1
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Joyce W, Warwicker J, Shiels HA, Perry SF. Evolution and divergence of teleost adrenergic receptors: why sometimes 'the drugs don't work' in fish. J Exp Biol 2023; 226:jeb245859. [PMID: 37823524 DOI: 10.1242/jeb.245859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Adrenaline and noradrenaline, released as hormones and/or neurotransmitters, exert diverse physiological functions in vertebrates, and teleost fishes are widely used as model organisms to study adrenergic regulation; however, such investigations often rely on receptor subtype-specific pharmacological agents (agonists and antagonists; see Glossary) developed and validated in mammals. Meanwhile, evolutionary (phylogenetic and comparative genomic) studies have begun to unravel the diversification of adrenergic receptors (ARs) and reveal that whole-genome duplications and pseudogenization events in fishes results in notable distinctions from mammals in their genomic repertoire of ARs, while lineage-specific gene losses within teleosts have generated significant interspecific variability. In this Review, we visit the evolutionary history of ARs (including α1-, α2- and β-ARs) to highlight the prominent interspecific differences in teleosts, as well as between teleosts and other vertebrates. We also show that structural modelling of teleost ARs predicts differences in ligand binding affinity compared with mammalian orthologs. To emphasize the difficulty of studying the roles of different AR subtypes in fish, we collate examples from the literature of fish ARs behaving atypically compared with standard mammalian pharmacology. Thereafter, we focus on specific case studies of the liver, heart and red blood cells, where our understanding of AR expression has benefited from combining pharmacological approaches with molecular genetics. Finally, we briefly discuss the ongoing advances in 'omics' technologies that, alongside classical pharmacology, will provide abundant opportunities to further explore adrenergic signalling in teleosts.
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Affiliation(s)
- William Joyce
- Department of Biology - Zoophysiology, Aarhus University, 8000 Aarhus C, Denmark
| | - Jim Warwicker
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Holly A Shiels
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Steve F Perry
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada, K1N 6N5
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2
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Papageorgiou L, Christou E, Louka E, Papakonstantinou E, Diakou I, Pierouli K, Dragoumani K, Bacopoulou F, Chrousos GP, Eliopoulos E, Vlachakis D. ADRA2B and HTR1A: An Updated Study of the Biogenic Amine Receptors Reveals Novel Conserved Motifs Which Play Key Role in Mental Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:79-99. [PMID: 37525034 DOI: 10.1007/978-3-031-31978-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Mental disorders are strongly connected with several psychiatric conditions including depression, bipolar disorder, schizophrenia, eating disorder, and suicides. There are many biological conditions and pathways that define these complicated illnesses. For example, eating disorders are complex mental health conditions that require the intervention of geneticists, psychiatrists, and medical experts in order to alleviate their symptoms. A patient with suicidal ideation should first be identified and consequently monitored by a similar team of specialists. Both genetics and epigenetics can shed light on eating disorders and suicides as they are found in the main core of such investigations. In the present study, an analysis has been performed on two specific members of the GPCR family toward drawing conclusions regarding their functionality and implementation in mental disorders. Specifically, evolutionary and structural studies on the adrenoceptor alpha 2b (ADRA2B) and the 5-hydroxytryptamine receptor 1A (HTR1A) have been carried out. Both receptors are classified in the biogenic amine receptors sub-cluster of the GPCRs and have been connected in many studies with mental diseases and malnutrition conditions. The major goal of this study is the investigation of conserved motifs among biogenic amine receptors that play an important role in this family signaling pathway, through an updated evolutionary analysis and the correlation of this information with the structural features of the HTR1A and ADRA2B. Furthermore, the structural comparison of ADRA2B, HTR1A, and other members of GPCRs related to mental disorders is performed.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Evangelia Christou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Effrosyni Louka
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece.
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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3
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Dieris M, Kowatschew D, Korsching SI. Olfactory function in the trace amine-associated receptor family (TAARs) evolved twice independently. Sci Rep 2021; 11:7807. [PMID: 33833329 PMCID: PMC8032801 DOI: 10.1038/s41598-021-87236-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/18/2021] [Indexed: 11/23/2022] Open
Abstract
Olfactory receptor families have arisen independently several times during evolution. The origin of taar genes, one of the four major vertebrate olfactory receptor families, is disputed. We performed a phylogenetic analysis making use of 96 recently available genomes, and report that olfactory functionality has arisen twice independently within the TAAR family, once in jawed and once in jawless fish. In lamprey, an ancestral gene expanded to generate a large family of olfactory receptors, while the sister gene in jawed vertebrates did not expand and is not expressed in olfactory sensory neurons. Both clades do not exhibit the defining TAAR motif, and we suggest naming them taar-like receptors (tarl). We have identified the evolutionary origin of both taar and tarl genes in a duplication of the serotonergic receptor 4 that occurred in the most recent common ancestor of vertebrates. We infer two ancestral genes in bony fish (TAAR12, TAAR13) which gave rise to the complete repertoire of mammalian olfactory taar genes and to class II of the taar repertoire of teleost fish. We follow their evolution in seventy-one bony fish genomes and report a high evolutionary dynamic, with many late gene birth events and both early and late gene death events.
