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Carter AM. Evolution of Placental Hormones: Implications for Animal Models. Front Endocrinol (Lausanne) 2022; 13:891927. [PMID: 35692413 PMCID: PMC9176407 DOI: 10.3389/fendo.2022.891927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 11/15/2022] Open
Abstract
Human placenta secretes a variety of hormones, some of them in large amounts. Their effects on maternal physiology, including the immune system, are poorly understood. Not one of the protein hormones specific to human placenta occurs outside primates. Instead, laboratory and domesticated species have their own sets of placental hormones. There are nonetheless several examples of convergent evolution. Thus, horse and human have chorionic gonadotrophins with similar functions whilst pregnancy-specific glycoproteins have evolved in primates, rodents, horses, and some bats, perhaps to support invasive placentation. Placental lactogens occur in rodents and ruminants as well as primates though evolved through duplication of different genes and with functions that only partially overlap. There are also placental hormones, such as the pregnancy-associated glycoproteins of ruminants, that have no equivalent in human gestation. This review focusses on the evolution of placental hormones involved in recognition and maintenance of pregnancy, in maternal adaptations to pregnancy and lactation, and in facilitating immune tolerance of the fetal semiallograft. The contention is that knowledge gained from laboratory and domesticated mammals can translate to a better understanding of human placental endocrinology, but only if viewed in an evolutionary context.
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Affiliation(s)
- Anthony M. Carter
- Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
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2
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Hansen-Estruch C, Cooper DK, Judd E. Physiological aspects of pig kidney xenotransplantation and implications for management following transplant. Xenotransplantation 2022; 29:e12743. [PMID: 35297098 PMCID: PMC9232961 DOI: 10.1111/xen.12743] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 02/19/2022] [Accepted: 03/03/2022] [Indexed: 12/16/2022]
Abstract
Successful organ transplantation between species is now possible, using genetic modifications. This article aims to provide a comprehensive overview of the differences and similarities in kidney function between humans, primates, and pigs, in preparation for pig-allograft to human xenotransplantation. The kidney, as the principal defender of body homeostasis, acts as a sensor, effector, and regulator of physiologic feedback systems. Considerations are made for anticipated effects on each system when a pig kidney is placed into a human recipient. Discussion topics include anatomy, global kidney function, sodium and water handling, kidney hormone production and response to circulating hormones, acid-base balance, and calcium and phosphorus handling. Based on available data, pig kidneys are anticipated to be compatible with human physiology, despite a few barriers.
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Affiliation(s)
- Christophe Hansen-Estruch
- Xenotransplantation Program, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David K.C. Cooper
- Xenotransplantation Program, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eric Judd
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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3
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Wallis M. Do some viruses use growth hormone, prolactin and their receptors to facilitate entry into cells?: Episodic evolution of hormones and receptors suggests host-virus arms races; related placental lactogens may provide protective viral decoys. Bioessays 2021; 43:e2000268. [PMID: 33521987 DOI: 10.1002/bies.202000268] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/30/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022]
Abstract
The molecular evolution of pituitary growth hormone and prolactin in mammals shows two unusual features: episodes of markedly accelerated evolution and, in some species, complex families of related proteins expressed in placenta and resulting from multiple gene duplications. Explanations of these phenomena in terms of physiological adaptations seem unconvincing. Here, I propose an alternative explanation, namely that these evolutionary features reflect the use of the hormones (and their receptors) as viral receptors. Episodes of rapid evolution can then be explained as due to "arms races" in which changes in the hormone lead to reduced interaction with the virus, and subsequent changes in the virus counteract this. Placental paralogues of the hormones could provide decoys that bind viruses, and protect the foetus against infection. The hypothesis implies that the extensive changes introduced into growth hormone, prolactin and their receptors during the course of mammalian evolution reflect viral interactions, not endocrine adaptations.
