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Yadav DK, Srivastava GP, Singh A, Singh M, Yadav N, Tuteja N. Proteome-wide analysis reveals G protein-coupled receptor-like proteins in rice ( Oryza sativa). PLANT SIGNALING & BEHAVIOR 2024; 19:2365572. [PMID: 38904257 PMCID: PMC11195488 DOI: 10.1080/15592324.2024.2365572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of transmembrane proteins in metazoans that mediate the regulation of various physiological responses to discrete ligands through heterotrimeric G protein subunits. The existence of GPCRs in plant is contentious, but their comparable crucial role in various signaling pathways necessitates the identification of novel remote GPCR-like proteins that essentially interact with the plant G protein α subunit and facilitate the transduction of various stimuli. In this study, we identified three putative GPCR-like proteins (OsGPCRLPs) (LOC_Os06g09930.1, LOC_Os04g36630.1, and LOC_Os01g54784.1) in the rice proteome using a stringent bioinformatics workflow. The identified OsGPCRLPs exhibited a canonical GPCR 'type I' 7TM topology, patterns, and biologically significant sites for membrane anchorage and desensitization. Cluster-based interactome mapping revealed that the identified proteins interact with the G protein α subunit which is a characteristic feature of GPCRs. Computational results showing the interaction of identified GPCR-like proteins with G protein α subunit and its further validation by the membrane yeast-two-hybrid assay strongly suggest the presence of GPCR-like 7TM proteins in the rice proteome. The absence of a regulator of G protein signaling (RGS) box in the C- terminal domain, and the presence of signature motifs of canonical GPCR in the identified OsGPCRLPs strongly suggest that the rice proteome contains GPCR-like proteins that might be involved in signal transduction.
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Affiliation(s)
- Dinesh K. Yadav
- Plant Molecular Biology and Genetic Engineering Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Gyan Prakash Srivastava
- Plant Molecular Biology and Genetic Engineering Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Ananya Singh
- Plant Molecular Biology and Genetic Engineering Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Madhavi Singh
- Plant Molecular Biology and Genetic Engineering Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Neelam Yadav
- Plant Molecular Biology and Genetic Engineering Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Narendra Tuteja
- Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Kundu A, Jaiswal N, Rao U, Somvanshi VS. Stringent in-silico identification of putative G-protein-coupled receptors (GPCRs) of the entomopathogenic nematode Heterorhabditis bacteriophora. J Nematol 2023; 55:20230038. [PMID: 38026552 PMCID: PMC10670001 DOI: 10.2478/jofnem-2023-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Indexed: 12/01/2023] Open
Abstract
The infective juveniles (IJs) of entomopathogenic nematode (EPN) Heterorhabditis bacteriophora find and infect their host insects in heterogeneous soil ecosystems by sensing a universal host cue (CO2) or insect/plant-derived odorants, which bind to various sensory receptors, including G protein-coupled receptors (GPCRs). Nematode chemosensory GPCRs (NemChRs) bind to a diverse set of ligands, including odor molecules. However, there is a lack of information on the NemChRs in EPNs. Here we identified 21 GPCRs in the H. bacteriophora genome sequence in a triphasic manner, combining various transmembrane detectors and GPCR predictors based on different algorithms, and considering inherent properties of GPCRs. The pipeline was validated by reciprocal BLAST, InterProscan, GPCR-CA, and NCBI CDD search. Functional classification of predicted GPCRs using Pfam revealed the presence of four NemChRs. Additionally, GPCRs were classified into various families based on the reciprocal BLAST approach into a frizzled type, a secretin type, and 19 rhodopsin types of GPCRs. Gi/o is the most abundant kind of G-protein, having a coupling specificity to all the fetched GPCRs. As the 21 GPCRs identified are expected to play a crucial role in the host-seeking behavior, these might be targeted to develop novel insect-pest management strategies by tweaking EPN IJ behavior, or to design novel anthelminthic drugs. Our new and stringent GPCR detection pipeline may also be used to identify GPCRs from the genome sequence of other organisms.
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Affiliation(s)
- Artha Kundu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi-12, India
| | - Nisha Jaiswal
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi-12, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi-12, India
| | - Vishal Singh Somvanshi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi-12, India
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3
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Characterization of a new type of neuronal 5-HT G- protein coupled receptor in the cestode nervous system. PLoS One 2021; 16:e0259104. [PMID: 34762657 PMCID: PMC8584985 DOI: 10.1371/journal.pone.0259104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
Cestodes are platyhelminth parasites with a wide range of hosts that cause neglected diseases. Neurotransmitter signaling is of critical importance for these parasites which lack circulatory, respiratory and digestive systems. For example, serotonin (5-HT) and serotonergic G-protein coupled receptors (5-HT GPCRs) play major roles in cestode motility, development and reproduction. In previous work, we deorphanized a group of 5-HT7 type GPCRs from cestodes. However, little is known about another type of 5-HT GPCR, the 5-HT1 clade, which has been studied in several invertebrate phyla but not in platyhelminthes. Three putative 5-HT GPCRs from Echinococcus canadensis, Mesocestoides vogae (syn. M. corti) and Hymenolepis microstoma were cloned, sequenced and bioinformatically analyzed. Evidence grouped these new sequences within the 5-HT1 clade of GPCRs but differences in highly conserved GPCR motifs were observed. Transcriptomic analysis, heterologous expression and immunolocalization studies were performed to characterize the E. canadensis receptor, called Eca-5-HT1a. Functional heterologous expression studies showed that Eca-5-HT1a is highly specific for serotonin. 5-Methoxytryptamine and α-methylserotonin, both known 5-HT GPCR agonists, give stimulatory responses whereas methysergide, a known 5-HT GPCR ligand, give an antagonist response in Eca-5-HT1a. Mutants obtained by the substitution of key predicted residues resulted in severe impairment of receptor activity, confirming that indeed, these residues have important roles in receptor function. Immunolocalization studies on the protoscolex stage from E. canadensis, showed that Eca-5-HT1a is localized in branched fibers which correspond to the nervous system of the parasite. The patterns of immunoreactive fibers for Eca-5-HT1a and for serotonin were intimately intertwined but not identical, suggesting that they are two separate groups of fibers. These data provide the first functional, pharmacological and localization report of a serotonergic receptor that putatively belongs to the 5-HT1 type of GPCRs in cestodes. The serotonergic GPCR characterized here may represent a new target for antiparasitic intervention.