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Affiliation(s)
- Milan Dieris
- Institute for Genetics, University At Cologne, Zülpicher Str. 47A, 50674, Cologne, Germany
| | - Daniel Kowatschew
- Institute for Genetics, University At Cologne, Zülpicher Str. 47A, 50674, Cologne, Germany
| | - Sigrun I Korsching
- Institute for Genetics, University At Cologne, Zülpicher Str. 47A, 50674, Cologne, Germany.
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4
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Ravhe IS, Krishnan A, Manoj N. Evolutionary history of histamine receptors: Early vertebrate origin and expansion of the H 3-H 4 subtypes. Mol Phylogenet Evol 2020; 154:106989. [PMID: 33059072 DOI: 10.1016/j.ympev.2020.106989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 12/22/2022]
Abstract
Histamine receptors belonging to the superfamily of G protein-coupled receptors (GPCRs) mediate the diverse biological effects of biogenic histamine. They are classified into four phylogenetically distinct subtypes H1-H4, each with a different binding affinity for histamine and divergent downstream signaling pathways. Here we present the evolutionary history of the histamine receptors using a phylogenetic approach complemented with comparative genomics analyses of the sequences, gene structures, and synteny of gene neighborhoods. The data indicate the earliest emergence of histamine-mediated GPCR signaling by a H2 in a prebilaterian ancestor. The analyses support a revised classification of the vertebrate H3-H4 receptor subtypes. We demonstrate the presence of the H4 across vertebrates, contradicting the currently held notion that H4 is restricted to mammals. These non-mammalian vertebrate H4 orthologs have been mistaken for H3. We also identify the presence of a new H3 subtype (H3B), distinct from the canonical H3 (H3A), and propose that the H3A, H3B, and H4 likely emerged from a H3 progenitor through the 1R/2R whole genome duplications in an ancestor of the vertebrates. It is apparent that the ability of the H1, H2, and H3-4 to bind histamine was acquired convergently. We identified genomic signatures suggesting that the H1 and H3-H4 shared a last common ancestor with the muscarinic receptor in a bilaterian predecessor whereas, the H2 and the α-adrenoreceptor shared a progenitor in a prebilaterian ancestor. Furthermore, site-specific analysis of the vertebrate subtypes revealed potential residues that may account for the functional divergence between them.
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Affiliation(s)
- Infant Sagayaraj Ravhe
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Arunkumar Krishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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Xu R, Pan L, Yang Y, Zhou Y. Characterizing transcriptome in female scallop Chlamys farreri provides new insights into the molecular mechanisms of reproductive regulation during ovarian development and spawn. Gene 2020; 758:144967. [PMID: 32707299 DOI: 10.1016/j.gene.2020.144967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/06/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
Bivalve mollusks are descendants of an early-Cambrian lineage and have successfully evolved unique strategies for reproduction. Nonetheless, the molecular mechanisms underlying reproductive regulation in mollusks remain to be elucidated. In this study, transcriptomes of ovary at four reproductive stages in female Chlamys farreri were characterized by RNA-Seq. Regarding signaling pathways, ECM-receptor interaction pathway, mTOR signaling pathway, Fanconi anemia pathway, FoxO signaling pathway, Wnt signaling pathway and Hedgehog signaling pathway were enriched during ovarian development processes. In addition, pathways related to energy metabolism such as Nitrogen metabolism and Arachidonic acid metabolism were enriched at spawn stage. Interestingly, Neuroactive ligand-receptor interaction was significantly enriched involved in ovarian development and spawn, and indicated the potential functions of nervous system on reproductive regulation in C. farreri. What's more, this study identified and characterized fourteen genes involved in "sex hormones synthesis and regulation", "ovarian development and spawn" and "maternal immunity" during the four reproductive stages in C. farreri. We determined that CYP17 uniquely affected gamete release by influencing the physiological balance among the steroid hormones and showed that receptors of the 5-HT and GABA neurotransmitters were tightly associated with ovarian maturation. Furthermore, to the best of our knowledge, this is the first study to report the maternal effect gene Zar1 in bivalve mollusks, likewise the maternal immunity genes displayed coordinated and cooperative expression during reproductive periods, which strengthened the environmental adaptation mechanisms of bivalves. Taken together, this study provides the first dynamic transcriptomic analysis of C. farreri at four key reproductive stages, which will assist in revealing the molecular mechanisms underlying bivalves on reproductive regulation in ovarian development and spawn.