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Affiliation(s)
- Michael Wallis
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, UK
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4
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Dhandare BC, Rather MA, Bhosale BP, Pawar R, Guttula PK, Pagarkar AU. Molecular modeling, docking and dynamic simulations of growth hormone receptor (GHR) of Labeo rohita. J Biomol Struct Dyn 2020; 40:3024-3037. [PMID: 33179589 DOI: 10.1080/07391102.2020.1844063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Growth hormones (GH) have diverse functions like growth promotion, metabolism, appetite, reproduction and social behavior in vertebrates, which is mediated through the growth hormone receptor (GHR). This work was aimed to analyze structural features, homology modeling and molecular docking of Labeo rohita GHR protein. A physicochemical characteristic, like molecular weight was 67.2 kDa and hydropathicity was 0.336. Protein modeling and structure confirmation of L. rohita GHR protein showed 92.7% residues are in the favored region. Selection of ligands and molecular docking shown Melengestrol and Riboflavin ligand showed uppermost binding energy values -7.8 and -7.3 kcal/mol. Molecular interactions describe conventional hydrogen bonding of Melengestrol was observed with VAL94, GLU97, GLU95, TRP57, PHE33, THR34, PRO35, ASP36, PRO37, ARG49, GLY292, LYS291, ILE290, ALA287, LYS289 residues. Riboflavin hydrogen bonds interaction was at PRO37, ASP36, PRO35, THR34, ARG49, SER144, VAL443, GLN442, PRO284, ASP294, ILE285, PRO286, SER408, ALA287, GLY292, LYS291, ILE290, PRO288, LYS287. Molecular dynamics simulation outcomes revealed that complex 2 (Riboflavin and GHR protein) is better than complex1 (Melengestrol and GHR protein). Overall, the results of the present work lead identification of novel molecules that may be agonistic of growth hormone receptor protein and can be used to surge growth in fish. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bhushan C Dhandare
- Department of Fisheries Biology, College of Fisheries, Fish Biotechnology Laboratory, Ratnagiri, Maharashtra, India
| | - Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries, Rangil-Gandarbal, Sher-e-Kashmir University of Agricultural Sciences and Technology-Kashmir (SKAUST-K), India
| | - B P Bhosale
- Department of Fisheries Biology, College of Fisheries, Fish Biotechnology Laboratory, Ratnagiri, Maharashtra, India
| | - Ravindra Pawar
- Department of Fisheries Biology, College of Fisheries, Fish Biotechnology Laboratory, Ratnagiri, Maharashtra, India
| | | | - A U Pagarkar
- Marine Biological Research Station (MBRS), Ratnagiri, Maharashtra, India
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5
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Cattini PA, Bock ME, Jin Y, Zanghi JA, Vakili H. A useful model to compare human and mouse growth hormone gene chromosomal structure, expression and regulation, and immune tolerance of human growth hormone analogues. Growth Horm IGF Res 2018; 42-43:58-65. [PMID: 30227383 DOI: 10.1016/j.ghir.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/15/2018] [Accepted: 09/06/2018] [Indexed: 11/25/2022]
Abstract
Human (h) pituitary growth hormone (GH) is both physiologically and clinically important. GH reaches its highest circulatory levels in puberty, where it contributes to energy homeostasis and somatogenic growth. GH also helps to maintain tissues and organs and, thus, health and homeostasis. A reduction in the rate of hGH production begins in middle age but if GH insufficiency occurs this may result in tissue degenerative and metabolic diseases. As a consequence, hGH is prescribed under conditions of GH deficiency and, because of its lipolytic activity, stimulation of hGH release has also been used to treat obesity. However, studies of normal GH production and particularly synthesis versus secretion are not feasible in humans as they require sampling normal pituitaries from living subjects. Furthermore, human (or primate) GH structure and, as such, regulation and potential function, is distinct from non-primate rodent GH. As a result, most information about hGH regulation comes from measurements of secreted levels of GH in humans. Thus, partially humanized hGH transgenic mice, generated containing fragments of human chromosome 17 that include the intact hGH gene locus and many thousands of flanking base pairs as well as the endogenous mouse (m) GH gene provide a potentially useful model. Here we review this mouse model in terms of its ability to allow comparison of hGH versus mGH gene expression, and specifically: (i) GH locus structure as well as regulated and rhythmic expression; (ii) their ability to model a clinical assessment of hGH production in response to overeating and hyperinsulinemia as well as a possible effect of exercise, and (iii) their hGH-related immune tolerance and thus potential for testing hGH-related analogue immunogenicity.
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Affiliation(s)
- Peter A Cattini
- Department of Physiology & Pathophysiology, University of Manitoba, Manitoba, Canada.
| | - Margaret E Bock
- Department of Physiology & Pathophysiology, University of Manitoba, Manitoba, Canada
| | - Yan Jin
- Department of Physiology & Pathophysiology, University of Manitoba, Manitoba, Canada
| | | | - Hana Vakili
- Department of Pathology, University of Texas Southwestern Medical Center, TX, USA
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6
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Sell C. Minireview: The Complexities of IGF/Insulin Signaling in Aging: Why Flies and Worms Are Not Humans. Mol Endocrinol 2015; 29:1107-13. [PMID: 26102060 DOI: 10.1210/me.2015-1074] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A remarkable plasticity in life span has been uncovered in recent years, offering hope that the basic mechanisms of aging and interventions that delay aging may be identified in the coming decades. Life span extension has been achieved by genetic manipulation in multiple organisms including Sarcomyces cervisae, Caenorhabditis elegans, and Drosophila melanogaster, resulting in more than a doubling of life span in some cases. Typically, a reduction in function has been the most effective approach to extending life span, and a reduction in the insulin/IGF-1 signaling pathway appears to provide the most robust increase in life span. This highly conserved pathway integrates growth/survival signals with nutrient status. In mammals, it comprises part of the neuroendocrine axis, a critical regulator of growth and development. Reduced functionality of the neuroendocrine axis itself promotes life span extension in mammals; however, reduced activity of the IGF-1 signaling pathway specifically leads to less robust increases in life span. This review examines the differences in the insulin/IGF-1 axis between invertebrate and mammalian systems and discusses implications of these differences in terms of life span modulation.
