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Salgueiro WG, Soares MV, Martins CF, Paula FR, Rios-Anjos RM, Carrazoni T, Mori MA, Müller RU, Aschner M, Dal Belo CA, Ávila DS. Dopaminergic modulation by quercetin: In silico and in vivo evidence using Caenorhabditis elegans as a model. Chem Biol Interact 2023; 382:110610. [PMID: 37348670 PMCID: PMC10527449 DOI: 10.1016/j.cbi.2023.110610] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 06/12/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Quercetin is a flavonol widely distributed in plants and has various described biological functions. Several studies have reported on its ability to restore neuronal function in a wide variety of disease models, including animal models of neurodegenerative disorders such as Parkinson's disease. Quercetin per se can act as a neuroprotector/neuromodulator, especially in diseases related to impaired dopaminergic neurotransmission. However, little is known about how quercetin interacts with the dopaminergic machinery. Here we employed the nematode Caenorhabditis elegans to study this putative interaction. After observing behavioral modulation, mutant analysis and gene expression in C. elegans upon exposure to quercetin at a concentration that does not protect against MPTP, we constructed a homology-based dopamine transporter protein model to conduct a docking study. This led to suggestive evidence on how quercetin may act as a dopaminergic modulator by interacting with C. elegans' dopamine transporter and alter the nematode's exploratory behavior. Consistent with this model, quercetin controls C. elegans behavior in a way dependent on the presence of both the dopamine transporter (dat-1), which is up-regulated upon quercetin exposure, and the dopamine receptor 2 (dop-2), which appears to be mandatory for dat-1 up-regulation. Our data propose an interaction with the dopaminergic machinery that may help to establish the effects of quercetin as a neuromodulator.
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Affiliation(s)
- Willian Goulart Salgueiro
- Research Group in Biochemistry and Toxicology in Caenorhabditis elegans (GBToxCe), Federal University of Pampa - UNIPAMPA, CEP 97500-970, Uruguaiana, RS, Brazil; Department of Biochemistry and Tissue Biology, University of Campinas, Monteiro Lobato Avenue, 255, Campinas, São Paulo, 13083-862, Brazil; Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, 50931, Germany; Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Marcell Valandro Soares
- Research Group in Biochemistry and Toxicology in Caenorhabditis elegans (GBToxCe), Federal University of Pampa - UNIPAMPA, CEP 97500-970, Uruguaiana, RS, Brazil; Department of Biochemistry and Molecular Biology, Post-graduate Program in Biological Sciences, Federal University of Santa Maria, Camobi, 97105-900, Santa Maria, RS, Brazil
| | - Cassiano Fiad Martins
- Research Group in Biochemistry and Toxicology in Caenorhabditis elegans (GBToxCe), Federal University of Pampa - UNIPAMPA, CEP 97500-970, Uruguaiana, RS, Brazil
| | - Fávero Reisdorfer Paula
- Laboratory for Development and Quality Control in Medicines (LDCQ), Federal University of Pampa, Uruguaiana, RS, Brazil
| | | | - Thiago Carrazoni
- Neurobiology and Toxinology Laboratory, (LANETOX), Federal University of Pampa - UNIPAMPA, CEP 97300-000, São Gabriel, RS, Brazil
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, University of Campinas, Monteiro Lobato Avenue, 255, Campinas, São Paulo, 13083-862, Brazil; Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, SP, Brazil; Experimental Medicine Research Cluster, University of Campinas, Campinas, SP, Brazil
| | - Roman-Ulrich Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, 50931, Germany; Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Cháriston André Dal Belo
- Department of Biochemistry and Molecular Biology, Post-graduate Program in Biological Sciences, Federal University of Santa Maria, Camobi, 97105-900, Santa Maria, RS, Brazil; Neurobiology and Toxinology Laboratory, (LANETOX), Federal University of Pampa - UNIPAMPA, CEP 97300-000, São Gabriel, RS, Brazil; Multidisciplinar Department, Federal University of São Paulo (UNIFESP), Angelica Street, 100- CEP 06110295, Osasco, SP, Brazil
| | - Daiana Silva Ávila
- Research Group in Biochemistry and Toxicology in Caenorhabditis elegans (GBToxCe), Federal University of Pampa - UNIPAMPA, CEP 97500-970, Uruguaiana, RS, Brazil; Department of Biochemistry and Molecular Biology, Post-graduate Program in Biological Sciences, Federal University of Santa Maria, Camobi, 97105-900, Santa Maria, RS, Brazil.