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Affiliation(s)
- Ruiyi Xu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Yingying Yang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yueyao Zhou
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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Moutkine I, Collins EL, Béchade C, Maroteaux L. Evolutionary considerations on 5-HT2 receptors. Pharmacol Res 2019; 140:14-20. [DOI: 10.1016/j.phrs.2018.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/13/2018] [Accepted: 09/13/2018] [Indexed: 10/28/2022]
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7
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Sukumar V, Liu H, Meisner S, French AS, Torkkeli PH. Multiple Biogenic Amine Receptor Types Modulate Spider, Cupiennius salei, Mechanosensory Neurons. Front Physiol 2018; 9:857. [PMID: 30050453 PMCID: PMC6052906 DOI: 10.3389/fphys.2018.00857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/15/2018] [Indexed: 12/02/2022] Open
Abstract
The biogenic amines octopamine (OA), tyramine (TA), dopamine (DA), serotonin (5-HT), and histamine (HA) affect diverse physiological and behavioral processes in invertebrates, but recent findings indicate that an additional adrenergic system exists in at least some invertebrates. Transcriptome analysis has made it possible to identify biogenic amine receptor genes in a wide variety of species whose genomes have not yet been sequenced. This approach provides new sequences for research into the evolutionary history of biogenic amine receptors and allows them to be studied in experimentally accessible animal models. The Central American Wandering spider, Cupiennius salei, is an experimental model for neurophysiological, developmental and behavioral research. We identified ten different biogenic amine receptors in C. salei transcriptomes. Phylogenetic analysis indicated that, in addition to the typical receptors for OA, TA, DA, and 5-HT in protostome invertebrates, spiders also have α1- and α2-adrenergic receptors, but lack TAR2 receptors and one invertebrate specific DA receptor type. In situ hybridization revealed four types of biogenic amine receptors expressed in C. salei mechanosensory neurons. We used intracellular electrophysiological experiments and pharmacological tools to determine how each receptor type contributes to modulation of these neurons. We show that arachnids have similar groups of biogenic amine receptors to other protostome invertebrates, but they lack two clades. We also clarify that arachnids and many other invertebrates have both α1- and α2-adrenergic, likely OA receptors. Our results indicate that in addition to an OAβ-receptor that regulates rapid and large changes in sensitivity via a Gs-protein activating a cAMP mediated pathway, the C. salei mechanosensory neurons have a constitutively active TAR1 and/or α2-adrenergic receptor type that adjusts the baseline sensitivity to a level appropriate for the behavioral state of the animal by a Gq-protein that mobilizes Ca2+.
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Affiliation(s)
- Vaishnavi Sukumar
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
| | - Hongxia Liu
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
| | - Shannon Meisner
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
| | - Andrew S French
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
| | - Päivi H Torkkeli
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
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8
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Verlinden H. Dopamine signalling in locusts and other insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 97:40-52. [PMID: 29680287 DOI: 10.1016/j.ibmb.2018.04.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/05/2018] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Dopamine is an important catecholamine neurotransmitter in invertebrates and vertebrates. It is biochemically derived from tyrosine via L-DOPA. It is most abundant in the central nervous system, but can also be produced in e.g. epidermal cells. Dopamine has conserved roles in the control of movement, pleasure, motivation, arousal and memory between invertebrate and vertebrate animals. It is crucial for melanisation and sclerotisation, important processes for the formation of the exoskeleton of insects and immune function. In this brief review I will discuss some general aspects of insect dopamine biosynthesis and breakdown, dopamine receptors and their pharmacology. In addition, I will provide a glance on the multitude of biological functions of dopamine in insects. More detail is provided concerning the putative roles of dopamine in phase related phenomena in locusts. Finally, molecular and pharmacological adjustments of insect dopamine signalling are discussed in the light of possible approaches towards insect pest management.
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Affiliation(s)
- Heleen Verlinden
- Department of Animal Physiology and Neurobiology, Zoological Institute, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium.