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Sajadi F, Paluzzi JPV. Hormonal regulation and functional role of the "renal" tubules in the disease vector, Aedes aegypti. VITAMINS AND HORMONES 2021; 117:189-225. [PMID: 34420581 DOI: 10.1016/bs.vh.2021.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Aedes aegypti mosquito is a vector responsible for transmitting various arboviruses including dengue and yellow fever. Their ability to regulate the ionic and water composition of their hemolymph is a major physiological phenomenon, allowing the mosquito to adapt to a range of ecological niches. Hematophagus insects, including the female A. aegypti, face the challenge of excess salt and water intake after a blood meal. Post-prandial diuresis is under rigorous control by neuroendocrine factors, acting on the Malpighian "renal" tubules (MTs), to regulate primary urine production. The MTs are made up of two cell types; mitochondria-rich principal cells, which facilitate active transport of Na+ and K+ cations across the membrane, and thin stellate cells, which allows for transepithelial Cl- secretion. The active driving force responsible for ion transport is the apical V-type H+ ATPase, which creates a proton gradient allowing for Na+ and/or K+ cation exchange through cation/H+ antiporters. Additionally, the basolaterally localized Na+-K+-2Cl- cotransporter (NKCC) is responsible for the transport of these ions from the hemolymph into the principal cells. Numerous studies have examined hormonal regulation of the mosquito MTs and identified several diuretics including serotonin (5HT), a calcitonin-related diuretic hormone 31 (DH31), a corticotropin-related factor like diuretic peptide (DH44), a kinin-related diuretic peptide, as well as anti-diuretic factors including CAPA peptides, all of which are known to regulate fluid and ion transport by the MTs. This review therefore focuses on the control of ionic homeostasis in A. aegypti mosquitoes, emphasizing the importance of the MTs, the channels and transporters involved in maintaining hydromineral balance, and the neuroendocrine regulation of both diuresis and anti-diuresis.
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Affiliation(s)
- Farwa Sajadi
- Department of Biology, York University, Toronto, ON, Canada
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5
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Calderón-Zamora L, Canizalez-Román A, León-Sicairos N, Aguilera-Mendez A, Huang F, Hong E, Villafaña S. Changes in expression of orphan receptors GPR99 and GPR107 during the development and establishment of hypertension in spontaneously hypertensive rats. J Recept Signal Transduct Res 2020; 41:558-565. [PMID: 33121311 DOI: 10.1080/10799893.2020.1835959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Hypertension is a disease, which in spite of existing treatments continues to have high morbidity and mortality, which suggests that there are other mechanisms involved in this pathology. In this sense, the orphan receptors are G protein-coupled receptor associated with various pathologies such as GPR99 which has been linked to mice develop left ventricular hypertrophy induced by blood pressure overload while GPR107 with patients with idiopathic pulmonary arterial hypertension. For this reason, the aim of this work was to study if the expression of the orphan receptors GPR99 and GPR107 are modified by arterial hypertension. Male SHR and WKY rats of 6-8 and 10-12 weeks old were used. The weight, systolic blood pressure and heart rate were measured, as well as the mRNA of the receptors GPR99 and GPR107 in the aorta, kidney, heart and brain by RT-PCR, also was realized an in silico analysis to predict which G protein could be coupled the orphan receptor GPR107. Our results showed that receptors GPR99 and GPR107 are expressed in the analyzed tissues and their expression profile tends to change at different ages and with the development of hypertension, for the other hand, the bioinformatics analysis for GPR107 showed that is coupled to Gi protein. Therefore, we do not rule out that GPR99 and GPR107 could be involved in the pathophysiology of hypertension and could be used as targets therapeutic in hypertension.
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Affiliation(s)
| | | | - Nidia León-Sicairos
- CIASaP, Facultad de Medicina, Universidad Autónoma de Sinaloa, Culiacán, México
| | - Asdrubal Aguilera-Mendez
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás Hidalgo, Morelia, México
| | - Fengyang Huang
- Laboratorio de Investigación de Farmacología, Hospital Infantil de México Federico Gómez (HIMFG), Ciudad de México, México
| | | | - Santiago Villafaña
- Laboratorio de Farmacología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
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6
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Antonakoudis A, Barbosa R, Kotidis P, Kontoravdi C. The era of big data: Genome-scale modelling meets machine learning. Comput Struct Biotechnol J 2020; 18:3287-3300. [PMID: 33240470 PMCID: PMC7663219 DOI: 10.1016/j.csbj.2020.10.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
With omics data being generated at an unprecedented rate, genome-scale modelling has become pivotal in its organisation and analysis. However, machine learning methods have been gaining ground in cases where knowledge is insufficient to represent the mechanisms underlying such data or as a means for data curation prior to attempting mechanistic modelling. We discuss the latest advances in genome-scale modelling and the development of optimisation algorithms for network and error reduction, intracellular constraining and applications to strain design. We further review applications of supervised and unsupervised machine learning methods to omics datasets from microbial and mammalian cell systems and present efforts to harness the potential of both modelling approaches through hybrid modelling.
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Affiliation(s)
| | | | | | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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Singh G, Inoue A, Gutkind JS, Russell RB, Raimondi F. PRECOG: PREdicting COupling probabilities of G-protein coupled receptors. Nucleic Acids Res 2020; 47:W395-W401. [PMID: 31143927 PMCID: PMC6602504 DOI: 10.1093/nar/gkz392] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/13/2019] [Accepted: 05/01/2019] [Indexed: 01/08/2023] Open
Abstract
G-protein coupled receptors (GPCRs) control multiple physiological states by transducing a multitude of extracellular stimuli into the cell via coupling to intra-cellular heterotrimeric G-proteins. Deciphering which G-proteins couple to each of the hundreds of GPCRs present in a typical eukaryotic organism is therefore critical to understand signalling. Here, we present PRECOG (precog.russelllab.org): a web-server for predicting GPCR coupling, which allows users to: (i) predict coupling probabilities for GPCRs to individual G-proteins instead of subfamilies; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features.
