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Kim DH, Kim MS, Lee JS, Yoon DS, Lee JS. Genome-wide identification of 769 G protein-coupled receptor (GPCR) genes from the marine medaka Oryzias melastigma. MARINE POLLUTION BULLETIN 2024; 207:116868. [PMID: 39173477 DOI: 10.1016/j.marpolbul.2024.116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
The marine medaka Oryzias melastigma is a useful fish model for marine and estuarine ecotoxicology studies and can be applied to field-based population genomics because of its distribution in Asian estuaries and other coastal areas. We identified 769 full-length G protein-coupled receptor genes in the O. melastigma genome and classified them into five distinct classes. A phylogenetic comparison of GPCR genes in O. melastigma to humans and two other small fish species revealed a high-level orthological relationship. Purinergic and chemokine receptors were highly differentiated in humans whereas significant differentiation of chemosensory receptors was evident in fish species. Our results suggest that the GPCR gene families among the species used in this study exhibit evidence of sporadic evolutionary processes. These results may help improve our understanding of the advanced repertoires of GPCR and expand our knowledge of physiological mechanisms of fish in response to various environmental stimuli.
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Affiliation(s)
- Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jin-Sol Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Deok-Seo Yoon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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Qin X, Jin X, Zhou K, Li H, Wang Q, Li W, Wang Q. EsGPCR89 regulates cerebral antimicrobial peptides through hemocytes in Eriocheir sinensis. FISH & SHELLFISH IMMUNOLOGY 2019; 95:151-162. [PMID: 31605765 DOI: 10.1016/j.fsi.2019.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/02/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
G protein-coupled receptors (GPCRs) are important transmembrane receptors that participate in diverse physiological processes including metabolism, cell growth and immune processes by transmitting extracellular signals to intracellular effectors. In this study, a gene belonging to the GPCR family was cloned from Eriocheir sinensis and named EsGPCR89. The full-length gene includes an open reading frame (ORF) of 465 amino acid residues, and bioinformatic analysis confirmed the high conservation between species. EsGPCR89 was detected in various tissues of E. sinensis, and was up-regulated in brain following Staphylococcus aureus infection. Expression levels of cerebral antimicrobial peptides (AMPs) were also up-regulated following bacterial challenge, reflecting their function in cerebral immunity. Additionally, EsGPCR89 silencing in hemocytes by RNA interference, down-regulated AMPs in brain after S. aureus infection. Moreover, through Immunisation assay and Polyacrylamide gel electrophoresis (SDS-PAGE) experiments, we could infer that bacterially infected hemocytes released effectors under the regulation of EsGPCR89, thereby activating transcription of cerebral AMPs. These results demonstrate that EsGPCR89 plays important roles in cerebral antimicrobial function via hemocytes.
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Affiliation(s)
- Xiang Qin
- State Key Laboratory of Estuarine and Coastal Research, and The Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Science, East China Normal University, Shanghai, PR China
| | - Xingkun Jin
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, PR China
| | - Kaimin Zhou
- State Key Laboratory of Estuarine and Coastal Research, and The Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Science, East China Normal University, Shanghai, PR China
| | - Hao Li
- State Key Laboratory of Estuarine and Coastal Research, and The Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Science, East China Normal University, Shanghai, PR China
| | - Qiying Wang
- State Key Laboratory of Estuarine and Coastal Research, and The Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Science, East China Normal University, Shanghai, PR China
| | - Weiwei Li
- State Key Laboratory of Estuarine and Coastal Research, and The Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Science, East China Normal University, Shanghai, PR China.
| | - Qun Wang
- State Key Laboratory of Estuarine and Coastal Research, and The Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Science, East China Normal University, Shanghai, PR China.
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Favara DM, Banham AH, Harris AL. ADGRL4/ELTD1 is a highly conserved angiogenesis-associated orphan adhesion GPCR that emerged with the first vertebrates and comprises 3 evolutionary variants. BMC Evol Biol 2019; 19:143. [PMID: 31299890 PMCID: PMC6626334 DOI: 10.1186/s12862-019-1445-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 05/27/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Our laboratory identified ADGRL4/ELTD1, an orphan GPCR belonging to the adhesion GPCR (aGPCR) family, as a novel regulator of angiogenesis and a potential anti-cancer therapeutic target. Little is known about how ADGRL4/ELTD1 (and aGPCRs in general) function, a problem compounded by a lack of known ligands or means of activation. With this in mind, we turned to computational evolutionary biology with the aim of better understanding ADGRL4/ELTD1. RESULTS We identified ADGRL4/ELTD1 as a highly conserved early angiogenic gene which emerged in the first true vertebrates (bony fish) approximately 435 million years ago (mya), evolving alongside key angiogenic genes VEGFR2 and DLL4. We identified 3 evolutionary ADGRL4/ELTD1 variants based on EGF domain deletions with variant 2 first emerging 101 mya (95% CI 96-105) in Afrotheria and 82 mya (95% CI 76-89) in Primates. Additionally, conservation mapping across all orthologues reveals highest level conservation in EGF Ca binding domain 1, suggesting that this motif plays an essential role, as well as specific regions of the GAIN domain, GPS motif and 7TM domain, suggesting possible activation mechanisms and ligand binding positions. Additionally, we found that ADGRL4/ELTD1 (a member aGPCR family 1) is possibly ancestral to members of aGPCR family 2. CONCLUSION This work establishes ADGRL4/ELTD1's evolution, sheds light on its possible activation and ligand binding zones, and establishes the first temporal references for the emergence of ADGRL4/ELTD1 variants during vertebrate evolution. Our approach is applicable to the greater aGPCR family and opens up new avenues for future experimental work.