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9
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Opazo JC, Zavala K, Miranda-Rottmann S, Araya R. Evolution of dopamine receptors: phylogenetic evidence suggests a later origin of the DRD 2l and DRD 4rs dopamine receptor gene lineages. PeerJ 2018; 6:e4593. [PMID: 29666757 PMCID: PMC5900934 DOI: 10.7717/peerj.4593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/17/2018] [Indexed: 01/11/2023] Open
Abstract
Dopamine receptors are integral membrane proteins whose endogenous ligand is dopamine. They play a fundamental role in the central nervous system and dysfunction of dopaminergic neurotransmission is responsible for the generation of a variety of neuropsychiatric disorders. From an evolutionary standpoint, phylogenetic relationships among the DRD1 class of dopamine receptors are still a matter of debate as in the literature different tree topologies have been proposed. In contrast, phylogenetic relationships among the DRD2 group of receptors are well understood. Understanding the time of origin of the different dopamine receptors is also an issue that needs further study, especially for the genes that have restricted phyletic distributions (e.g., DRD2l and DRD4rs). Thus, the goal of this study was to investigate the evolution of dopamine receptors, with emphasis on shedding light on the phylogenetic relationships among the D1 class of dopamine receptors and the time of origin of the DRD2l and DRD4rs gene lineages. Our results recovered the monophyly of the two groups of dopamine receptors. Within the DRD1 group the monophyly of each paralog was recovered with strong support, and phylogenetic relationships among them were well resolved. Within the DRD1 class of dopamine receptors we recovered the sister group relationship between the DRD1C and DRD1E, and this clade was recovered sister to a cyclostome sequence. The DRD1 clade was recovered sister to the aforementioned clade, and the group containing DRD5 receptors was sister to all other DRD1 paralogs. In agreement with the literature, among the DRD2 class of receptors, DRD2 was recovered sister to DRD3, whereas DRD4 was sister to the DRD2/DRD3 clade. According to our phylogenetic tree, the DRD2l and DRD4rs gene lineages would have originated in the ancestor of gnathostomes between 615 and 473 mya. Conservation of sequences required for dopaminergic neurotransmission and small changes in regulatory regions suggest a functional refinement of the dopaminergic pathways along evolution.
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Affiliation(s)
- Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | | | - Roberto Araya
- Department of Neurosciences, Faculty of Medicine, University of Montreal, Montreal, Canada
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Céspedes HA, Zavala K, Vandewege MW, Opazo JC. Evolution of the α 2-adrenoreceptors in vertebrates: ADRA2D is absent in mammals and crocodiles. Gen Comp Endocrinol 2017. [PMID: 28622977 DOI: 10.1016/j.ygcen.2017.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Evolutionary studies of genes that have been functionally characterized and whose variation has been associated with pathological conditions represent an opportunity to understand the genetic basis of pathologies. α2-Adrenoreceptors (ADRA2) are a class of G protein-coupled receptors that regulate several physiological processes including blood pressure, platelet aggregation, insulin secretion, lipolysis, and neurotransmitter release. This gene family has been extensively studied from a molecular/physiological perspective, yet much less is known about its evolutionary history. Accordingly, the goal of this study was to investigate the evolutionary history of α2-adrenoreceptors (ADRA2) in vertebrates. Our results show that in addition to the three well-recognized α2-adrenoreceptor genes (ADRA2A, ADRA2B and ADRA2C), we recovered a clade that corresponds to the fourth member of the α2-adrenoreceptor gene family (ADRA2D). We also recovered a clade that possesses two ADRA2 sequences found in two lamprey species. Furthermore, our results show that mammals and crocodiles are characterized by possessing three α2-adrenoreceptor genes, whereas all other vertebrate groups possess the full repertoire of α2-adrenoreceptor genes. Among vertebrates ADRA2D seems to be a dispensable gene, as it was lost two independent times during the evolutionary history of the group. Additionally, we found that most examined species possess the most common alleles described for humans; however, there are cases in which non-human mammals possess the alternative variant. Finally, transcript abundance profiles revealed that during the early evolutionary history of gnathostomes, the expression of ADRA2D in different taxonomic groups became specialized to different tissues, but in the ancestor of sarcopterygians this specialization would have been lost.
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Affiliation(s)
- Héctor A Céspedes
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Michael W Vandewege
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; David Rockefeller Center For Latin American Studies, Harvard University, Cambridge, MA 02138, USA.