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Affiliation(s)
- Christian Sell
- Drexel University College of Medicine, Philadelphia, Pennsylvania 19102
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7
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Integrated Genomics Approaches in Evolutionary and Ecological Endocrinology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:299-319. [DOI: 10.1007/978-94-007-7347-9_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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8
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Chuong EB, Hannibal RL, Green SL, Baker JC. Evolutionary perspectives into placental biology and disease. Appl Transl Genom 2013; 2:64-69. [PMID: 27896057 PMCID: PMC5121266 DOI: 10.1016/j.atg.2013.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 07/27/2013] [Indexed: 12/29/2022]
Abstract
In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal-fetal conflict shapes both basic placental and reproductive biology - in all species - will provide key insights into diseases of pregnancy.
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Affiliation(s)
- Edward B Chuong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roberta L Hannibal
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sherril L Green
- Department of Comparative Medicine, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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9
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Natural selection and adaptive evolution of leptin. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-012-5635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Pérez-Maya AA, Rodríguez-Sánchez IP, de Jong P, Wallis M, Barrera-Saldaña HA. The chimpanzee GH locus: composition, organization, and evolution. Mamm Genome 2012; 23:387-98. [DOI: 10.1007/s00335-012-9392-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 12/31/2011] [Indexed: 12/27/2022]
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11
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Evidence for positive selection on the leptin gene in Cetacea and Pinnipedia. PLoS One 2011; 6:e26579. [PMID: 22046310 PMCID: PMC3203152 DOI: 10.1371/journal.pone.0026579] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Accepted: 09/29/2011] [Indexed: 01/21/2023] Open
Abstract
The leptin gene has received intensive attention and scientific investigation for its importance in energy homeostasis and reproductive regulation in mammals. Furthermore, study of the leptin gene is of crucial importance for public health, particularly for its role in obesity, as well as for other numerous physiological roles that it plays in mammals. In the present work, we report the identification of novel leptin genes in 4 species of Cetacea, and a comparison with 55 publicly available leptin sequences from mammalian genome assemblies and previous studies. Our study provides evidence for positive selection in the suborder Odontoceti (toothed whales) of the Cetacea and the family Phocidae (earless seals) of the Pinnipedia. We also detected positive selection in several leptin gene residues in these two lineages. To test whether leptin and its receptor evolved in a coordinated manner, we analyzed 24 leptin receptor gene (LPR) sequences from available mammalian genome assemblies and other published data. Unlike the case of leptin, our analyses did not find evidence of positive selection for LPR across the Cetacea and Pinnipedia lineages. In line with this, positively selected sites identified in the leptin genes of these two lineages were located outside of leptin receptor binding sites, which at least partially explains why co-evolution of leptin and its receptor was not observed in the present study. Our study provides interesting insights into current understanding of the evolution of mammalian leptin genes in response to selective pressures from life in an aquatic environment, and leads to a hypothesis that new tissue specificity or novel physiologic functions of leptin genes may have arisen in both odontocetes and phocids. Additional data from other species encompassing varying life histories and functional tests of the adaptive role of the amino acid changes identified in this study will help determine the factors that promote the adaptive evolution of the leptin genes in marine mammals.
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12
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Wildman DE. Review: Toward an integrated evolutionary understanding of the mammalian placenta. Placenta 2011; 32 Suppl 2:S142-5. [PMID: 21306776 PMCID: PMC3437765 DOI: 10.1016/j.placenta.2011.01.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/05/2011] [Accepted: 01/06/2011] [Indexed: 11/27/2022]
Abstract
The placenta is fundamentally important for the success of pregnancy. Disruptions outside the normal range for placental function can result in pregnancy failure and other complications. The anatomy of the placenta varies greatly across mammals, as do key parameters in pregnancy such as neonatal body mass, length of gestation and number of offspring per pregnancy. An accurate understanding of the evolution of the mammalian placenta will require at minimum the integration of anatomical, developmental, physiological, genetic, and epigenetic data. Currently available data suggest that the placenta is a dynamic organ that has evolved rapidly in a lineage specific manner. Examination of the placenta from the perspective of human evolution shows that many anatomical features of the human placenta are relatively conserved. Despite the anatomical conservation of the human placenta there are many recently evolved placenta-specific genes (e.g. CGB, LGALS13, GH2) that are important in the development and function of the human placenta. Other mammalian genomes have also evolved specific suites of placenta-expressed genes. For example, rodents have undergone expansions of the cathepsin and prolactin families, and artiodactyls have expanded their suite of pregnancy-associated glycoproteins. In addition to lineage specific birth and death of gene family members, the pattern of imprinted loci varies greatly among species. Taken together, these studies suggest that a strategy reliant upon the sampling of placentally expressed and imprinted genes from a phylogenetically diverse range of species is appropriate for unraveling the conserved and derived aspects of placental biology.