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Affiliation(s)
- David M. Favara
- Balliol College, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Alison H. Banham
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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Krishnan A, Nijmeijer S, de Graaf C, Schiöth HB. Classification, Nomenclature, and Structural Aspects of Adhesion GPCRs. Handb Exp Pharmacol 2016; 234:15-41. [PMID: 27832482 DOI: 10.1007/978-3-319-41523-9_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Representation of the nine distinct aGPCR subfamilies and their unique N-terminal domain architecture. The illustration also shows the extracellular structural feature shared by all aGPCRs (except ADGRA1), known as the GPCR autoproteolysis-inducing (GAIN) domain, that mediates autoproteolysis and subsequent attachment of the cleaved NTF and CTF fragments The adhesion family of G protein-coupled receptors (aGPCRs) is unique among all GPCR families with long N-termini and multiple domains that are implicated in cell-cell and cell-matrix interactions. Initially, aGPCRs in the human genome were phylogenetically classified into nine distinct subfamilies based on their 7TM sequence similarity. This phylogenetic grouping of genes into subfamilies was found to be in congruence in closely related mammals and other vertebrates as well. Over the years, aGPCR repertoires have been mapped in many species including model organisms, and, currently, there is a growing interest in exploring the pharmacological aspects of aGPCRs. Nonetheless, the aGPCR nomenclature has been highly diverse because experts in the field have used different names for different family members based on their characteristics (e.g., epidermal growth factor-seven-span transmembrane (EGF-TM7)), but without harmonization with regard to nomenclature efforts. In order to facilitate naming of orthologs and other genetic variants in different species in the future, the Adhesion-GPCR Consortium, together with the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification, proposed a unified nomenclature for aGPCRs. Here, we review the classification and the most recent/current nomenclature of aGPCRs and as well discuss the structural topology of the extracellular domain (ECD)/N-terminal fragment (NTF) that is comparable with this 7TM subfamily classification. Of note, we systematically describe the structural domains in the ECD of aGPCR subfamilies and highlight their role in aGPCR-protein interactions.
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Affiliation(s)
- Arunkumar Krishnan
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, 593, Uppsala, 75 124, Sweden
| | - Saskia Nijmeijer
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, 1081HV, The Netherlands
| | - Chris de Graaf
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, 1081HV, The Netherlands
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, 593, Uppsala, 75 124, Sweden.
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Campos TDL, Young ND, Korhonen PK, Hall RS, Mangiola S, Lonie A, Gasser RB. Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics. Parasit Vectors 2014; 7:242. [PMID: 24884876 PMCID: PMC4100253 DOI: 10.1186/1756-3305-7-242] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 05/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Schistosomiasis is a parasitic disease affecting ~200 million people worldwide. Schistosoma haematobium and S. mansoni are two relatively closely related schistosomes (blood flukes), and the causative agents of urogenital and hepatointestinal schistosomiasis, respectively. The availability of genomic, transcriptomic and proteomic data sets for these two schistosomes now provides unprecedented opportunities to explore their biology, host interactions and schistosomiasis at the molecular level. A particularly important group of molecules involved in a range of biological and developmental processes in schistosomes and other parasites are the G protein-coupled receptors (GPCRs). Although GPCRs have been studied in schistosomes, there has been no detailed comparison of these receptors between closely related species. Here, using a genomic-bioinformatic approach, we identified and characterised key GPCRs in S. haematobium and S. mansoni (two closely related species of schistosome). METHODS Using a Hidden Markov Model (HMM) and Support Vector Machine (SVM)-based pipeline, we classified and sub-classified GPCRs of S. haematobium and S. mansoni, combined with phylogenetic and transcription analyses. RESULTS We identified and classified classes A, B, C and F as well as an unclassified group of GPCRs encoded in the genomes of S. haematobium and S. mansoni. In addition, we characterised ligand-specific subclasses (i.e. amine, peptide, opsin and orphan) within class A (rhodopsin-like). CONCLUSIONS Most GPCRs shared a high degree of similarity and conservation, except for members of a particular clade (designated SmGPR), which appear to have diverged between S. haematobium and S. mansoni and might explain, to some extent, some of the underlying biological differences between these two schistosomes. The present set of annotated GPCRs provides a basis for future functional genomic studies of cellular GPCR-mediated signal transduction and a resource for future drug discovery efforts in schistosomes.
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Affiliation(s)
| | - Neil D Young
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia.
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Sequence-structure based phylogeny of GPCR Class A Rhodopsin receptors. Mol Phylogenet Evol 2014; 74:66-96. [PMID: 24503482 DOI: 10.1016/j.ympev.2014.01.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/17/2014] [Accepted: 01/24/2014] [Indexed: 11/23/2022]
Abstract
Current methods of G protein coupled receptors (GPCRs) phylogenetic classification are sequence based and therefore inappropriate for highly divergent sequences, sharing low sequence identity. In this study, sequence structure profile based alignment generated by PROMALS3D was used to understand the GPCR Class A Rhodopsin superfamily evolution using the MEGA 5 software. Phylogenetic analysis included a combination of Neighbor-Joining method and Maximum Likelihood method, with 1000 bootstrap replicates. Our study was able to identify potential ligand association for Class A Orphans and putative/unclassified Class A receptors with no cognate ligand information: GPR21 and GPR52 with fatty acids; GPR75 with Neuropeptide Y; GPR82, GPR18, GPR141 with N-arachidonylglycine; GPR176 with Free fatty acids, GPR10 with Tachykinin & Neuropeptide Y; GPR85 with ATP, ADP & UDP glucose; GPR151 with Galanin; GPR153 and GPR162 with Adrenalin, Noradrenalin; GPR146, GPR139, GPR142 with Neuromedin, Ghrelin, Neuromedin U-25 & Thyrotropin-releasing hormone; GPR171 with ATP, ADP & UDP Glucose; GPR88, GPR135, GPR161, GPR101with 11-cis-retinal; GPR83 with Tackykinin; GPR148 with Prostanoids, GPR109b, GPR81, GPR31with ATP & UTP and GPR150 with GnRH I & GnRHII. Furthermore, we suggest that this study would prove useful in re-classification of receptors, selecting templates for homology modeling and identifying ligands which may show cross reactivity with other GPCRs as signaling via multiple ligands play a significant role in disease modulation.
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Stäubert C, Le Duc D, Schöneberg T. Examining the Dynamic Evolution of G Protein-Coupled Receptors. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-62703-779-2_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Yan J, Jia H, Ma Z, Ye H, Zhou M, Su L, Liu J, Guo AY. The evolutionary analysis reveals domain fusion of proteins with Frizzled-like CRD domain. Gene 2013; 533:229-39. [PMID: 24135643 DOI: 10.1016/j.gene.2013.09.083] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/18/2013] [Accepted: 09/23/2013] [Indexed: 10/26/2022]
Abstract
Frizzleds (FZDs) are transmembrane receptors in the Wnt signaling pathway and they play pivotal roles in developments. The Frizzled-like extracellular Cysteine-rich domain (Fz-CRD) has been identified in FZDs and other proteins. The origin and evolution of these proteins with Fz-CRD is the main interest of this study. We found that the Fz-CRD exists in FZD, SFRP, RTK, MFRP, CPZ, CORIN, COL18A1 and other proteins. Our systematic analysis revealed that the Fz-CRD domain might have originated in protists and then fused with the Frizzled-like seven-transmembrane domain (7TM) to form the FZD receptors, which duplicated and diversified into about 11 members in Vertebrates. The SFRPs and RTKs with the Fz-CRD were found in sponge and expanded in Vertebrates. Other proteins with Fz-CRD may have emerged during Vertebrate evolution through domain fusion. Moreover, we found a glycosylation site and several conserved motifs in FZDs, which may be related to Wnt interaction. Based on these results, we proposed a model showing that the domain fusion and expansion of Fz-CRD genes occurred in Metazoa and Vertebrates. Our study may help to pave the way for further research on the conservation and diversification of Wnt signaling functions during evolution.