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Affiliation(s)
- Gurdeep Singh
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert B Russell
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Francesco Raimondi
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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8
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Inoue A, Raimondi F, Kadji FMN, Singh G, Kishi T, Uwamizu A, Ono Y, Shinjo Y, Ishida S, Arang N, Kawakami K, Gutkind JS, Aoki J, Russell RB. Illuminating G-Protein-Coupling Selectivity of GPCRs. Cell 2019; 177:1933-1947.e25. [PMID: 31160049 DOI: 10.1016/j.cell.2019.04.044] [Citation(s) in RCA: 325] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/28/2019] [Accepted: 04/25/2019] [Indexed: 12/20/2022]
Abstract
Heterotrimetic G proteins consist of four subfamilies (Gs, Gi/o, Gq/11, and G12/13) that mediate signaling via G-protein-coupled receptors (GPCRs), principally by receptors binding Gα C termini. G-protein-coupling profiles govern GPCR-induced cellular responses, yet receptor sequence selectivity determinants remain elusive. Here, we systematically quantified ligand-induced interactions between 148 GPCRs and all 11 unique Gα subunit C termini. For each receptor, we probed chimeric Gα subunit activation via a transforming growth factor-α (TGF-α) shedding response in HEK293 cells lacking endogenous Gq/11 and G12/13 proteins, and complemented G-protein-coupling profiles through a NanoBiT-G-protein dissociation assay. Interrogation of the dataset identified sequence-based coupling specificity features, inside and outside the transmembrane domain, which we used to develop a coupling predictor that outperforms previous methods. We used the predictor to engineer designer GPCRs selectively coupled to G12. This dataset of fine-tuned signaling mechanisms for diverse GPCRs is a valuable resource for research in GPCR signaling.
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Affiliation(s)
- Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan; Advanced Research & Development Programs for Medical Innovation (PRIME), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo 100-0004, Japan; Advanced Research & Development Programs for Medical Innovation (LEAP), AMED, Chiyoda-ku, Tokyo 100-0004, Japan.
| | - Francesco Raimondi
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
| | | | - Gurdeep Singh
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Takayuki Kishi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Akiharu Uwamizu
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Yuki Ono
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Yuji Shinjo
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Satoru Ishida
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Nadia Arang
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan; Advanced Research & Development Programs for Medical Innovation (LEAP), AMED, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Robert B Russell
- CellNetworks, Bioquant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
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Calderón-Zamora L, Ruiz-Hernandez A, Romero-Nava R, León-Sicairos N, Canizalez-Román A, Hong E, Huang F, Villafaña S. Possible involvement of orphan receptors GPR88 and GPR124 in the development of hypertension in spontaneously hypertensive rat. Clin Exp Hypertens 2017; 39:513-519. [PMID: 28678544 DOI: 10.1080/10641963.2016.1273949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hypertension (HBP) is a chronic disease characterized by increased blood pressure, which despite several treatments maintains a high morbi-mortality, which suggests that there are other mechanisms involved in this pathology, within which the orphan receptors could be candidates for the treatment of the HBP; these receptors are called orphan receptors because their ligand is unknown. These receptors have been suggested to participate in some pathologies because they are associated with various systems such as GPR88, which has been linked to the dopaminergic system, and GPR124 with angiogenesis, suggesting that these receptors could take part in HBP. Hence, the aim of this work was to study the expression of orphan receptors GPR88 and GPR124 in various tissues of normotensive and hypertensive rats. We used Wistar Kyoto (WKY) and spontaneously hypertensive rat (SHR) of 6-8 and 10-12 weeks of age and we determined systolic blood pressure (SBP), heart rate, as well as mRNA of GPR88 and GPR124 receptors by reverse transcription polymerase chain reaction (RT-PCR) in the aorta, heart, kidney, and brain. Our results showed that GPR88 and GPR124 were expressed in all analyzed tissues, but their expression is dependent on the age and development of HBP because their expression tends to be modified as HBP is established. Therefore, we conclude that GPR88 and GPR124 receptors may be involved in the development or maintenance of high blood pressure.
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Affiliation(s)
- L Calderón-Zamora
- a Laboratorio de Señalización Intracelular, Sección de Posgrado , Escuela Superior de Medicina del Instituto Politécnico Nacional Ciudad de México , México
| | - A Ruiz-Hernandez
- a Laboratorio de Señalización Intracelular, Sección de Posgrado , Escuela Superior de Medicina del Instituto Politécnico Nacional Ciudad de México , México
| | - R Romero-Nava
- a Laboratorio de Señalización Intracelular, Sección de Posgrado , Escuela Superior de Medicina del Instituto Politécnico Nacional Ciudad de México , México
| | - N León-Sicairos
- b CIASaP, Facultad de Medicina , Universidad Autónoma de Sinaloa Culiacán , Sinaloa , México
| | - A Canizalez-Román
- b CIASaP, Facultad de Medicina , Universidad Autónoma de Sinaloa Culiacán , Sinaloa , México
| | - E Hong
- c Departamento de Farmacobiología , Centro de Investigación y de Estudios Avanzados , Ciudad de México , México
| | - F Huang
- d Departamento de Farmacología y Toxicología , Hospital Infantil de México Federico Gómez (HIMFG) , Ciudad de México , México
| | - S Villafaña
- a Laboratorio de Señalización Intracelular, Sección de Posgrado , Escuela Superior de Medicina del Instituto Politécnico Nacional Ciudad de México , México
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Rourke JL, Dranse HJ, Sinal CJ. CMKLR1 and GPR1 mediate chemerin signaling through the RhoA/ROCK pathway. Mol Cell Endocrinol 2015; 417:36-51. [PMID: 26363224 DOI: 10.1016/j.mce.2015.09.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/31/2015] [Accepted: 09/01/2015] [Indexed: 12/14/2022]
Abstract
Chemerin is an adipose-derived hormone that regulates immunity and energy homesotasis. To date, all known chemerin functions have been attributed to activation of the G protein-coupled receptor chemokine-like receptor-1 (CMKLR1). Chemerin is also the only known ligand for a second receptor, G protein-coupled receptor-1 (GPR1), whose signaling and function remains unknown. This study investigated the in vitro signal transduction mechanisms of CMKLR1 and GPR1 using a panel of luciferase-reporters and pathway-specific inhibitors. Herein we report the novel finding that chemerin signals through a RhoA and rho-associated protein kinase (ROCK)-dependent pathway for activation of the transcriptional regulator serum-response factor (SRF). Despite similarities in RhoA/ROCK, Gαi/o, and MAPK signaling, we also demonstrate species-specific and receptor-dependent variations in GPR1 and CMKLR1 signaling and expression of the SRF target genes EGR1, FOS and VCL. Moreover, we demonstrate that signaling through p38, Gαi/o, RhoA, and ROCK is required for chemerin-mediated chemotaxis of L1.2 lymphocytes and AGS gastric adenocarcinoma cells. These results provide, to our knowledge, the first empirical evidence that GPR1 is a functional chemerin receptor and identify RhoA/SRF as a novel chemerin-signaling axis via both CMKLR1 and GPR1.