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Gao AW, El Alam G, Lalou A, Li TY, Molenaars M, Zhu Y, Overmyer KA, Shishkova E, Hof K, Bou Sleiman M, Houtkooper RH, Coon JJ, Auwerx J. Multi-omics analysis identifies essential regulators of mitochondrial stress response in two wild-type C. elegans strains. iScience 2022; 25:103734. [PMID: 35118355 PMCID: PMC8792074 DOI: 10.1016/j.isci.2022.103734] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/02/2021] [Accepted: 12/31/2021] [Indexed: 11/28/2022] Open
Abstract
The mitochondrial unfolded protein response (UPRmt) is a promising pharmacological target for aging and age-related diseases. However, the integrative analysis of the impact of UPRmt activation on different signaling layers in animals with different genetic backgrounds is lacking. Here, we applied systems approaches to investigate the effect of UPRmt induced by doxycycline (Dox) on transcriptome, proteome, and lipidome in two genetically divergent worm strains, named N2 and CB4856. From the integrated omics datasets, we found that Dox prolongs lifespan of both worm strains through shared and strain-specific mechanisms. Specifically, Dox strongly impacts mitochondria, upregulates defense response, and lipid metabolism, while decreasing triglycerides. We further validated that lipid genes acs-2/20 and fat-7/6 were required for Dox-induced UPRmt and longevity in N2 and CB4856 worms, respectively. Our data have translational value as they indicate that the beneficial effects of Dox-induced UPRmt on lifespan are consistent across different genetic backgrounds through different regulators. Dox extends lifespan of N2 and CB4856 via shared and strain-specific mechanisms Dox controls mitochondria, defense responses, and lipid metabolism in both strains Dox-mediated longevity requires acs-2/20 in N2 and fat-7/6 in CB4856 worms
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Affiliation(s)
- Arwen W. Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Gaby El Alam
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Amélia Lalou
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Terytty Yang Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, AZ, the Netherlands
| | - Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Katherine A. Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
| | - Kevin Hof
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, AZ, the Netherlands
| | - Joshua J. Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Corresponding author
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Ferkey DM, Sengupta P, L’Etoile ND. Chemosensory signal transduction in Caenorhabditis elegans. Genetics 2021; 217:iyab004. [PMID: 33693646 PMCID: PMC8045692 DOI: 10.1093/genetics/iyab004] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Chemosensory neurons translate perception of external chemical cues, including odorants, tastants, and pheromones, into information that drives attraction or avoidance motor programs. In the laboratory, robust behavioral assays, coupled with powerful genetic, molecular and optical tools, have made Caenorhabditis elegans an ideal experimental system in which to dissect the contributions of individual genes and neurons to ethologically relevant chemosensory behaviors. Here, we review current knowledge of the neurons, signal transduction molecules and regulatory mechanisms that underlie the response of C. elegans to chemicals, including pheromones. The majority of identified molecules and pathways share remarkable homology with sensory mechanisms in other organisms. With the development of new tools and technologies, we anticipate that continued study of chemosensory signal transduction and processing in C. elegans will yield additional new insights into the mechanisms by which this animal is able to detect and discriminate among thousands of chemical cues with a limited sensory neuron repertoire.