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Affiliation(s)
- Jun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China; Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China; Department of Applied Physics, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, PR China
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Nowling RJ, Abrudan JL, Shoue DA, Abdul-Wahid B, Wadsworth M, Stayback G, Collins FH, McDowell MA, Izaguirre JA. Identification of novel arthropod vector G protein-coupled receptors. Parasit Vectors 2013; 6:150. [PMID: 23705687 PMCID: PMC3680159 DOI: 10.1186/1756-3305-6-150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/18/2013] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The control of vector-borne diseases, such as malaria, dengue fever, and typhus fever is often achieved with the use of insecticides. Unfortunately, insecticide resistance is becoming common among different vector species. There are currently no chemical alternatives to these insecticides because new human-safe classes of molecules have yet to be brought to the vector-control market. The identification of novel targets offer opportunities for rational design of new chemistries to control vector populations. One target family, G protein-coupled receptors (GPCRs), has remained relatively under explored in terms of insecticide development. METHODS A novel classifier, Ensemble*, for vector GPCRs was developed. Ensemble* was validated and compared to existing classifiers using a set of all known GPCRs from Aedes aegypti, Anopheles gambiae, Apis Mellifera, Drosophila melanogaster, Homo sapiens, and Pediculus humanus. Predictions for unidentified sequences from Ae. aegypti, An. gambiae, and Pe. humanus were validated. Quantitative RT-PCR expression analysis was performed on previously-known and newly discovered Ae. aegypti GPCR genes. RESULTS We present a new analysis of GPCRs in the genomes of Ae, aegypti, a vector of dengue fever, An. gambiae, a primary vector of Plasmodium falciparum that causes malaria, and Pe. humanus, a vector of epidemic typhus fever, using a novel GPCR classifier, Ensemble*, designed for insect vector species. We identified 30 additional putative GPCRs, 19 of which we validated. Expression of the newly discovered Ae. aegypti GPCR genes was confirmed via quantitative RT-PCR. CONCLUSION A novel GPCR classifier for insect vectors, Ensemble*, was developed and GPCR predictions were validated. Ensemble* and the validation pipeline were applied to the genomes of three insect vectors (Ae. aegypti, An. gambiae, and Pe. humanus), resulting in the identification of 52 GPCRs not previously identified, of which 11 are predicted GPCRs, and 19 are predicted and confirmed GPCRs.
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Affiliation(s)
- Ronald J Nowling
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Jenica L Abrudan
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Douglas A Shoue
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Badi’ Abdul-Wahid
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Mariha Wadsworth
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Gwen Stayback
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Frank H Collins
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, 46656, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Mary Ann McDowell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Jesús A Izaguirre
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
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Gopurappilly R, Ogawa S, Parhar IS. Functional significance of GnRH and kisspeptin, and their cognate receptors in teleost reproduction. Front Endocrinol (Lausanne) 2013; 4:24. [PMID: 23482509 PMCID: PMC3591744 DOI: 10.3389/fendo.2013.00024] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 02/22/2013] [Indexed: 12/18/2022] Open
Abstract
Guanine nucleotide binding protein (G-protein)-coupled receptors (GPCRs) are eukaryotic transmembrane proteins found in all living organisms. Their versatility and roles in several physiological processes make them the single largest family of drug targets. Comparative genomic studies using various model organisms have provided useful information about target receptors. The similarity of the genetic makeup of teleosts to that of humans and other vertebrates aligns with the study of GPCRs. Gonadotropin-releasing hormone (GnRH) represents a critical step in the reproductive process through its cognate GnRH receptors (GnRHRs). Kisspeptin (Kiss1) and its cognate GPCR, GPR54 (=kisspeptin receptor, Kiss-R), have recently been identified as a critical signaling system in the control of reproduction. The Kiss1/Kiss-R system regulates GnRH release, which is vital to pubertal development and vertebrate reproduction. This review highlights the physiological role of kisspeptin-Kiss-R signaling in the reproductive neuroendocrine axis in teleosts through the modulation of GnRH release. Moreover, we also review the recent developments in GnRHR and Kiss-R with respect to their structural variants, signaling mechanisms, ligand interactions, and functional significance. Finally, we discuss the recent progress in identifying many teleost GnRH-GnRHR and kisspeptin-Kiss-R systems and consider their physiological significance in the control of reproduction.
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Affiliation(s)
- Renjitha Gopurappilly
- Brain Research Institute, School of Medicine and Health Sciences, Monash University Sunway CampusSelangor, Malaysia
| | - Satoshi Ogawa
- Brain Research Institute, School of Medicine and Health Sciences, Monash University Sunway CampusSelangor, Malaysia
| | - Ishwar S. Parhar
- Brain Research Institute, School of Medicine and Health Sciences, Monash University Sunway CampusSelangor, Malaysia
- *Correspondence: Ishwar S. Parhar, Brain Research Institute, School of Medicine and Health Sciences, Monash University Sunway Campus, Petaling Jaya 46150, Selangor, Malaysia. e-mail:
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Zamanian M, Kimber MJ, McVeigh P, Carlson SA, Maule AG, Day TA. The repertoire of G protein-coupled receptors in the human parasite Schistosoma mansoni and the model organism Schmidtea mediterranea. BMC Genomics 2011; 12:596. [PMID: 22145649 PMCID: PMC3261222 DOI: 10.1186/1471-2164-12-596] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 12/06/2011] [Indexed: 12/31/2022] Open
Abstract
Background G protein-coupled receptors (GPCRs) constitute one of the largest groupings of eukaryotic proteins, and represent a particularly lucrative set of pharmaceutical targets. They play an important role in eukaryotic signal transduction and physiology, mediating cellular responses to a diverse range of extracellular stimuli. The phylum Platyhelminthes is of considerable medical and biological importance, housing major pathogens as well as established model organisms. The recent availability of genomic data for the human blood fluke Schistosoma mansoni and the model planarian Schmidtea mediterranea paves the way for the first comprehensive effort to identify and analyze GPCRs in this important phylum. Results Application of a novel transmembrane-oriented approach to receptor mining led to the discovery of 117 S. mansoni GPCRs, representing all of the major families; 105 Rhodopsin, 2 Glutamate, 3 Adhesion, 2 Secretin and 5 Frizzled. Similarly, 418 Rhodopsin, 9 Glutamate, 21 Adhesion, 1 Secretin and 11 Frizzled S. mediterranea receptors were identified. Among these, we report the identification of novel receptor groupings, including a large and highly-diverged Platyhelminth-specific Rhodopsin subfamily, a planarian-specific Adhesion-like family, and atypical Glutamate-like receptors. Phylogenetic analysis was carried out following extensive gene curation. Support vector machines (SVMs) were trained and used for ligand-based classification of full-length Rhodopsin GPCRs, complementing phylogenetic and homology-based classification. Conclusions Genome-wide investigation of GPCRs in two platyhelminth genomes reveals an extensive and complex receptor signaling repertoire with many unique features. This work provides important sequence and functional leads for understanding basic flatworm receptor biology, and sheds light on a lucrative set of anthelmintic drug targets.