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Affiliation(s)
- D E Wildman
- Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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13
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Cooper DN, Chen JM, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutat 2010; 31:631-55. [PMID: 20506564 DOI: 10.1002/humu.21260] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of reported germline mutations in human nuclear genes, either underlying or associated with inherited disease, has now exceeded 100,000 in more than 3,700 different genes. The availability of these data has both revolutionized the study of the morbid anatomy of the human genome and facilitated "personalized genomics." With approximately 300 new "inherited disease genes" (and approximately 10,000 new mutations) being identified annually, it is pertinent to ask how many "inherited disease genes" there are in the human genome, how many mutations reside within them, and where such lesions are likely to be located? To address these questions, it is necessary not only to reconsider how we define human genes but also to explore notions of gene "essentiality" and "dispensability."Answers to these questions are now emerging from recent novel insights into genome structure and function and through complete genome sequence information derived from multiple individual human genomes. However, a change in focus toward screening functional genomic elements as opposed to genes sensu stricto will be required if we are to capitalize fully on recent technical and conceptual advances and identify new types of disease-associated mutation within noncoding regions remote from the genes whose function they disrupt.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom.
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14
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Rodríguez-Sánchez IP, Tejero ME, Cole SA, Comuzzie AG, Nathanielsz PW, Wallis M, Barrera-Saldaña HA. Growth hormone-related genes from baboon (Papio hamadryas): Characterization, placental expression and evolutionary aspects. Gene 2010; 450:1-7. [PMID: 19651193 PMCID: PMC3088510 DOI: 10.1016/j.gene.2009.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 06/22/2009] [Accepted: 07/21/2009] [Indexed: 11/25/2022]
Abstract
Pregnancy is a complex physiological condition, and the growth hormone (GH)-related hormones produced in the placenta, which emerged during the evolution of primates, are thought to play an important metabolic role in pregnancy that is not yet fully understood. The aim of this study was to identify the genes and transcription products of the GH family in baboon (Papio hamadryas) and to assess these in relation to the evolution of this gene family. GH-related transcripts were amplified using total RNA from placental tissue, by reverse transcription coupled to polymerase chain reaction (RT-PCR). Three different GH-related transcripts were identified in baboon placental tissue, with two encoding chorionic somatomammotropins (CSH) and one the placental variant of GH (GH-2). The CSH transcripts showed some minor allelic variation, and a splice variant of CSH-C that retains its in-frame third intron. Gene sequences for GH-1 (probably representing the GH gene expressed primarily in the pituitary gland), GH-2 and the two CSHs were identified in the baboon genomic database, together with a CSH-related pseudogene. Phylogenetic analysis of the baboon GH-related sequences, together with those of a related Old World monkey, macaque, and ape outgroup (human), showed the equivalence of the genes in baboon and macaque, and revealed evidence for several episodes of rapid adaptive evolution. Many of the substitutions seen during the evolution of these placental proteins have occurred in the receptor-binding sites, especially site 2, contrasting with the strong conservation of the hydrophobic core.