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Affiliation(s)
- Jillian L Rourke
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Helen J Dranse
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
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11
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Gu Q, Ding YS, Zhang TL. An ensemble classifier based prediction of G-protein-coupled receptor classes in low homology. Neurocomputing 2015. [DOI: 10.1016/j.neucom.2014.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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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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13
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Siehler S. G12/13-dependent signaling of G-protein-coupled receptors: disease context and impact on drug discovery. Expert Opin Drug Discov 2013; 2:1591-604. [PMID: 23488903 DOI: 10.1517/17460441.2.12.1591] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
G-protein-coupled receptors (GPCRs) transmit extracellular signals across the plasma membrane via intracellular activation of heterotrimeric G proteins. The signal transduction pathways of Gs, Gi and Gq protein families are widely studied, whereas signaling properties of G12 proteins are only emerging. Many GPCRs were found to couple to G12/13 proteins in addition to coupling to one or more other types of G proteins. G12/13 proteins couple GPCRs to activation of the small monomeric GTPase RhoA. Activation of RhoA modulates various downstream effector systems relevant to diseases such as hypertension, artherosclerosis, asthma and cancer. GPCR screening assays exist for Gs-, Gi- and Gq-linked pathways, whereas a drug-screening assay for the G12-Rho pathway was developed only recently. The review gives an overview of the present understanding of the G12/13-related biology of GPCRs.
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Affiliation(s)
- Sandra Siehler
- Novartis Institutes for BioMedical Research Basel, Center for Proteomic Chemistry, Novartis Pharma AG, WSJ-88.2.05, 4002 Basel, Switzerland +41 61 324 8946 ; +41 61 324 2870 ;
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14
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Latek D, Pasznik P, Carlomagno T, Filipek S. Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison. PLoS One 2013; 8:e56742. [PMID: 23468878 PMCID: PMC3585245 DOI: 10.1371/journal.pone.0056742] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/14/2013] [Indexed: 11/19/2022] Open
Abstract
UNLABELLED G-protein coupled receptors (GPCRs) are targets of nearly one third of the drugs at the current pharmaceutical market. Despite their importance in many cellular processes the crystal structures are available for less than 20 unique GPCRs of the Rhodopsin-like class. Fortunately, even though involved in different signaling cascades, this large group of membrane proteins has preserved a uniform structure comprising seven transmembrane helices that allows quite reliable comparative modeling. Nevertheless, low sequence similarity between the GPCR family members is still a serious obstacle not only in template selection but also in providing theoretical models of acceptable quality. An additional level of difficulty is the prediction of kinks and bulges in transmembrane helices. Usage of multiple templates and generation of alignments based on sequence profiles may increase the rate of success in difficult cases of comparative modeling in which the sequence similarity between GPCRs is exceptionally low. Here, we present GPCRM, a novel method for fast and accurate generation of GPCR models using averaging of multiple template structures and profile-profile comparison. In particular, GPCRM is the first GPCR structure predictor incorporating two distinct loop modeling techniques: Modeller and Rosetta together with the filtering of models based on the Z-coordinate. We tested our approach on all unique GPCR structures determined to date and report its performance in comparison with other computational methods targeting the Rhodopsin-like class. We also provide a database of precomputed GPCR models of the human receptors from that class. AVAILABILITY GPCRM SERVER AND DATABASE: http://gpcrm.biomodellab.eu.
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Affiliation(s)
- Dorota Latek
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- * E-mail: (DL); (SF)
| | - Pawel Pasznik
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Teresa Carlomagno
- EMBL, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Slawomir Filipek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- * E-mail: (DL); (SF)
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15
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Ku GM, Pappalardo Z, Luo CC, German MS, McManus MT. An siRNA screen in pancreatic beta cells reveals a role for Gpr27 in insulin production. PLoS Genet 2012; 8:e1002449. [PMID: 22253604 PMCID: PMC3257298 DOI: 10.1371/journal.pgen.1002449] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 11/18/2011] [Indexed: 11/18/2022] Open
Abstract
The prevalence of type 2 diabetes in the United States is projected to double or triple by 2050. We reasoned that the genes that modulate insulin production might be new targets for diabetes therapeutics. Therefore, we developed an siRNA screening system to identify genes important for the activity of the insulin promoter in beta cells. We created a subclone of the MIN6 mouse pancreatic beta cell line that expresses destabilized GFP under the control of a 362 base pair fragment of the human insulin promoter and the mCherry red fluorescent protein under the control of the constitutively active rous sarcoma virus promoter. The ratio of the GFP to mCherry fluorescence of a cell indicates its insulin promoter activity. As G protein coupled receptors (GPCRs) have emerged as novel targets for diabetes therapies, we used this cell line to screen an siRNA library targeting all known mouse GPCRs. We identified several known GPCR regulators of insulin secretion as regulators of the insulin promoter. One of the top positive regulators was Gpr27, an orphan GPCR with no known role in beta cell function. We show that knockdown of Gpr27 reduces endogenous mouse insulin promoter activity and glucose stimulated insulin secretion. Furthermore, we show that Pdx1 is important for Gpr27's effect on the insulin promoter and insulin secretion. Finally, the over-expression of Gpr27 in 293T cells increases inositol phosphate levels, while knockdown of Gpr27 in MIN6 cells reduces inositol phosphate levels, suggesting this orphan GPCR might couple to Gq/11. In summary, we demonstrate a MIN6-based siRNA screening system that allows rapid identification of novel positive and negative regulators of the insulin promoter. Using this system, we identify Gpr27 as a positive regulator of insulin production. Pancreatic beta cells are the only physiologic source of insulin. When these cells are destroyed in type 1 diabetics, there is uncontrolled hyperglycemia from complete insulin deficiency. In type 2 diabetes, these same cells fail to increase insulin secretion to compensate for peripheral insulin resistance leading to relative insulin deficiency. We constructed a novel screening system to find new regulators of insulin production in this critical cell type. Here, we describe a screen of the G protein coupled receptors (GPCRs) and show a role for orphan GPCR, Gpr27, in insulin promoter activity and insulin secretion. We propose that Gpr27 is a novel target for diabetes therapeutics.