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Affiliation(s)
- Mostafa Zamanian
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA.
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Dong C, Zhang P. A putative G protein-coupled receptor involved in innate immune defense of Procambarus clarkii against bacterial infection. Comp Biochem Physiol A Mol Integr Physiol 2011; 161:95-101. [PMID: 21964155 DOI: 10.1016/j.cbpa.2011.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/18/2011] [Accepted: 09/19/2011] [Indexed: 01/10/2023]
Abstract
The immune functions of G protein-coupled receptor (GPCR) were widely investigated in mammals. However, limited researches on immune function of GPCRs were reported in invertebrates. In the present study, the immune functions of HP1R gene, a putative GPCR identified from red swamp crayfish Procambarus clarkii were reported. Expression of HP1R gene was significant up-regulated in response to heat-killed Aeromonas hydrophila challenge. HP1R gene silencing mediated by RNA interference significantly enhanced the susceptibility of red swamp crayfish to A. hydrophila and Vibrio alginolyticus, indicating that HP1R was required for red swamp crayfish to defend against bacterial challenge. In HP1R-silenced crayfish, increased bacterial burden and decreased THC in response to bacterial challenge were observed when compared with control crayfish. No significant difference of proPO gene expression was observed between HP1R-silenced and control crayfish after challenge with heat-killed A. hydrophila. However, PO activity in response to bacterial challenge was significantly reduced in HP1R-silenced crayfish. The results collectively indicated that HP1R was an important immune molecule which was required for red swamp crayfish to defend against bacterial infection.
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Affiliation(s)
- Chaohua Dong
- College of Life Science, Qingdao Agricultural University, Qingdao 266109, China.
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Kurtenbach S, Mayer C, Pelz T, Hatt H, Leese F, Neuhaus EM. Molecular evolution of a chordate specific family of G protein-coupled receptors. BMC Evol Biol 2011; 11:234. [PMID: 21827690 PMCID: PMC3238225 DOI: 10.1186/1471-2148-11-234] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 08/09/2011] [Indexed: 11/23/2022] Open
Abstract
Background Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important characteristics, vertebrates obtained a well developed brain, anterior sensory structures, a closed circulatory system and gills or lungs as blood oxygenation systems. The duplication of pre-existing genes had profound evolutionary implications for the developmental complexity in vertebrates, since mutations modifying the function of a duplicated protein can lead to novel functions, improving the evolutionary success. Results We analyzed here the evolution of the GPRC5 family of G protein-coupled receptors by comprehensive similarity searches and found that the receptors are only present in chordates and that the size of the receptor family expanded, likely due to genome duplication events in the early history of vertebrate evolution. We propose that a single GPRC5 receptor coding gene originated in a stem chordate ancestor and gave rise by duplication events to a gene family comprising three receptor types (GPRC5A-C) in vertebrates, and a fourth homologue present only in mammals (GPRC5D). Additional duplications of GPRC5B and GPRC5C sequences occurred in teleost fishes. The finding that the expression patterns of the receptors are evolutionarily conserved indicates an important biological function of these receptors. Moreover, we found that expression of GPRC5B is regulated by vitamin A in vivo, confirming previous findings that linked receptor expression to retinoic acid levels in tumor cell lines and strengthening the link between the receptor expression and the development of a complex nervous system in chordates, known to be dependent on retinoic acid signaling. Conclusions GPRC5 receptors, a class of G protein-coupled receptors with unique sequence characteristics, may represent a molecular novelty that helped non-chordates to become chordates.
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Affiliation(s)
- Stefan Kurtenbach
- 1Department of Cell Physiology, Ruhr University Bochum, Universitaetsstrasse150, 44801 Bochum, Germany
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Pelé J, Abdi H, Moreau M, Thybert D, Chabbert M. Multidimensional scaling reveals the main evolutionary pathways of class A G-protein-coupled receptors. PLoS One 2011; 6:e19094. [PMID: 21544207 PMCID: PMC3081337 DOI: 10.1371/journal.pone.0019094] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 03/16/2011] [Indexed: 11/21/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) constitute the largest family of transmembrane receptors in the human genome. Understanding the mechanisms which drove the evolution of such a large family would help understand the specificity of each GPCR sub-family with applications to drug design. To gain evolutionary information on class A GPCRs, we explored their sequence space by metric multidimensional scaling analysis (MDS). Three-dimensional mapping of human sequences shows a non-uniform distribution of GPCRs, organized in clusters that lay along four privileged directions. To interpret these directions, we projected supplementary sequences from different species onto the human space used as a reference. With this technique, we can easily monitor the evolutionary drift of several GPCR sub-families from cnidarians to humans. Results support a model of radiative evolution of class A GPCRs from a central node formed by peptide receptors. The privileged directions obtained from the MDS analysis are interpretable in terms of three main evolutionary pathways related to specific sequence determinants. The first pathway was initiated by a deletion in transmembrane helix 2 (TM2) and led to three sub-families by divergent evolution. The second pathway corresponds to the differentiation of the amine receptors. The third pathway corresponds to parallel evolution of several sub-families in relation with a covarion process involving proline residues in TM2 and TM5. As exemplified with GPCRs, the MDS projection technique is an important tool to compare orthologous sequence sets and to help decipher the mutational events that drove the evolution of protein families.