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Affiliation(s)
- Irám Pablo Rodríguez-Sánchez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
| | - Maria Elizabeth Tejero
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX, USA
| | - Shelley A. Cole
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX, USA
| | - Anthony G. Comuzzie
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX, USA
- Southwest National Primate Research Center, San Antonio, TX, USA
| | - Peter W. Nathanielsz
- Center for Pregnancy and Newborn Research, University of Texas Health Science Center Medical School, Department of Obstetrics and Gynecology, San Antonio, TX, USA
| | - Michael Wallis
- Biochemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QG.U.K
| | - Hugo A. Barrera-Saldaña
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, México
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15
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Ancient origin of placental expression in the growth hormone genes of anthropoid primates. Proc Natl Acad Sci U S A 2009; 106:17083-8. [PMID: 19805162 DOI: 10.1073/pnas.0908377106] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In anthropoid primates, growth hormone (GH) genes have undergone at least 2 independent locus expansions, one in platyrrhines (New World monkeys) and another in catarrhines (Old World monkeys and apes). In catarrhines, the GH cluster has a pituitary-expressed gene called GH1; the remaining GH genes include placental GHs and placental lactogens. Here, we provide cDNA sequence evidence that the platyrrhine GH cluster also includes at least 3 placenta expressed genes and phylogenetic evidence that placenta expressed anthropoid GH genes have undergone strong adaptive evolution, whereas pituitary-expressed GH genes have faced strict functional constraint. Our phylogenetic evidence also points to lineage-specific gene gain and loss in early placental mammalian evolution, with at least three copies of the GH gene present at the time of the last common ancestor (LCA) of primates, rodents, and laurasiatherians. Anthropoid primates and laurasiatherians share gene descendants of one of these three copies, whereas rodents and strepsirrhine primates each maintain a separate copy. Eight of the amino-acid replacements that occurred on the lineage leading to the LCA of extant anthropoids have been implicated in GH signaling at the maternal-fetal interface. Thus, placental expression of GH may have preceded the separate series of GH gene duplications that occurred in catarrhines and platyrrhines (i.e., the roles played by placenta-expressed GHs in human pregnancy may have a longer evolutionary history than previously appreciated).
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16
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Menzies BR, Shaw G, Fletcher TP, Renfree MB. Early onset of ghrelin production in a marsupial. Mol Cell Endocrinol 2009; 299:266-73. [PMID: 19026714 DOI: 10.1016/j.mce.2008.10.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 10/17/2008] [Accepted: 10/20/2008] [Indexed: 11/17/2022]
Abstract
Ghrelin regulates appetite in mammals and can stimulate growth hormone (GH) release from the pituitary. In rats and humans, ghrelin cells appear in the stomach during late fetal life. Nevertheless, the role of ghrelin in early mammalian development is not well understood. Marsupials deliver highly altricial young that weigh less than 1g so they must feed and digest milk at a comparatively immature stage of development. Since they complete their growth and differentiation while in the pouch, they are accessible models in which to determine the time course of ghrelin production during development. We examined the distribution of gastric ghrelin cells, plasma ghrelin concentrations and pituitary expression of the ghrelin receptor (ghsr-1alpha) and GH in the tammar wallaby, Macropus eugenii. There were ghrelin immunopositive cells in the developing mesenchyme of the stomach from day 10 post partum (pp) to day 150pp. Subsequently ghrelin protein in the fore-stomach declined and was absent by day 250pp but remained in the gastric cells of the hind-stomach. Ghrelin was detected in the developing pancreas from day 10pp but was absent by day 150pp and in the adult. Pituitary ghsr-1alpha expression and plasma concentrations of ghrelin increased significantly up to day 70-120pp while GH expression was also elevated, declining with GH to reach adult levels by day 180pp. These results demonstrate an early onset of gastric ghrelin expression in the tammar in concert with a functional stomach at a relatively earlier stage than that of developmentally more mature eutherian young.
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Affiliation(s)
- Brandon R Menzies
- Department of Zoology, The University of Melbourne, Royal Parade, 3010 Victoria, Australia.
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17
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Menzies BR, Shaw G, Fletcher TP, Pask AJ, Renfree MB. Exon 3 of the growth hormone receptor (GH-R) is specific to eutherian mammals. Mol Cell Endocrinol 2008; 296:64-8. [PMID: 18706474 DOI: 10.1016/j.mce.2008.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 07/14/2008] [Indexed: 11/21/2022]
Abstract
Growth hormone receptor (GH-R) plays a critical role in the control of growth and metabolism in all vertebrates. GH-R consists of 9 coding exons (2-10) in all eutherian mammals, while the chicken only has 8 coding exons, and does not have an orthologous region to exon 3 in eutherians. To further understand the evolutionary origins of exon 3 of the GH-R in eutherians we cloned the full-length GH-R sequence in a marsupial, the tammar wallaby to determine whether exon 3 was present or absent in marsupial liver cDNA. There was no evidence for the presence of an exon 3 containing mRNA in sequence of tammar pouch young and adult livers. We next examined the genomes of the platypus (a monotreme mammal) and the grey short-tailed opossum (another marsupial). Like the tammar, the GH-R gene of neither species contained an exon 3. GH receptor can obviously function in the absence of this exon, raising speculation about the function of this domain, if any, in eutherians. A comparison of exon 3 protein sequences within 16 species of eutherian mammals showed that there was approximately 75% homology in the domain but only 3 of the 21 amino acids were identical (Leu12, Gln13 and Pro17). Interestingly, we detected greater evolutionary divergence in exon 3 sequences from species that have variants of GH or prolactin (PRL) in their placentas. These data show that exon 3 was inserted into the GH-R after the divergence of the marsupial and eutherian lineages at least 130 million years ago.