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Affiliation(s)
- Denise M Ferkey
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Noelle D L’Etoile
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
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Duguet TB, Glebov A, Hussain A, Kulkarni S, Mochalkin I, Geary TG, Rashid M, Spangenberg T, Ribeiro P. Identification of annotated bioactive molecules that impair motility of the blood fluke Schistosoma mansoni. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 13:73-88. [PMID: 32531750 PMCID: PMC7284125 DOI: 10.1016/j.ijpddr.2020.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 01/21/2023]
Abstract
Neglected tropical diseases are of growing worldwide concern and schistosomiasis, caused by parasitic flatworms, continues to be a major threat with more than 200 million people requiring preventive treatment. As praziquantel (PZQ) remains the treatment of choice, an urgent need for alternative treatments motivates research to identify new lead compounds that would complement PZQ by filling the therapeutic gaps associated with this treatment. Because impairing parasite neurotransmission remains a core strategy for control of parasitic helminths, we screened a library of 708 compounds with validated biological activity in humans on the blood fluke Schistosoma mansoni, measuring their effect on the motility on schistosomulae and adult worms. The primary phenotypic screen performed on schistosomulae identified 70 compounds that induced changes in viability and/or motility. Screening different concentrations and incubation times identified molecules with fast onset of activity on both life stages at low concentration (1 μM). To complement this study, similar assays were performed with chemical analogs of the cholinomimetic drug arecoline and the calcilytic molecule NPS-2143, two compounds that rapidly inhibited schistosome motility; 17 arecoline and 302 NPS-2143 analogs were tested to enlarge the pool of schistosomicidal molecules. Finally, validated hit compounds were tested on three functionally-validated neuroregulatory S. mansoni G-protein coupled receptors (GPCRs): Sm5HTR (serotonin-sensitive), SmGPR2 (histamine) and SmD2 (dopamine), revealing NPS-2143 and analogs as potent inhibitors of dopamine/epinine responses on both human and S. mansoni GPCRs. This study highlights the potential for repurposing known human therapeutic agents for potential schistosomicidal effects and expands the list of hits for further progression.
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Affiliation(s)
- Thomas B Duguet
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada.
| | - Anastasia Glebov
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Asimah Hussain
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | | | - Igor Mochalkin
- EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Timothy G Geary
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Mohammed Rashid
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Thomas Spangenberg
- Global Health Institute of Merck, Ares Trading S.A., a subsidiary of Merck KGaA (Darmstadt, Germany), Eysins, Switzerland.
| | - Paula Ribeiro
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
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Ascaroside Pheromones: Chemical Biology and Pleiotropic Neuronal Functions. Int J Mol Sci 2019; 20:ijms20163898. [PMID: 31405082 PMCID: PMC6719183 DOI: 10.3390/ijms20163898] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/1970] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022] Open
Abstract
Pheromones are neuronal signals that stimulate conspecific individuals to react to environmental stressors or stimuli. Research on the ascaroside (ascr) pheromones in Caenorhabditis elegans and other nematodes has made great progress since ascr#1 was first isolated and biochemically defined in 2005. In this review, we highlight the current research on the structural diversity, biosynthesis, and pleiotropic neuronal functions of ascr pheromones and their implications in animal physiology. Experimental evidence suggests that ascr biosynthesis starts with conjugation of ascarylose to very long-chain fatty acids that are then processed via peroxisomal β-oxidation to yield diverse ascr pheromones. We also discuss the concentration and stage-dependent pleiotropic neuronal functions of ascr pheromones. These functions include dauer induction, lifespan extension, repulsion, aggregation, mating, foraging and detoxification, among others. These roles are carried out in coordination with three G protein-coupled receptors that function as putative pheromone receptors: SRBC-64/66, SRG-36/37, and DAF-37/38. Pheromone sensing is transmitted in sensory neurons via DAF-16-regulated glutamatergic neurotransmitters. Neuronal peroxisomal fatty acid β-oxidation has important cell-autonomous functions in the regulation of neuroendocrine signaling, including neuroprotection. In the future, translation of our knowledge of nematode ascr pheromones to higher animals might be beneficial, as ascr#1 has some anti-inflammatory effects in mice. To this end, we propose the establishment of pheromics (pheromone omics) as a new subset of integrated disciplinary research area within chemical ecology for system-wide investigation of animal pheromones.