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Affiliation(s)
- Julien Pelé
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
| | - Hervé Abdi
- School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
| | - Matthieu Moreau
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
| | - David Thybert
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
| | - Marie Chabbert
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
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Nordström KJV, Sällman Almén M, Edstam MM, Fredriksson R, Schiöth HB. Independent HHsearch, Needleman--Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families. Mol Biol Evol 2011; 28:2471-80. [PMID: 21402729 DOI: 10.1093/molbev/msr061] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several families of G protein-coupled receptors (GPCRs) show no significant sequence similarities to each other, and it has been debated which of them share a common origin. We developed and performed integrated and independent HHsearch, Needleman--Wunsch-based and motif analyses on more than 6,600 unique GPCRs from 12 species. Moreover, we mined the evolutionary important Trichoplax adhaerens, Nematostella vectensis, Thalassiosira pseudonana, and Strongylocentrotus purpuratus genomes, revealing remarkably rich vertebrate-like GPCR repertoires already in the early Metazoan species. We found strong evidence that the Adhesion and Frizzled families are children to the cyclic AMP (cAMP) family with HHsearch homology probabilities of 99.8% and 99.4%, respectively, also supported by the Needleman--Wunsch analysis and several motifs. We also found that the large Rhodopsin family is likely a child of the cAMP family with an HHsearch homology probability of 99.4% and conserved motifs. Therefore, we suggest that the Adhesion and Frizzled families originated from the cAMP family in an event close to that which gave rise to the Rhodopsin family. We also found convincing evidence that the Rhodopsin family is parent to the important sensory families; Taste 2 and Vomeronasal type 1 as well as the Nematode chemoreceptor families. The insect odorant, gustatory, and Trehalose receptors, frequently referred to as GPCRs, form a separate cluster without relationship to the other families, and we propose, based on these and others' results, that these families are ligand-gated ion channels rather than GPCRs. Overall, we suggest common descent of at least 97% of the GPCRs sequences found in humans.
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Affiliation(s)
- Karl J V Nordström
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, Uppsala, Sweden
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Sarkar A, Kumar S, Sundar D. The G protein-coupled receptors in the pufferfish Takifugu rubripes. BMC Bioinformatics 2011; 12 Suppl 1:S3. [PMID: 21342560 PMCID: PMC3044285 DOI: 10.1186/1471-2105-12-s1-s3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as "molecular switches" in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and their role in several physiological functions, being active players in detecting the presence of light, a variety of smells and tastes, amino acids, nucleotides, lipids, chemicals etc. in the environment of the cell. Comparative genomic studies on model organisms provide information on target receptors in humans and their function. The Japanese teleost Fugu has been identified as one of the smallest vertebrate genomes and a compact model to study the human genome, owing to the great similarity in its gene repertoire with that of human and other vertebrates. Thus the characterization of the GPCRs of Fugu would provide insights to the evolution of the vertebrate genome. RESULTS We classified the GPCRs in the Fugu genome and our analysis of its 316 membrane-bound receptors, available on the public databases as well as from literature, detected 298 GPCRs that were grouped into five main families according to the GRAFS classification system (namely, Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin). We also identified 18 other GPCRs that could not be grouped under the GRAFS family and hence were classified as 'Other 7TM' receptors. On comparison of the GPCR information from the Fugu genome with those in the human and chicken genomes, we detected 96.83% (306/316) and 96.51% (305/316) orthology in GPCRs among the Fugu-human genomes and Fugu-chicken genomes, respectively. CONCLUSIONS This study reveals the position of pisces in vertebrate evolution from the GPCR perspective. Fugu can act as a reference model for the human genome for other protein families as well, going by the high orthology observed for GPCRs between Fugu and human. The evolutionary comparison of GPCR sequences between key vertebrate classes of mammals, birds and fish will help in identifying key functional residues and motifs so as to fill in the blanks in the evolution of GPCRs in vertebrates.
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Affiliation(s)
- Anita Sarkar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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Schiöth HB, Nordström KJV, Fredriksson R. The adhesion GPCRs; gene repertoire, phylogeny and evolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 706:1-13. [PMID: 21618822 DOI: 10.1007/978-1-4419-7913-1_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Adhesion family is unique among the GPCR (G protein-coupled receptor) families because of several features including long N-termini with multiple domains. The gene repertoire has recently been mined in great detail in several species including mouse, rat, dog, chicken and the early vertebrate Branchiostoma (Branchiostoma floridae) and one of the most primitive animals, the cniderian Nematostella (Nematostella vectensis). There is a one-to-one relationship of the rodent (mouse and rat) and human orthologues with the exception the EMR2 and EMR3 that do not seem to have orthologues in either rat or mouse. All 33 human Adhesion GPCR genes are present in the dog genome but the dog genome also contains 5 additional full-length Adhesion genes. The dog and human Adhesion orthologues have higher average protein sequence identity than the rodent (rat and mouse) and the human sequences. The Adhesion family is well-represented in chicken with 21 one-to-one orthologous with humans, while 12 human Adhesion GPCRs lack a chicken ortholog. Branchiostoma has rich repertoire of Adhesion GPCRs with at least 37 genes. Moreover, the Adhesion GPCRs in Branchiostoma have several novel domains their N-termini, like Somatomedin B, Kringle, Lectin C-type, SRCR, LDLa, Immunoglobulin I-set, CUB and TNFR. Nematostella has also Adhesion GPCRs that are show domain structure and sequence similarities in the transmembrane regions with different classes of mammalian GPCRs. The Nematostella genome has a unique set of Adhesion-like sequences lacking GPS domains. There is considerable evidence showing that the Adhesion family is ancestral to the peptide hormone binding Secretin family of GPCRs.
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Affiliation(s)
- Helgi B Schiöth
- Department of Neuroscience, Biomedical Center, Box 593, 75 124 Uppsala, Sweden.
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Ji Y, Zhang Z, Hu Y. The repertoire of G-protein-coupled receptors in Xenopus tropicalis. BMC Genomics 2009; 10:263. [PMID: 19508718 PMCID: PMC2709155 DOI: 10.1186/1471-2164-10-263] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 06/09/2009] [Indexed: 01/06/2023] Open
Abstract
Background The G-protein-coupled receptor (GPCR) superfamily represents the largest protein family in the human genome. These proteins have a variety of physiological functions that give them well recognized roles in clinical medicine. In Xenopus tropicalis, a widely used animal model for physiology research, the repertoire of GPCRs may help link the GPCR evolutionary history in vertebrates from teleost fish to mammals. Results We have identified 1452 GPCRs in the X. tropicalis genome. Phylogenetic analyses classified these receptors into the following seven families: Glutamate, Rhodopsin, Adhesion, Frizzled, Secretin, Taste 2 and Vomeronasal 1. Nearly 70% of X. tropicalis GPCRs are represented by the following three types of receptors thought to receive chemosensory information from the outside world: olfactory, vomeronasal 1 and vomeronasal 2 receptors. Conclusion X. tropicalis shares a more similar repertoire of GPCRs with mammals than it does with fish. An examination of the three major groups of receptors related to olfactory/pheromone detection shows that in X. tropicalis, these groups have undergone lineage specific expansion. A comparison of GPCRs in X. tropicalis, teleost fish and mammals reveals the GPCR evolutionary history in vertebrates.