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Affiliation(s)
- Gregory M. Ku
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Zachary Pappalardo
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
| | - Chun Chieh Luo
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
| | - Michael S. German
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Michael T. McManus
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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16
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Classification of G proteins and prediction of GPCRs-G proteins coupling specificity using continuous wavelet transform and information theory. Amino Acids 2011; 43:793-804. [PMID: 22086210 DOI: 10.1007/s00726-011-1133-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 10/20/2011] [Indexed: 10/15/2022]
Abstract
The coupling between G protein-coupled receptors (GPCRs) and guanine nucleotide-binding proteins (G proteins) regulates various signal transductions from extracellular space into the cell. However, the coupling mechanism between GPCRs and G proteins is still unknown, and experimental determination of their coupling specificity and function is both expensive and time consuming. Therefore, it is significant to develop a theoretical method to predict the coupling specificity between GPCRs and G proteins as well as their function using their primary sequences. In this study, a novel four-layer predictor (GPCRsG_CWTIT) based on support vector machine (SVM), continuous wavelet transform (CWT) and information theory (IT) is developed to classify G proteins and predict the coupling specificity between GPCRs and G proteins. SVM is used for construction of models. CWT and IT are used to characterize the primary structure of protein. Performance of GPCRsG_CWTIT is evaluated with cross-validation test on various working dataset. The overall accuracy of the G proteins at the levels of class and family is 98.23 and 85.42%, respectively. The accuracy of the coupling specificity prediction varies from 74.60 to 94.30%. These results indicate that the proposed predictor is an effective and feasible tool to predict the coupling specificity between GPCRs and G proteins as well as their functions using only the protein full sequence. The establishment of such an accurate prediction method will facilitate drug discovery by improving the ability to identify and predict protein-protein interactions. GPCRsG_CWTIT and dataset can be acquired freely on request from the authors.
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17
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Abstract
Apelin is a newly discovered peptide hormone that has recently been linked to insulin resistance and obesity. Data collected from both the clinical and basic research settings show that apelin: (i) is correlated with the states of insulin resistance and obesity; (ii) stimulates glucose utilization; (iii) decreases insulin secretion; and (iv) negatively regulates catecholamine-mediated lipolysis. These and other lines of evidence demonstrate that apelin may be a potentially viable candidate in the search for treatments for Type 2 diabetes and the insulin resistance (metabolic syndrome). The present review summarizes the literature on the regulation by apelin of glucose and lipid metabolism and the signaling pathways involved.
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Affiliation(s)
- Shiming Xu
- Department of Medicine/Cardiovascular Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
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18
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Yellow submarine of the Wnt/Frizzled signaling: submerging from the G protein harbor to the targets. Biochem Pharmacol 2011; 82:1311-9. [PMID: 21689640 DOI: 10.1016/j.bcp.2011.06.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 05/30/2011] [Accepted: 06/02/2011] [Indexed: 10/18/2022]
Abstract
The Wnt/Frizzled signaling pathway plays multiple functions in animal development and, when deregulated, in human disease. The G-protein coupled receptor (GPCR) Frizzled and its cognate heterotrimeric Gi/o proteins initiate the intracellular signaling cascades resulting in cell fate determination and polarization. In this review, we summarize the knowledge on the ligand recognition, biochemistry, modifications and interacting partners of the Frizzled proteins viewed as GPCRs. We also discuss the effectors of the heterotrimeric Go protein in Frizzled signaling. One group of these effectors is represented by small GTPases of the Rab family, which amplify the initial Wnt/Frizzled signal. Another effector is the negative regulator of Wnt signaling Axin, which becomes deactivated in response to Go action. The discovery of the GPCR properties of Frizzled receptors not only provides mechanistic understanding to their signaling pathways, but also paves new avenues for the drug discovery efforts.
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19
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DeMars G, Fanelli F, Puett D. The extreme C-terminal region of Gαs differentially couples to the luteinizing hormone and beta2-adrenergic receptors. Mol Endocrinol 2011; 25:1416-30. [PMID: 21622536 DOI: 10.1210/me.2011-0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The mechanisms of G protein coupling to G protein-coupled receptors (GPCR) share general characteristics but may exhibit specific interactions unique for each GPCR/G protein partnership. The extreme C terminus (CT) of G protein α-subunits has been shown to be important for association with GPCR. Hypothesizing that the extreme CT of Gα(s) is an essential component of the molecular landscape of the GPCR, human LH receptor (LHR), and β(2)-adrenergic receptor (β(2)-AR), a model cell system was created for the expression and manipulation of Gα(s) subunits in LHR(+) s49 ck cells that lack endogenous Gα(s). On the basis of studies involving truncations, mutations, and chain extensions of Gα(s), the CT was found to be necessary for LHR and β(2)-AR signaling. Some general similarities were found for the responses of the two receptors, but significant differences were also noted. Computational modeling was performed with a combination of comparative modeling, molecular dynamics simulations, and rigid body docking. The resulting models, focused on the Gα(s) CT, are supported by the experimental observations and are characterized by the interaction of the four extreme CT amino acid residues of Gα(s) with residues in LHR and β(2)-AR helix 3, (including R of the DRY motif), helix 6, and intracellular loop 2. This portion of Gα(s) recognizes the same regions of the two GPCR, although with differences in the details of selected interactions. The predicted longer cytosolic extensions of helices 5 and 6 of β(2)-AR are expected to contribute significantly to differences in Gα(s) recognition by the two receptors.