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Affiliation(s)
- Brandon R Menzies
- Department of Zoology, The University of Melbourne, Victoria, Australia.
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18
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Markov GV, Paris M, Bertrand S, Laudet V. The evolution of the ligand/receptor couple: a long road from comparative endocrinology to comparative genomics. Mol Cell Endocrinol 2008; 293:5-16. [PMID: 18634845 DOI: 10.1016/j.mce.2008.06.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 05/14/2008] [Accepted: 06/11/2008] [Indexed: 12/16/2022]
Abstract
Comparative endocrinology considers the evolution of bioregulatory systems and the anatomical structures and molecules that constitute the neuroendocrine and endocrine systems. One aim of comparative endocrinology is to trace the origins of the main endocrine systems. The understanding of the evolution of the ligand/receptor couple is central to this objective. One classical approach to tackle this question is the characterization of receptors and ligands in various types of non-model organisms using as a starting point the knowledge accumulated on classical models such as mammals (mainly human and mouse) and arthropods (with Drosophila among other insects). In this review we discuss the potential caveats associated to this two-by-two comparison between a classical model and non-model organisms. We suggest that the use of an evolutionary approach involving comparisons of several organisms in a coherent framework permits reconstruction of the most probable scenarios. The use of the vast amount of genomic data now available, coupled to functional experiments, offers unprecedented possibilities to trace back the origins of the main ligand/receptor couples.
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Pazos F, Valencia A. Protein co-evolution, co-adaptation and interactions. EMBO J 2008; 27:2648-55. [PMID: 18818697 PMCID: PMC2556093 DOI: 10.1038/emboj.2008.189] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 08/28/2008] [Indexed: 01/28/2023] Open
Abstract
Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes (‘co-adaptation') from other forces that, in a less specific way, can also create general patterns of co-evolution.
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Affiliation(s)
- Florencio Pazos
- Structure of Macromolecules, Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
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Growth hormone and in vitro maturation of rhesus macaque oocytes and subsequent embryo development. J Assist Reprod Genet 2008; 25:145-58. [PMID: 18278582 DOI: 10.1007/s10815-008-9208-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 02/04/2008] [Indexed: 10/22/2022] Open
Abstract
PURPOSE The objective of this study was to use a nonhuman primate model to examine the effects of growth hormone (GH) on oocyte in vitro maturation (IVM). METHODS Immunocytochemistry confirmed the presence of GH receptors in rhesus cumulus oocyte complexes and the cytoplasm of embryonic blastomeres. Recombinant human GH (r-hGH) was added to IVM medium and cumulus expansion, nuclear maturation, cytoplasmic maturation and embryo development were analyzed. RESULTS Cumulus expansion was highest in the presence of 1 and 10 ng/ml r-hGH. The addition of r-hGH during IVM increased the percentage of embryos progressing to at least the 9-16 cell stage. In a separate study, 100 ng/ml r-hGH was supplemented to IVM and embryo culture medium and no effect was observed. CONCLUSIONS The presence of GH receptors along with increased cumulus expansion and embryos progressing to the 9-16 cell stage supports the hypothesis that r-hGH may be involved in oocyte maturation.
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Varvio SL, Iso-Touru T, Kantanen J, Viitala S, Tapio I, Mäki-Tanila A, Zerabruk M, Vilkki J. Molecular anatomy of the cytoplasmic domain of bovine growth hormone receptor, a quantitative trait locus. Proc Biol Sci 2008; 275:1525-34. [PMID: 18381258 DOI: 10.1098/rspb.2008.0181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Quantitative trait loci (QTL) studies have indicated growth hormone receptor (GHR) as a candidate gene affecting cattle milk yield and composition. In order to characterize genetic variation at GHR in cattle, we studied European and East African breeds with different histories of selection, and Bos grunniens, Ovis aries, Sus scrofa, Bison bison and Rangifer tarandus as references. We sequenced most of the cytoplasmic domain (900 bp of exon 10), 89 bp of exon 8, including the putative causative mutation for the QTL effect, and 390 bp of intron 8 for comparison. In the cytoplasmic domain, seven synonymous and seven non-synonymous single nucleotide polymorphisms (SNP) were identified in cattle. Three non-synonymous SNPs were found in sheep and one synonymous SNP in yak, while other studied species were monomorphic. Three major haplotypes were observed, one unique to African breeds, one unique to European breeds and one shared. Bison and yak haplotypes are derivatives of the European haplotype lineage. Most of the exon 10 non-synonymous cattle SNPs appear at phylogenetically highly conserved sites. The polymorphisms in exon 10 cluster around a ruminant-specific tyrosine residue, suggesting that this site may act as an additional signalling domain of GHR in ruminants. Alternative explanations for the persistent polymorphism include balancing selection, hitch-hiking, pleiotropic or sexually antagonistic fitness effects or relaxed functional constraints.