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Affiliation(s)
- Yanping Ji
- Shanghai Institute of Brain Functional Genomics, East China Normal University, 3663 Zhongshan Road N,, Shanghai, 200062, PR China.
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19
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Haitina T, Fredriksson R, Foord SM, Schiöth HB, Gloriam DE. The G protein-coupled receptor subset of the dog genome is more similar to that in humans than rodents. BMC Genomics 2009; 10:24. [PMID: 19146662 PMCID: PMC2651185 DOI: 10.1186/1471-2164-10-24] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 01/15/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The dog is an important model organism and it is considered to be closer to humans than rodents regarding metabolism and responses to drugs. The close relationship between humans and dogs over many centuries has lead to the diversity of the canine species, important genetic discoveries and an appreciation of the effects of old age in another species. The superfamily of G protein-coupled receptors (GPCRs) is one of the largest gene families in most mammals and the most exploited in terms of drug discovery. An accurate comparison of the GPCR repertoires in dog and human is valuable for the prediction of functional similarities and differences between the species. RESULTS We searched the dog genome for non-olfactory GPCRs and obtained 353 full-length GPCR gene sequences, 18 incomplete sequences and 13 pseudogenes. We established relationships between human, dog, rat and mouse GPCRs resolving orthologous pairs and species-specific duplicates. We found that 12 dog GPCR genes are missing in humans while 24 human GPCR genes are not part of the dog GPCR repertoire. There is a higher number of orthologous pairs between dog and human that are conserved as compared with either mouse or rat. In almost all cases the differences observed between the dog and human genomes coincide with other variations in the rodent species. Several GPCR gene expansions characteristic for rodents are not found in dog. CONCLUSION The repertoire of dog non-olfactory GPCRs is more similar to the repertoire in humans as compared with the one in rodents. The comparison of the dog, human and rodent repertoires revealed several examples of species-specific gene duplications and deletions. This information is useful in the selection of model organisms for pharmacological experiments.
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Affiliation(s)
- Tatjana Haitina
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Robert Fredriksson
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - Steven M Foord
- GlaxoSmithKline Pharmaceuticals, New Frontiers Science Park, 3rd Avenue, Harlow CM19 5AW, UK
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden
| | - David E Gloriam
- GlaxoSmithKline Pharmaceuticals, New Frontiers Science Park, 3rd Avenue, Harlow CM19 5AW, UK
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Nordström KJV, Lagerström MC, Wallér LMJ, Fredriksson R, Schiöth HB. The Secretin GPCRs descended from the family of Adhesion GPCRs. Mol Biol Evol 2008; 26:71-84. [PMID: 18845549 DOI: 10.1093/molbev/msn228] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Adhesion G-protein-coupled receptors (GPCRs) are the most complex gene family among GPCRs with large genomic size, multiple introns, and a fascinating flora of functional domains, though the evolutionary origin of this family has been obscure. Here we studied the evolution of all class B (7tm2)-related genes, including the Adhesion, Secretin, and Methuselah families of GPCRs with a focus on nine genomes. We found that the cnidarian genome of Nematostella vectensis has a remarkably rich set of Adhesion GPCRs with a broad repertoire of N-terminal domains although this genome did not have any Secretin GPCRs. Moreover, the single-celled and colony-forming eukaryotes Monosiga brevicollis and Dictyostelium discoideum contain Adhesion-like GPCRs although these genomes do not have any Secretin GPCRs suggesting that the Adhesion types of GPCRs are the most ancient among class B GPCRs. Phylogenetic analysis found Adhesion group V (that contains GPR133 and GPR144) to be the closest relative to the Secretin family in the Adhesion family. Moreover, Adhesion group V sequences in N. vectensis share the same splice site setup as the Secretin GPCRs. Additionally, one of the most conserved motifs in the entire Secretin family is only found in group V of the Adhesion family. We suggest therefore that the Secretin family of GPCRs could have descended from group V Adhesion GPCRs. We found a set of unique Adhesion-like GPCRs in N. vectensis that have long N-termini containing one Somatomedin B domain each, which is a domain configuration similar to that of a set of Adhesion-like GPCRs found in Branchiostoma floridae. These sequences show slight similarities to Methuselah sequences found in insects. The extended class B GPCRs have a very complex evolutionary history with several species-specific expansions, and we identified at least 31 unique N-terminal domains originating from other protein classes. The overall N-terminal domain structure, however, concurs with the phylogenetic analysis of the transmembrane domains, thus enabling us to track the origin of most of the subgroups.
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Affiliation(s)
- Karl J V Nordström
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
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Kamesh N, Aradhyam GK, Manoj N. The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis. BMC Evol Biol 2008; 8:129. [PMID: 18452600 PMCID: PMC2396169 DOI: 10.1186/1471-2148-8-129] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2007] [Accepted: 05/01/2008] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND G protein-coupled receptors (GPCRs) constitute a large family of integral transmembrane receptor proteins that play a central role in signal transduction in eukaryotes. The genome of the protochordate Ciona intestinalis has a compact size with an ancestral complement of many diversified gene families of vertebrates and is a good model system for studying protochordate to vertebrate diversification. An analysis of the Ciona repertoire of GPCRs from a comparative genomic perspective provides insight into the evolutionary origins of the GPCR signalling system in vertebrates. RESULTS We have identified 169 gene products in the Ciona genome that code for putative GPCRs. Phylogenetic analyses reveal that Ciona GPCRs have homologous representatives from the five major GRAFS (Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin) families concomitant with other vertebrate GPCR repertoires. Nearly 39% of Ciona GPCRs have unambiguous orthologs of vertebrate GPCR families, as defined for the human, mouse, puffer fish and chicken genomes. The Rhodopsin family accounts for ~68% of the Ciona GPCR repertoire wherein the LGR-like subfamily exhibits a lineage specific gene expansion of a group of receptors that possess a novel domain organisation hitherto unobserved in metazoan genomes. CONCLUSION Comparison of GPCRs in Ciona to that in human reveals a high level of orthology of a protochordate repertoire with that of vertebrate GPCRs. Our studies suggest that the ascidians contain the basic ancestral complement of vertebrate GPCR genes. This is evident at the subfamily level comparisons since Ciona GPCR sequences are significantly analogous to vertebrate GPCR subfamilies even while exhibiting Ciona specific genes. Our analysis provides a framework to perform future experimental and comparative studies to understand the roles of the ancestral chordate versions of GPCRs that predated the divergence of the urochordates and the vertebrates.