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Affiliation(s)
- Geneva DeMars
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229, USA
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20
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Yue P, Jin H, Xu S, Aillaud M, Deng AC, Azuma J, Kundu RK, Reaven GM, Quertermous T, Tsao PS. Apelin decreases lipolysis via G(q), G(i), and AMPK-Dependent Mechanisms. Endocrinology 2011; 152:59-68. [PMID: 21047945 PMCID: PMC3033059 DOI: 10.1210/en.2010-0576] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The release of free fatty acids (FFAs) from adipocytes (i.e. lipolysis) is increased in obesity and is a contributory factor to the development of insulin resistance. A recently identified adipokine, apelin, is up-regulated in states of obesity. Although apelin is secreted by adipocytes, its functions in them remain largely unknown. To determine whether apelin affects lipolysis, FFA, glycerol, and leptin levels, as well as abdominal adiposity, were measured at baseline and after reintroduction of exogenous apelin in apelin-null mice. To examine apelin's effects in vitro, isoproterenol-induced FFA/glycerol release, and hormone-sensitive lipase (HSL) and acetyl CoA carboxylase phosphorylation were investigated in 3T3-L1 cells and isolated wild-type adipocytes. Serum FFA, glycerol, and leptin concentrations, as well as abdominal adiposity, were significantly increased in apelin-null vs. wild-type mice; these changes were ameliorated in response to exogenous apelin. Apelin also reduced isoproterenol-induced FFA release in adipocytes isolated from wild-type but not APJ-null mice. In 3T3-L1 cells and isolated adipocytes, apelin attenuated isoproterenol-induced FFA/glycerol release. Apelin's inhibition was reversed by pertussis toxin, the G(q) inhibitor glycoprotein antagonist 2A, and the AMP-activated protein kinase inhibitors compound C and dorsomorphin. Apelin increased HSL phosphorylation at Ser-565 and also abrogated isoproterenol-induced HSL phosphorylation at Ser-563. Notably, apelin increased acetyl CoA carboxylase phosphorylation, suggesting AMPK activation. In conclusion, apelin negatively regulates lipolysis. Its actions may be mediated by pathways involving G(q), G(i), and AMP-activated protein kinase.
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Affiliation(s)
- Patrick Yue
- Department of Medicine/Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California 94350, USA
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21
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Krsmanovic LZ, Hu L, Leung PK, Feng H, Catt KJ. The hypothalamic GnRH pulse generator: multiple regulatory mechanisms. Trends Endocrinol Metab 2009; 20:402-8. [PMID: 19740674 PMCID: PMC2769988 DOI: 10.1016/j.tem.2009.05.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 05/04/2009] [Accepted: 05/05/2009] [Indexed: 12/30/2022]
Abstract
Pulsatile secretion of gonadotropin-releasing hormone (GnRH) release is an intrinsic property of hypothalamic GnRH neurons. Pulse generation has been attributed to multiple specific mechanisms, including spontaneous electrical activity of GnRH neurons, calcium and cAMP signaling, a GnRH receptor autocrine regulatory component, a GnRH concentration-dependent switch in GnRH receptor (GnRH-R) coupling to specific G proteins, the expression of G protein-coupled receptors (GPCRs) and steroid receptors, and homologous and heterologous interactions between cell membrane receptors expressed in GnRH neurons. The coexistence of multiple regulatory mechanisms for pulsatile GnRH secretion provides a high degree of redundancy in maintaining this crucial component of the mammalian reproductive process. These studies provide insights into the basic cellular and molecular mechanisms involved in GnRH neuronal function.
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Affiliation(s)
- Lazar Z Krsmanovic
- Section on Hormonal Regulation, Program on Developmental Endocrinology and Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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22
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Park HC, Eo HS, Kim W. A computational approach for the classification of protein tyrosine kinases. Mol Cells 2009; 28:195-200. [PMID: 19756393 DOI: 10.1007/s10059-009-0122-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 07/20/2009] [Indexed: 10/20/2022] Open
Abstract
Protein tyrosine kinases (PTKs) play a central role in the modulation of a wide variety of cellular events such as differentiation, proliferation and metabolism, and their unregulated activation can lead to various diseases including cancer and diabetes. PTKs represent a diverse family of proteins including both receptor tyrosine kinases (RTKs) and non-receptor tyrosine kinases (NRTKs). Due to the diversity and important cellular roles of PTKs, accurate classification methods are required to better understand and differentiate different PTKs. In addition, PTKs have become important targets for drugs, providing a further need to develop novel methods to accurately classify this set of important biological molecules. Here, we introduce a novel statistical model for the classification of PTKs that is based on their structural features. The approach allows for both the recognition of PTKs and the classification of RTKs into their subfamilies. This novel approach had an overall accuracy of 98.5% for the identification of PTKs, and 99.3% for the classification of RTKs.
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Affiliation(s)
- Hyun-Chul Park
- Program in Bioinformatics, Seoul National University, Korea
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23
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Abstract
G protein-coupled receptors (GPCRs) represent a large family of seven transmembrane receptors, which communicate extracellular signals into the cellular lumen. The human genome contains 720-800 GPCRs, and their diverse signal characteristics are determined by their specific tissue and subcellular expression profiles, as well as their coupling profile to the various G protein families (G(s), G(i), G(q), G(12)). The G protein coupling pattern links GPCR activation to the specific downstream effector pathways. G(12/13) signalling of GPCRs has been studied only recently in more detail, and involves activation of RhoGTPase nucleotide exchange factors (RhoGEFs). Four mammalian RhoGEFs regulated by G(12/13) proteins are known: p115-RhoGEF, PSD-95/Disc-large/ZO-1 homology-RhoGEF, leukemia-associated RhoGEF and lymphoid blast crisis-RhoGEF. These link GPCRs to activation of the small monomeric GTPase RhoA, and other downstream effectors. Misregulated G(12/13) signalling is involved in multiple pathophysiological conditions such as cancer, cardiovascular diseases, arterial and pulmonary hypertension, and bronchial asthma. Specific targeting of G(12/13) signalling-related diseases of GPCRs hence provides novel therapeutic approaches. Assays to quantitatively measure GPCR-mediated activation of G(12/13) are only emerging, and are required to understand the G(12/13)-linked pharmacology. The review gives an overview of G(12/13) signalling of GPCRs with a focus on RhoGEF proteins as the immediate mediators of G(12/13) activation.
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Affiliation(s)
- Sandra Siehler
- Novartis Institutes for BioMedical Research Basel, Center for Proteomic Chemistry, Novartis Pharma AG, Basel, Switzerland.
