Affiliation(s)
- Amir B Cohanim
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Israel
| | - Etya Amsalem
- Department of Entomology, Huck Institutes of the Life Sciences, Pennsylvania State University
| | - Rana Saad
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Israel
| | - DeWayne Shoemaker
- Department of Entomology and Plant Pathology, University of Tennessee
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Israel
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