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Affiliation(s)
- N Kamesh
- Department of Biotechnology, Bhupat and Jyothi Mehta School of Biosciences Building, Indian Institute of Technology Madras, Chennai 600036, India.
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Metpally RPR, Vigneshwar R, Sowdhamini R. Genome inventory and analysis of nuclear hormone receptors in Tetraodon nigroviridis. J Biosci 2007; 32:43-50. [PMID: 17426379 DOI: 10.1007/s12038-007-0005-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear hormone receptors (NRs) form a large superfamily of ligand-activated transcription factors, which regulate genes underlying a wide range of (patho) physiological phenomena. Availability of the full genome sequence of Tetraodon nigroviridis facilitated a genome wide analysis of the NRs in fish genome. Seventy one NRs were found in Tetraodon and were compared with mammalian and fish NR family members. In general, there is a higher representation of NRs in fish genomes compared to mammalian ones. They showed high diversity across classes as observed by phylogenetic analysis. Nucleotide substitution rates show strong negative selection among fish NRs except for pregnane x receptor (PxR), estrogen receptor (ER) and liver x receptor (LxR). This may be attributed to crucial role played by them in metabolism and detoxification of xenobiotic and endobiotic compounds and might have resulted in slight positive selection. Chromosomal mapping and pairwise comparisons of NR distribution in Tetraodon and humans led to the identification of nine syntenic NR regions, of which three are common among fully sequenced vertebrate genomes. Gene structure analysis shows strong conservation of exon structures among orthologoues. Whereas paralogous members show different splicing patterns with intron gain or loss and addition or substitution of exons played a major role in evolution of NR superfamily.
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Affiliation(s)
- Raghu Prasad Rao Metpally
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India
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Levoye A, Jockers R. [GPCRs heterodimerization: a new way towards the discovery of function for the orphan receptors?]. Med Sci (Paris) 2007; 23:746-50. [PMID: 17875294 DOI: 10.1051/medsci/20072389746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs), also called seven transmembrane domain (7TM) proteins, represent the largest family of cell surface receptors. GPCRs control a variety of physiological processes, are involved in multiple diseases and are major drug targets. Despite a vast effort of academic and industrial research, more than one hundred receptors remain orphans. These orphan GPCRs offer a great potential for drug discovery, as almost 60% of currently prescribed drugs target GPCRs. Deorphenization strategies have concentrated mainly on the identification of the natural ligands of these proteins. Recent advances have shown that orphan GPCRs, similar to orphan nuclear receptors, can regulate the function of non-orphan receptors by heterodimerization. These findings not only help to better understand the extraordinary diversity of GPCRs, but also open new perspectives for the identification of the function of these orphan receptors that hold great therapeutic potential.
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Affiliation(s)
- Angélique Levoye
- Institut Pasteur, Laboratoire de Pathogénie Virale Moléculaire, INSERM U819, Département de Virologie, 28, rue du Docteur Roux, 75724, Paris, France.
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Davies MN, Gloriam DE, Secker A, Freitas AA, Mendao M, Timmis J, Flower DR. Proteomic applications of automated GPCR classification. Proteomics 2007; 7:2800-14. [PMID: 17639603 DOI: 10.1002/pmic.200700093] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The G-protein coupled receptor (GPCR) superfamily fulfils various metabolic functions and interacts with a diverse range of ligands. There is a lack of sequence similarity between the six classes that comprise the GPCR superfamily. Moreover, most novel GPCRs found have low sequence similarity to other family members which makes it difficult to infer properties from related receptors. Many different approaches have been taken towards developing efficient and accurate methods for GPCR classification, ranging from motif-based systems to machine learning as well as a variety of alignment-free techniques based on the physiochemical properties of their amino acid sequences. This review describes the inherent difficulties in developing a GPCR classification algorithm and includes techniques previously employed in this area.
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Schiöth HB, Nordström KJV, Fredriksson R. Mining the gene repertoire and ESTs for G protein-coupled receptors with evolutionary perspective. Acta Physiol (Oxf) 2007; 190:21-31. [PMID: 17428229 DOI: 10.1111/j.1365-201x.2007.01694.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The purpose of this article was to review recent progress in mining the gene repertoire and expressed sequence tags (ESTs) for the super-family of G protein-coupled receptors (GPCRs) in the form of a proceeding from the Nordic GPCR meeting held at the Nobel Forum, Karolinska Institute in August 2006. We update and give an overview of the expansion of the main families of GPCRs; Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin (GRAFS) in perspective of fully sequenced genomes. We look into the most recent findings including the work that has been carried out on the spotted green puffer fish (Tetraodon nigroviridis), mouse (Mus musculus), chicken (Gallus gallus), slime mold (Dictyostelium discoideum) and the plant pathogenic fungus Magnaporthe grisea. We use examples from our recent work on chicken GPCRs to highlight the importance of detailed assembly and curation of sequences and how that can affect percentage similarity and phylogeny. ESTs can give valuable information about expression patterns. GPCRs have comparatively low numbers of EST suggesting that GPCRs are in generally expressed in lower amount than other genes. We discuss similarities in the evolution of the trace amine associated receptors with other sensory receptors.
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Affiliation(s)
- H B Schiöth
- Department of Neuroscience, Uppsala University, Uppsala, Sweden.