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Affiliation(s)
- S-L Varvio
- Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
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22
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Survey of retail milk composition as affected by label claims regarding farm-management practices. ACTA ACUST UNITED AC 2008; 108:1198-203. [PMID: 18589029 DOI: 10.1016/j.jada.2008.04.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 01/29/2008] [Indexed: 11/23/2022]
Abstract
A trend in food labeling is to make claims related to agricultural management, and this is occurring with dairy labels. A survey study was conducted to compare retail milk for quality (antibiotics and bacterial counts), nutritional value (fat, protein, and solids-not-fat), and hormonal composition (somatotropin, insulin-like growth factor-1 [IGF-1], estradiol, and progesterone) as affected by three label claims related to dairy-cow management: conventional, recombinant bovine somatotropin (rbST)-free (processor-certified not from cows supplemented with rbST), or organic (follows US Department of Agriculture organic practices). Retail milk samples (n=334) from 48 states were collected. Based on a statistical analysis that reflected the sampling schema and distributions appropriate to the various response variables, minor differences were observed for conventional, rbST-free, and organic milk labels. Conventionally labeled milk had the lowest (P<0.05) bacterial counts compared to either milk labeled rbST-free or organic; however, these differences were not biologically meaningful. In addition, conventionally labeled milk had significantly less (P<0.05) estradiol and progesterone than organic milk (4.97 vs 6.40 pg/mL and 12.0 vs 13.9 ng/mL, respectively). Milk labeled rbST-free had similar concentrations of progesterone vs conventional milk and similar concentrations of estradiol vs organic milk. Concentrations of IGF-1 in milk were similar between conventional milk and milk labeled rbST-free. Organic milk had less (P<0.05) IGF-1 than either conventional or rbST-free milk (2.73 ng/mL vs 3.12 and 3.04 ng/mL, respectively). The macronutrient profiles of the different milks were similar, except for a slight increase in protein in organic milk (about 0.1% greater for organic compared to other milks). Label claims were not related to any meaningful differences in the milk compositional variables measured. It is important for food and nutrition professionals to know that conventional, rbST-free, and organic milk are compositionally similar so they can serve as a key resource to consumers who are making milk purchase (and consumption) decisions in a marketplace where there are misleading milk label claims.
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Juan D, Pazos F, Valencia A. Co-evolution and co-adaptation in protein networks. FEBS Lett 2008; 582:1225-30. [DOI: 10.1016/j.febslet.2008.02.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 02/08/2008] [Indexed: 10/22/2022]
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Kurbel S, Gulam D, Kovacić D, Mihaljević I, Faj D. Mutations that modulate receptor-hormone congruency as a cause of the primate GH receptor species specificity. Theory Biosci 2008; 123:435-40. [PMID: 18202875 DOI: 10.1016/j.thbio.2004.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Accepted: 10/29/2004] [Indexed: 11/26/2022]
Abstract
Peptide hormones depend on reliable recognition by their receptors. Any mutation that compromises recognition of hormone and receptor molecules is dangerous, the carrier animal would not procreate and the mutation would be lost. Although, most of the hormones from one mammalian species are active when injected into another, the incompatibility of human GH receptor toward nonprimate GHs is a notable exception. It is reported that the coevolution of GH and GHR in primates includes two crucial steps (Mol. Biol. Evol. 18 (2001) 945). The first was mutation of GH His-->Asp at position 171 that happened before the split of Old world and New world monkeys. The second event was Leu-->Arg change at position 43 in the GH receptor molecule that happened in the ancestor of Old world monkeys. The proposed model is based on the possibility that certain mutations can modify the surface of one of interacting molecules to form a confined empty space, a niche in the otherwise congruent hormone/receptor interface. Altoough affinity between molecules is probably slightly reduced, recognition and function are not compromised in this special case. Further mutations of hormone and receptor molecules are allowed under the condition that they remain confined to the niche space. Mutations that do not compromise hormone function can be passed to offsprings. If the consequent mutation of one molecule change its shape to fill the niche space, further mutations without function loss will become less probable. Without the niche space, the phase of fast evolution is closed and both genes become conserved. In this setting, accumulated mutations before the niche closing mutation are the cause of species specificity. To become a dominant variety, carrier animals must possess survival advantage in comparison to the carriers of other less advantageous mutations.