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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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Ikeda M, Sugihara M, Suwa M. SEVENS: a database for comprehensive GPCR genes obtained from genomes: -Update to 68 eukaryotes. Biophys Physicobiol 2018; 15:104-110. [PMID: 29892516 PMCID: PMC5992857 DOI: 10.2142/biophysico.15.0_104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/25/2018] [Indexed: 12/01/2022] Open
Abstract
We report the development of the SEVENS database, which contains information on G-protein coupled receptor (GPCR) genes that are identified with high confidence levels (A, B, C, and D) from various eukaryotic genomes, by using a pipeline comprising bioinformatics softwares, including a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. SEVENS compiles detailed information on GPCR genes, such as chromosomal mapping position, phylogenetic tree, sequence similarity to known genes, and protein function described by motif/domain and transmembrane helices. They are presented in a user-friendly interface. Because of the comprehensive gene findings from genomes, SEVENS contains a larger data set than that of previous databases and enables the performance of a genome-scale overview of all the GPCR genes. We surveyed the complete genomes of 68 eukaryotes, and found that there were between 6 and 3,470 GPCR genes for each genome (Level A data). Within these genes, the number of receptors for various molecules, including biological amines, peptides, and lipids, were conserved in mammals, birds, and fishes, whereas the numbers of odorant receptors and pheromone receptors were highly diverse in mammals. SEVENS is freely available at http://sevens.cbrc.jp or http://sevens.chem.aoyama.ac.jp.
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Affiliation(s)
- Masami Ikeda
- Aoyama Gakuin University, College of Science and Engineering, Sagamihara, Kanagawa 252-5258, Japan
| | - Minoru Sugihara
- Meiji Pharmaceutical University, Pharmaceutical Education and Research Center, Kiyose, Tokyo 204-8588, Japan
| | - Makiko Suwa
- Aoyama Gakuin University, College of Science and Engineering, Sagamihara, Kanagawa 252-5258, Japan
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Patel S. Pathogenicity-associated protein domains: The fiercely-conserved evolutionary signatures. GENE REPORTS 2017; 7:127-141. [PMID: 32363241 PMCID: PMC7185390 DOI: 10.1016/j.genrep.2017.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 12/15/2022]
Abstract
Proteins have highly conserved domains that determine their functionality. Out of the thousands of domains discovered so far across all living forms, some of the predominant clinically-relevant domains include IENR1, HNHc, HELICc, Pro-kuma_activ, Tryp_SPc, Lactamase_B, PbH1, ChtBD3, CBM49, acidPPc, G3P_acyltransf, RPOL8c, KbaA, HAMP, HisKA, Hr1, Dak2, APC2, Citrate_ly_lig, DALR, VKc, YARHG, WR1, PWI, ZnF_BED, TUDOR, MHC_II_beta, Integrin_B_tail, Excalibur, DISIN, Cadherin, ACTIN, PROF, Robl_LC7, MIT, Kelch, GAS2, B41, Cyclin_C, Connexin_CCC, OmpH, Bac_rhodopsin, AAA, Knot1, NH, Galanin, IB, Elicitin, ACTH, Cache_2, CHASE, AgrB, PRP, IGR, and Antimicrobial21. These domains are distributed in nucleases/helicases, proteases, esterases, lipases, glycosylase, GTPases, phosphatases, methyltransferases, acyltransferase, acetyltransferase, polymerase, kinase, ligase, synthetase, oxidoreductase, protease inhibitors, nucleic acid binding proteins, adhesion and immunity-related proteins, cytoskeletal component-manipulating proteins, lipid biosynthesis and metabolism proteins, membrane-associated proteins, hormone-like and signaling proteins, etc. These domains are ubiquitous stretches or folds of the proteins in pathogens and allergens. Pathogenesis alleviation efforts can benefit enormously if the characteristics of these domains are known. Hence, this review catalogs and discusses the role of such pivotal domains, suggesting hypotheses for better understanding of pathogenesis at molecular level. Proteins have highly conserved regions or domains across pathogens and allergens. Knowledge on these critical domains can facilitate our understanding of pathogenesis mechanisms. Such immune manipulation-related domains include IENR1, HNHc, HELICc, ACTIN, PROF, Robl_LC7, OmpH etc. These domains are presnt in enzyme, transcription regulators, adhesion proteins, and hormones. This review discusses and hypothesizes on these domains.