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24
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Leung T, Humbert JE, Stauffer AM, Giger KE, Chen H, Tsai HJ, Wang C, Mirshahi T, Robishaw JD. The orphan G protein-coupled receptor 161 is required for left-right patterning. Dev Biol 2008; 323:31-40. [PMID: 18755178 DOI: 10.1016/j.ydbio.2008.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 07/28/2008] [Accepted: 08/01/2008] [Indexed: 11/18/2022]
Abstract
Gpr161 (also known as RE2) is an orphan G protein-coupled receptor (GPCR) that is expressed during embryonic development in zebrafish. Determining its biological function has proven difficult due to lack of knowledge regarding its natural or synthetic ligands. Here, we show that targeted knockdown of gpr161 disrupts asymmetric gene expression in the lateral plate mesoderm, resulting in aberrant looping of the heart tube. This is associated with elevated Ca(2+) levels in cells lining the Kupffer's vesicle and normalization of Ca(2+) levels, by over-expression of ncx1 or pmca-RNA, is able to partially rescue the cardiac looping defect in gpr161 knockdown embryos. Taken together, these data support a model in which gpr161 plays an essential role in left-right (L-R) patterning by modulating Ca(2+) levels in the cells surrounding the Kupffer's vesicle.
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MESH Headings
- Amino Acid Sequence
- Animals
- Animals, Genetically Modified
- Body Patterning/genetics
- Body Patterning/physiology
- Calcium/metabolism
- Calcium Signaling
- Embryo, Nonmammalian/metabolism
- Embryo, Nonmammalian/physiology
- Gene Expression Regulation, Developmental
- In Situ Hybridization
- Models, Biological
- Molecular Sequence Data
- Oligonucleotides, Antisense/pharmacology
- Protein Structure, Tertiary
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Receptors, G-Protein-Coupled/physiology
- Sequence Homology, Amino Acid
- Zebrafish/embryology
- Zebrafish/genetics
- Zebrafish/metabolism
- Zebrafish Proteins/antagonists & inhibitors
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
- Zebrafish Proteins/physiology
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Affiliation(s)
- Tinchung Leung
- Weis Center for Research, Geisinger Clinic, Danville, PA 17822, USA.
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25
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Gookin TE, Kim J, Assmann SM. Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling. Genome Biol 2008; 9:R120. [PMID: 18671868 PMCID: PMC2530877 DOI: 10.1186/gb-2008-9-7-r120] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2008] [Revised: 04/19/2008] [Accepted: 07/31/2008] [Indexed: 11/10/2022] Open
Abstract
Computational prediction and in vivo protein coupling experiments identify candidate plant G-protein coupled receptors in Arabidopsis, rice and poplar. Background The classic paradigm of heterotrimeric G-protein signaling describes a heptahelical, membrane-spanning G-protein coupled receptor that physically interacts with an intracellular Gα subunit of the G-protein heterotrimer to transduce signals. G-protein coupled receptors comprise the largest protein superfamily in metazoa and are physiologically important as they sense highly diverse stimuli and play key roles in human disease. The heterotrimeric G-protein signaling mechanism is conserved across metazoa, and also readily identifiable in plants, but the low sequence conservation of G-protein coupled receptors hampers the identification of novel ones. Using diverse computational methods, we performed whole-proteome analyses of the three dominant model plant species, the herbaceous dicot Arabidopsis thaliana (mouse-eared cress), the monocot Oryza sativa (rice), and the woody dicot Populus trichocarpa (poplar), to identify plant protein sequences most likely to be GPCRs. Results Our stringent bioinformatic pipeline allowed the high confidence identification of candidate G-protein coupled receptors within the Arabidopsis, Oryza, and Populus proteomes. We extended these computational results through actual wet-bench experiments where we tested over half of our highest ranking Arabidopsis candidate G-protein coupled receptors for the ability to physically couple with GPA1, the sole Gα in Arabidopsis. We found that seven out of eight tested candidate G-protein coupled receptors do in fact interact with GPA1. We show through G-protein coupled receptor classification and molecular evolutionary analyses that both individual G-protein coupled receptor candidates and candidate G-protein coupled receptor families are conserved across plant species and that, in some cases, this conservation extends to metazoans. Conclusion Our computational and wet-bench results provide the first step toward understanding the diversity, conservation, and functional roles of plant candidate G-protein coupled receptors.
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Affiliation(s)
- Timothy E Gookin
- Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA.
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26
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Shimamura T, Hiraki K, Takahashi N, Hori T, Ago H, Masuda K, Takio K, Ishiguro M, Miyano M. Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region. J Biol Chem 2008; 283:17753-6. [PMID: 18463093 PMCID: PMC2440622 DOI: 10.1074/jbc.c800040200] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 04/15/2008] [Indexed: 01/26/2023] Open
Abstract
G-protein-coupled receptors play a key step in cellular signal transduction cascades by transducing various extracellular signals via G-proteins. Rhodopsin is a prototypical G-protein-coupled receptor involved in the retinal visual signaling cascade. We determined the structure of squid rhodopsin at 3.7A resolution, which transduces signals through the G(q) protein to the phosphoinositol cascade. The structure showed seven transmembrane helices and an amphipathic helix H8 has similar geometry to structures from bovine rhodopsin, coupling to G(t), and human beta(2)-adrenergic receptor, coupling to G(s). Notably, squid rhodopsin contains a well structured cytoplasmic region involved in the interaction with G-proteins, and this region is flexible or disordered in bovine rhodopsin and human beta(2)-adrenergic receptor. The transmembrane helices 5 and 6 are longer and extrude into the cytoplasm. The distal C-terminal tail contains a short hydrophilic alpha-helix CH after the palmitoylated cysteine residues. The residues in the distal C-terminal tail interact with the neighboring residues in the second cytoplasmic loop, the extruded transmembrane helices 5 and 6, and the short helix H8. Additionally, the Tyr-111, Asn-87, and Asn-185 residues are located within hydrogen-bonding distances from the nitrogen atom of the Schiff base.