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Lagerström MC, Hellström AR, Gloriam DE, Larsson TP, Schiöth HB, Fredriksson R. The G protein-coupled receptor subset of the chicken genome. PLoS Comput Biol 2007; 2:e54. [PMID: 16741557 PMCID: PMC1472694 DOI: 10.1371/journal.pcbi.0020054] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 04/06/2006] [Indexed: 11/23/2022] Open
Abstract
G protein–coupled receptors (GPCRs) are one of the largest families of proteins, and here we scan the recently sequenced chicken genome for GPCRs. We use a homology-based approach, utilizing comparisons with all human GPCRs, to detect and verify chicken GPCRs from translated genomic alignments and Genscan predictions. We present 557 manually curated sequences for GPCRs from the chicken genome, of which 455 were previously not annotated. More than 60% of the chicken Genscan gene predictions with a human ortholog needed curation, which drastically changed the average percentage identity between the human–chicken orthologous pairs (from 56.3% to 72.9%). Of the non-olfactory chicken GPCRs, 79% had a one-to-one orthologous relationship to a human GPCR. The Frizzled, Secretin, and subgroups of the Rhodopsin families have high proportions of orthologous pairs, although the percentage of amino acid identity varies. Other groups show large differences, such as the Adhesion family and GPCRs that bind exogenous ligands. The chicken has only three bitter Taste 2 receptors, and it also lacks an ortholog to human TAS1R2 (one of three GPCRs in the human genome in the Taste 1 receptor family [TAS1R]), implying that the chicken's ability and mode of detecting both bitter and sweet taste may differ from the human's. The chicken genome contains at least 229 olfactory receptors, and the majority of these (218) originate from a chicken-specific expansion. To our knowledge, this dataset of chicken GPCRs is the largest curated dataset from a single gene family from a non-mammalian vertebrate. Both the updated human GPCR dataset, as well the chicken GPCR dataset, are available for download. Man and chicken are very different, but how is that difference related to our respective gene repertoire? The authors studied the family of G protein–coupled receptors (GPCRs), which in man contains about 791 proteins. These are found in the cell membrane, where they recognize substances, thereby functioning as mediators of signals across the cellular membrane. GPCRs respond to physiologically important substances such as hormones and neurotransmitters. In this paper, the publicly available genomic sequence from the domestic chicken is used to identify the entire repertoire of GPCRs in this species. The authors found 557 GPCRs and compared the chicken and human receptors; they concluded that out of the 328 chicken receptors that are not involved in olfaction, more than 250 have a corresponding human receptor. The majority of the differences between the chicken and man are within three groups of GPCRs—the receptors for olfaction, bitter taste, and the receptors involved in the immune system. The chicken GPCR sequences obtained here will be useful for identification of GPCRs in other species that are more distantly related to man, such as fish or insects. The domestic chicken represents the leading experimental model among the avian species and also serves as an important source of food worldwide.
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Affiliation(s)
| | | | - David E Gloriam
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | | | - Helgi B Schiöth
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Robert Fredriksson
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
- * To whom correspondence should be addressed. E-mail:
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Evolution of secretin family GPCR members in the metazoa. BMC Evol Biol 2006; 6:108. [PMID: 17166275 PMCID: PMC1764030 DOI: 10.1186/1471-2148-6-108] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Accepted: 12/13/2006] [Indexed: 11/10/2022] Open
Abstract
Background Comparative approaches using protostome and deuterostome data have greatly contributed to understanding gene function and organismal complexity. The family 2 G-protein coupled receptors (GPCRs) are one of the largest and best studied hormone and neuropeptide receptor families. They are suggested to have arisen from a single ancestral gene via duplication events. Despite the recent identification of receptor members in protostome and early deuterostome genomes, relatively little is known about their function or origin during metazoan divergence. In this study a comprehensive description of family 2 GPCR evolution is given based on in silico and expression analyses of the invertebrate receptor genes. Results Family 2 GPCR members were identified in the invertebrate genomes of the nematodes C. elegans and C. briggsae, the arthropods D. melanogaster and A. gambiae (mosquito) and in the tunicate C. intestinalis. This suggests that they are of ancient origin and have evolved through gene/genome duplication events. Sequence comparisons and phylogenetic analyses have demonstrated that the immediate gene environment, with regard to gene content, is conserved between the protostome and deuterostome receptor genomic regions. Also that the protostome genes are more like the deuterostome Corticotrophin Releasing Factor (CRF) and Calcitonin/Calcitonin Gene-Related Peptide (CAL/CGRP) receptors members than the other family 2 GPCR members. The evolution of family 2 GPCRs in deuterostomes is characterised by acquisition of new family members, with SCT (Secretin) receptors only present in tetrapods. Gene structure is characterised by an increase in intron number with organismal complexity with the exception of the vertebrate CAL/CGRP receptors. Conclusion The family 2 GPCR members provide a good example of gene duplication events occurring in tandem with increasing organismal complexity during metazoan evolution. The putative ancestral receptors are proposed to be more like the deuterostome CAL/CGRP and CRF receptors and this may be associated with their fundamental role in calcium regulation and the stress response, both of which are essential for survival.
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Affiliation(s)
- N Srinivasan
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560 012; India
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Metpally RPR, Sowdhamini R. Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors. BMC Genomics 2005; 6:106. [PMID: 16091152 PMCID: PMC1192796 DOI: 10.1186/1471-2164-6-106] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 08/10/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cell-membrane G-protein coupled receptors (GPCRs) are one of the largest known superfamilies and are the main focus of intense pharmaceutical research due to their key role in cell physiology and disease. A large number of putative GPCRs are 'orphans' with no identified natural ligands. The first step in understanding the function of orphan GPCRs is to identify their ligands. Phylogenetic clustering methods were used to elucidate the chemical nature of receptor ligands, which led to the identification of natural ligands for many orphan receptors. We have clustered human and Drosophila receptors with known ligands and orphans through cross genome phylogenetic analysis and hypothesized higher relationship of co-clustered members that would ease ligand identification, as related receptors share ligands with similar structure or class. RESULTS Cross-genome phylogenetic analyses were performed to identify eight major groups of GPCRs dividing them into 32 clusters of 371 human and 113 Drosophila proteins (excluding olfactory, taste and gustatory receptors) and reveal unexpected levels of evolutionary conservation across human and Drosophila GPCRs. We also observe that members of human chemokine receptors, involved in immune response, and most of nucleotide-lipid receptors (except opsins) do not have counterparts in Drosophila. Similarly, a group of Drosophila GPCRs (methuselah receptors), associated in aging, is not present in humans. CONCLUSION Our analysis suggests ligand class association to 52 unknown Drosophila receptors and 95 unknown human GPCRs. A higher level of phylogenetic organization was revealed in which clusters with common domain architecture or cellular localization or ligand structure or chemistry or a shared function are evident across human and Drosophila genomes. Such analyses will prove valuable for identifying the natural ligands of Drosophila and human orphan receptors that can lead to a better understanding of physiological and pathological roles of these receptors.
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Affiliation(s)
- Raghu Prasad Rao Metpally
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore 560065, INDIA
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore 560065, INDIA
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