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Key Words
- CARDs, caspase activation and recruitment domains
- CBM, carbohydrate binding module
- CTD, C-terminal domain
- ChtBD, chitin-binding domain
- Diversification
- HNHc, homing endonucleases
- HTH, helix-turn-helix
- IENR1, intron-encoded endonuclease repeat
- Immune manipulation
- PAMPs, pathogen associated molecular patterns
- Pathogenesis
- Phylogenetic conservation
- Protein domains
- SMART, Simple Modular Architecture Research Tool
- Shuffling
- UDG, uracil DNA glycosylase
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego 92182, USA
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Sewelam N, Kazan K, Schenk PM. Global Plant Stress Signaling: Reactive Oxygen Species at the Cross-Road. FRONTIERS IN PLANT SCIENCE 2016; 7:187. [PMID: 26941757 PMCID: PMC4763064 DOI: 10.3389/fpls.2016.00187] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/04/2016] [Indexed: 05/18/2023]
Abstract
Current technologies have changed biology into a data-intensive field and significantly increased our understanding of signal transduction pathways in plants. However, global defense signaling networks in plants have not been established yet. Considering the apparent intricate nature of signaling mechanisms in plants (due to their sessile nature), studying the points at which different signaling pathways converge, rather than the branches, represents a good start to unravel global plant signaling networks. In this regard, growing evidence shows that the generation of reactive oxygen species (ROS) is one of the most common plant responses to different stresses, representing a point at which various signaling pathways come together. In this review, the complex nature of plant stress signaling networks will be discussed. An emphasis on different signaling players with a specific attention to ROS as the primary source of the signaling battery in plants will be presented. The interactions between ROS and other signaling components, e.g., calcium, redox homeostasis, membranes, G-proteins, MAPKs, plant hormones, and transcription factors will be assessed. A better understanding of the vital roles ROS are playing in plant signaling would help innovate new strategies to improve plant productivity under the circumstances of the increasing severity of environmental conditions and the high demand of food and energy worldwide.
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Affiliation(s)
- Nasser Sewelam
- Botany Department, Faculty of Science, Tanta UniversityTanta, Egypt
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization Agriculture, Queensland Bioscience Precinct, St LuciaQLD, Australia
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, BrisbaneQLD, Australia
| | - Peer M. Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sciences, The University of Queensland, BrisbaneQLD, Australia
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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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Nagarathnam B, Karpe SD, Harini K, Sankar K, Iftekhar M, Rajesh D, Giji S, Archunan G, Balakrishnan V, Gromiha MM, Nemoto W, Fukui K, Sowdhamini R. DOR - a Database of Olfactory Receptors - Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes. Bioinform Biol Insights 2014; 8:147-58. [PMID: 25002814 PMCID: PMC4069036 DOI: 10.4137/bbi.s14858] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/20/2014] [Accepted: 03/20/2014] [Indexed: 11/05/2022] Open
Abstract
Olfaction is the response to odors and is mediated by a class of membrane-bound proteins called olfactory receptors (ORs). An understanding of these receptors serves as a good model for basic signal transduction mechanisms and also provides important clues for the strategies adopted by organisms for their ultimate survival using chemosensory perception in search of food or defense against predators. Prior research on cross-genome phylogenetic analyses from our group motivated the addressal of conserved evolutionary trends, clustering, and ortholog prediction of ORs. The database of olfactory receptors (DOR) is a repository that provides sequence and structural information on ORs of selected organisms (such as Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, and Homo sapiens). Users can download OR sequences, study predicted membrane topology, and obtain cross-genome sequence alignments and phylogeny, including three-dimensional (3D) structural models of 100 selected ORs and their predicted dimer interfaces. The database can be accessed from http://caps.ncbs.res.in/DOR. Such a database should be helpful in designing experiments on point mutations to probe into the possible dimerization modes of ORs and to even understand the evolutionary changes between different receptors.