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27
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Theodoropoulou MC, Bagos PG, Spyropoulos IC, Hamodrakas SJ. gpDB: a database of GPCRs, G-proteins, effectors and their interactions. ACTA ACUST UNITED AC 2008; 24:1471-2. [PMID: 18441001 DOI: 10.1093/bioinformatics/btn206] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
UNLABELLED gpDB is a publicly accessible, relational database, containing information about G-proteins, G-protein coupled receptors (GPCRs) and effectors, as well as information concerning known interactions between these molecules. The sequences are classified according to a hierarchy of different classes, families and subfamilies based on literature search. The main innovation besides the classification of G-proteins, GPCRs and effectors is the relational model of the database, describing the known coupling specificity of GPCRs to their respective alpha subunits of G-proteins, and also the specific interaction between G-proteins and their effectors, a unique feature not available in any other database. AVAILABILITY http://bioinformatics.biol.uoa.gr/gpDB CONTACT: shamodr@biol.uoa.gr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Margarita C Theodoropoulou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 157 01, Greece
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Jiang Z, Guan C, Zhou Y. Computational prediction of the coupling specificity of g protein-coupled receptors. Appl Biochem Biotechnol 2007; 141:109-18. [PMID: 17625269 DOI: 10.1007/s12010-007-9213-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 04/17/2006] [Accepted: 05/16/2006] [Indexed: 10/23/2022]
Abstract
G protein-coupled receptors (GPCRs) represent one of the most important categories of membrane proteins that play important roles in signaling pathways. GPCRs transduce the extracellular stimuli into intracellular second messengers via their coupling to specific class of heterotrimeric GTP-binding proteins (G proteins) and the subsequent regulation of a diverse variety of effectors. Understanding the coupling specificity of GPCRs is critical for further comprehending their function, and is of tremendous clinical significance because GPCRs are the most successful drug targets. This minireview addresses the computational approaches that have been created for the prediction of coupling specificity of GPCRs and highlights the perspective of bioinformatics strategies that may be used to tackle this important task. In addition, some of the important resources of this field are also provided.
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Affiliation(s)
- Zhenran Jiang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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29
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Ono T, Hishigaki H. Prediction of GPCR-G protein coupling specificity using features of sequences and biological functions. GENOMICS PROTEOMICS & BIOINFORMATICS 2007; 4:238-44. [PMID: 17531799 PMCID: PMC5054072 DOI: 10.1016/s1672-0229(07)60004-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Understanding the coupling specificity between G protein-coupled receptors (GPCRs) and specific classes of G proteins is important for further elucidation of receptor functions within a cell. Increasing information on GPCR sequences and the G protein family would facilitate prediction of the coupling properties of GPCRs. In this study, we describe a novel approach for predicting the coupling specificity between GPCRs and G proteins. This method uses not only GPCR sequences but also the functional knowledge generated by natural language processing, and can achieve 92.2% prediction accuracy by using the C4.5 algorithm. Furthermore, rules related to GPCR-G protein coupling are generated. The combination of sequence analysis and text mining improves the prediction accuracy for GPCR-G protein coupling specificity, and also provides clues for understanding GPCR signaling.
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Affiliation(s)
- Toshihide Ono
- Laboratory of Bioinformatics, Otsuka Pharmaceutical Co., Ltd., Kawauchi-cho, Tokushima 771-0192, Japan.
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30
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Lu F, Li J, Jiang Z. Computational identification and analysis of G protein-coupled receptor targets. Drug Dev Res 2007. [DOI: 10.1002/ddr.20148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Mann S, Li J, Chen YPP. A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts. Nucleic Acids Res 2006; 35:e12. [PMID: 17170007 PMCID: PMC1802591 DOI: 10.1093/nar/gkl1024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 10/25/2006] [Accepted: 11/14/2006] [Indexed: 11/14/2022] Open
Abstract
The computational approach for identifying promoters on increasingly large genomic sequences has led to many false positives. The biological significance of promoter identification lies in the ability to locate true promoters with and without prior sequence contextual knowledge. Prior approaches to promoter modelling have involved artificial neural networks (ANNs) or hidden Markov models (HMMs), each producing adequate results on small scale identification tasks, i.e. narrow upstream regions. In this work, we present an architecture to support prokaryote promoter identification on large scale genomic sequences, i.e. not limited to narrow upstream regions. The significant contribution involved the hybrid formed via aggregation of the profile HMM with the ANN, via Viterbi scoring optimizations. The benefit obtained using this architecture includes the modelling ability of the profile HMM with the ability of the ANN to associate elements composing the promoter. We present the high effectiveness of the hybrid approach in comparison to profile HMMs and ANNs when used separately. The contribution of Viterbi optimizations is also highlighted for supporting the hybrid architecture in which gains in sensitivity (+0.3), specificity (+0.65) and precision (+0.54) are achieved over existing approaches.
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Affiliation(s)
- Scott Mann
- School of Engineering and Information Technology, Deakin UniversityVictoria, Australia
| | - Jinyan Li
- Institute for Infocomm ResearchSingapore 119613
| | - Yi-Ping Phoebe Chen
- School of Engineering and Information Technology, Deakin UniversityVictoria, Australia
- Australian Research Council Centre in BioinformaticsMelbourne, Australia
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32
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Abstract
A subset of melanopsin-expressing retinal ganglion cells has been identified to be directly photosensitive (pRGCs), modulating a range of behavioral and physiological responses to light. Recent expression studies of melanopsin have provided compelling evidence that melanopsin is the photopigment of the pRGCs. However, the mechanism by which melanopsin transduces light information remains an open question. This review discusses the signaling pathways that may underlie melanopsin-dependent phototransduction in native pRGCs, as well as the many exciting challenges ahead.
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Affiliation(s)
- Stuart Peirson
- Division of Neuroscience and Mental Health, Department of Cellular and Molecular Neuroscience, Faculty of Medicine, Charing Cross Hospital, Imperial College London, London W6 8RF, United Kingdom.
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33
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Ghimire GD, Imai K, Akazawa F, Tsuji T, Sonoyama M, Mitaku S. Physicochemical properties of amino acid sequences of G-proteins for understanding GPCR-G-protein coupling. CHEM-BIO INFORMATICS JOURNAL 2006. [DOI: 10.1273/cbij.6.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ganga D. Ghimire
- Tokyo University of Agriculture and Technology, Department of Biotechnology
| | - Kenichiro Imai
- Nagoya University, School of Engineering, Department of Applied Physics
| | - Fumitsugu Akazawa
- Tokyo University of Agriculture and Technology, Department of Biotechnology
| | - Toshiyuki Tsuji
- Nagoya University, School of Engineering, Department of Applied Physics
| | - Masashi Sonoyama
- Nagoya University, School of Engineering, Department of Applied Physics
| | - Shigeki Mitaku
- Nagoya University, School of Engineering, Department of Applied Physics
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