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11
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Zavala K, Vandewege MW, Hoffmann FG, Opazo JC. Evolution of the β-adrenoreceptors in vertebrates. Gen Comp Endocrinol 2017; 240:129-137. [PMID: 27769631 DOI: 10.1016/j.ygcen.2016.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 10/13/2016] [Accepted: 10/17/2016] [Indexed: 11/19/2022]
Abstract
The study of the evolutionary history of genes related to human disease lies at the interface of evolution and medicine. These studies provide the evolutionary context on which medical researchers should work, and are also useful in providing information to suggest further genetic experiments, especially in model species where genetic manipulations can be made. Here we studied the evolution of the β-adrenoreceptor gene family in vertebrates with the aim of adding an evolutionary framework to the already abundant physiological information. Our results show that in addition to the three already described vertebrate β-adrenoreceptor genes there is an additional group containing cyclostome sequences. We suggest that β-adrenoreceptors diversified as a product of the two whole genome duplications that occurred in the ancestor of vertebrates. Gene expression patterns are in general consistent across species, suggesting that expression dynamics were established early in the evolutionary history of vertebrates, and have been maintained since then. Finally, amino acid polymorphisms that are associated to pathological conditions in humans appear to be common in non-human mammals, suggesting that the phenotypic effects of these mutations depend on epistatic interaction with other positions. The evolutionary analysis of the β-adrenoreceptors delivers new insights about the diversity of these receptors in vertebrates, the evolution of the expression patterns and a comparative perspective regarding the polymorphisms that in humans are linked to pathological conditions.
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Affiliation(s)
- Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, MS, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
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12
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Spielman SJ, Wan S, Wilke CO. A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation. Genetics 2016; 204:499-511. [PMID: 27535929 PMCID: PMC5068842 DOI: 10.1534/genetics.115.185264] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 08/11/2016] [Indexed: 11/18/2022] Open
Abstract
Two broad paradigms exist for inferring [Formula: see text] the ratio of nonsynonymous to synonymous substitution rates, from coding sequences: (i) a one-rate approach, where [Formula: see text] is represented with a single parameter, or (ii) a two-rate approach, where [Formula: see text] and [Formula: see text] are estimated separately. The performances of these two approaches have been well studied in the specific context of proper model specification, i.e., when the inference model matches the simulation model. By contrast, the relative performances of one-rate vs. two-rate parameterizations when applied to data generated according to a different mechanism remain unclear. Here, we compare the relative merits of one-rate and two-rate approaches in the specific context of model misspecification by simulating alignments with mutation-selection models rather than with [Formula: see text]-based models. We find that one-rate frameworks generally infer more accurate [Formula: see text] point estimates, even when [Formula: see text] varies among sites. In other words, modeling [Formula: see text] variation may substantially reduce accuracy of [Formula: see text] point estimates. These results appear to depend on the selective constraint operating at a given site. For sites under strong purifying selection ([Formula: see text]), one-rate and two-rate models show comparable performances. However, one-rate models significantly outperform two-rate models for sites under moderate-to-weak purifying selection. We attribute this distinction to the fact that, for these more quickly evolving sites, a given substitution is more likely to be nonsynonymous than synonymous. The data will therefore be relatively enriched for nonsynonymous changes, and modeling [Formula: see text] contributes excessive noise to [Formula: see text] estimates. We additionally find that high levels of divergence among sequences, rather than the number of sequences in the alignment, are more critical for obtaining precise point estimates.
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Affiliation(s)
- Stephanie J Spielman
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712
| | - Suyang Wan
- School of Physics and Astronomy, The University of Minnesota, Minneapolis, Minnesota 55455
| | - Claus O Wilke
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712
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Tamvacakis AN, Senatore A, Katz PS. Identification of genes related to learning and memory in the brain transcriptome of the mollusc, Hermissenda crassicornis. Learn Mem 2015; 22:617-21. [PMID: 26572652 PMCID: PMC4749734 DOI: 10.1101/lm.038158.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 09/28/2015] [Indexed: 11/25/2022]
Abstract
The sea slug Hermissenda crassicornis (Mollusca, Gastropoda, Nudibranchia) has been studied extensively in associative learning paradigms. However, lack of genetic information previously hindered molecular-level investigations. Here, the Hermissenda brain transcriptome was sequenced and assembled de novo, producing 165,743 total transcripts. Orthologs of 95 genes implicated in learning were identified. These included genes for a serotonin receptor and a GABA-B receptor subunit that had not been previously described in molluscs, as well as an adenylyl cyclase gene not previously described in gastropods. This study illustrates the Hermissenda transcriptome's potential as an important genetic tool in future learning and memory research.
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Affiliation(s)
- Arianna N Tamvacakis
- Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-4010, USA
| | - Adriano Senatore
- Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-4010, USA
| | - Paul S Katz
- Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-4010, USA
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