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Affiliation(s)
| | - Snehal D Karpe
- National Center for Biological Sciences (TIFR), Bangalore, India
| | - Krishnan Harini
- National Center for Biological Sciences (TIFR), Bangalore, India
| | - Kannan Sankar
- Birla Institute of Technology and Science, Pilani, India. ; Presently in: Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA
| | | | - Durairaj Rajesh
- Department of Animal Sciences, Bharathidasan University, Tiruchirapalli, Tamil Nadu, India
| | - Sadasivam Giji
- National Center for Biological Sciences (TIFR), Bangalore, India
| | - Govidaraju Archunan
- Department of Animal Sciences, Bharathidasan University, Tiruchirapalli, Tamil Nadu, India
| | - Veluchamy Balakrishnan
- Department of Biotechnology, K.S. Rangasamy College of Technology, Tiruchengode, Tamil Nadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Wataru Nemoto
- Current Address: Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama, 350-0394, Japan
| | - Kazhuhiko Fukui
- Molecular Profiling Research Center for Drug Discover, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku,Tokyo, Japan
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Cardoso JC, Félix RC, Fonseca VG, Power DM. Feeding and the rhodopsin family g-protein coupled receptors in nematodes and arthropods. Front Endocrinol (Lausanne) 2012; 3:157. [PMID: 23264768 PMCID: PMC3524798 DOI: 10.3389/fendo.2012.00157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/22/2012] [Indexed: 12/13/2022] Open
Abstract
In vertebrates, receptors of the rhodopsin G-protein coupled superfamily (GPCRs) play an important role in the regulation of feeding and energy homeostasis and are activated by peptide hormones produced in the brain-gut axis. These peptides regulate appetite and energy expenditure by promoting or inhibiting food intake. Sequence and function homologs of human GPCRs involved in feeding exist in the nematode roundworm, Caenorhabditis elegans (C. elegans), and the arthropod fruit fly, Drosophila melanogaster (D. melanogaster), suggesting that the mechanisms that regulate food intake emerged early and have been conserved during metazoan radiation. Nematodes and arthropods are the most diverse and successful animal phyla on Earth. They can survive in a vast diversity of environments and have acquired distinct life styles and feeding strategies. The aim of the present review is to investigate if this diversity has affected the evolution of invertebrate GPCRs. Homologs of the C. elegans and D. melanogaster rhodopsin receptors were characterized in the genome of other nematodes and arthropods and receptor evolution compared. With the exception of bombesin receptors (BBR) that are absent from nematodes, a similar gene complement was found. In arthropods, rhodopsin GPCR evolution is characterized by species-specific gene duplications and deletions and in nematodes by gene expansions in species with a free-living stage and gene deletions in representatives of obligate parasitic taxa. Based upon variation in GPCR gene number and potentially divergent functions within phyla we hypothesize that life style and feeding diversity practiced by nematodes and arthropods was one factor that contributed to rhodopsin GPCR gene evolution. Understanding how the regulation of food intake has evolved in invertebrates will contribute to the development of novel drugs to control nematodes and arthropods and the pests and diseases that use them as vectors.
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Affiliation(s)
- João C.R. Cardoso
- Molecular Comparative Endocrinology, Centre of Marine Sciences, Universidade do AlgarveFaro, Portugal
- *Correspondence: João C.R. Cardoso, Molecular Comparative Endocrinology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal. e-mail:
| | - Rute C. Félix
- Molecular Comparative Endocrinology, Centre of Marine Sciences, Universidade do AlgarveFaro, Portugal
| | - Vera G. Fonseca
- Molecular Comparative Endocrinology, Centre of Marine Sciences, Universidade do AlgarveFaro, Portugal
| | - Deborah M. Power
- Molecular Comparative Endocrinology, Centre of Marine Sciences, Universidade do AlgarveFaro, Portugal
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