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Affiliation(s)
- Sven Kurbel
- Department of Physiology, Osijek Medical Faculty, Osijek Clinical Hospital, Huttlera 4, 31000, Osijek, Croatia,
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25
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Wallis M. Mammalian genome projects reveal new growth hormone (GH) sequences. Characterization of the GH-encoding genes of armadillo (Dasypus novemcinctus), hedgehog (Erinaceus europaeus), bat (Myotis lucifugus), hyrax (Procavia capensis), shrew (Sorex araneus), ground squirrel (Spermophilus tridecemlineatus), elephant (Loxodonta africana), cat (Felis catus) and opossum (Monodelphis domestica). Gen Comp Endocrinol 2008; 155:271-9. [PMID: 17574247 DOI: 10.1016/j.ygcen.2007.05.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2007] [Revised: 04/20/2007] [Accepted: 05/07/2007] [Indexed: 11/29/2022]
Abstract
Mammalian growth hormone (GH) sequences have been shown previously to display episodic evolution: the sequence is generally strongly conserved but on at least two occasions during mammalian evolution (on lineages leading to higher primates and ruminants) bursts of rapid evolution occurred. However, the number of mammalian orders studied previously has been relatively limited, and the availability of sequence data via mammalian genome projects provides the potential for extending the range of GH gene sequences examined. Complete or nearly complete GH gene sequences for six mammalian species for which no data were previously available have been extracted from the genome databases-Dasypus novemcinctus (nine-banded armadillo), Erinaceus europaeus (western European hedgehog), Myotis lucifugus (little brown bat), Procavia capensis (cape rock hyrax), Sorex araneus (European shrew), Spermophilus tridecemlineatus (13-lined ground squirrel). In addition incomplete data for several other species have been extended. Examination of the data in detail and comparison with previously available sequences has allowed assessment of the reliability of deduced sequences. Several of the new sequences differ substantially from the consensus sequence previously determined for eutherian GHs, indicating greater variability than previously recognised, and confirming the episodic pattern of evolution. The episodic pattern is not seen for signal sequences, 5' upstream sequence or synonymous substitutions-it is specific to the mature protein sequence, suggesting that it relates to the hormonal function. The substitutions accumulated during the course of GH evolution have occurred mainly on the side of the hormone facing away from the receptor, in a non-random fashion, and it is suggested that this may reflect interaction of the receptor-bound hormone with other proteins or small ligands.
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Affiliation(s)
- Michael Wallis
- Biochemistry Department, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9QG, UK.
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Yuri T, Kimball RT, Braun EL, Braun MJ. Duplication of Accelerated Evolution and Growth Hormone Gene in Passerine Birds. Mol Biol Evol 2007; 25:352-61. [DOI: 10.1093/molbev/msm260] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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27
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A simple model of co-evolutionary dynamics caused by epistatic selection. J Theor Biol 2007; 250:48-65. [PMID: 17923137 DOI: 10.1016/j.jtbi.2007.08.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 08/30/2007] [Accepted: 08/30/2007] [Indexed: 01/07/2023]
Abstract
Epistasis is the dependency of the effect of a mutation on the genetic background in which it occurs. Epistasis has been widely documented and implicated in the evolution of species barriers and the evolution of genetic architecture. Here we propose a simple model to formalize the idea that epistasis can also lead to co-evolutionary patterns in molecular evolution of interacting genes. This model epistasis is represented by the influence of one gene substitution on the fitness rank of the resident allele at another locus. We assume that increasing or decreasing fitness rank occur equally likely. In simulations we show that this form of epistasis leads to co-evolution in the sense that the length of an adaptive walk between interacting loci is highly correlated. This effect is caused by episodes of elevated rate of evolution in both loci simultaneously. We find that the influence of epistasis on these measures of co-evolutionary dynamics is relatively robust to the details of the model. The main factor influencing the correlation in evolutionary rates is the probability that a substitution will have an epistatic effect, but the strength of epistasis or the asymmetry of the initial fitness ranks of the alleles have only a minor effect. We suggest that covariance in rates of evolution among loci could be used to detect epistasis among loci.
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28
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Wallis OC, Wallis M. Evolution of growth hormone in primates: the GH gene clusters of the New World monkeys marmoset (Callithrix jacchus) and white-fronted capuchin (Cebus albifrons). J Mol Evol 2006; 63:591-601. [PMID: 17009125 DOI: 10.1007/s00239-006-0039-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Accepted: 06/26/2006] [Indexed: 10/24/2022]
Abstract
The GH gene cluster in marmoset, Callithrix jacchus, comprises eight GH-like genes and pseudogenes and appears to have arisen as a consequence of gene duplications occurring independently of those leading to the human GH gene cluster. We report here the complete sequence of the marmoset GH gene locus, including the intergenic regions and 5' and 3' flanking sequence, and a study of the multiple GH-like genes of an additional New World monkey (NWM), the white-fronted capuchin, Cebus albifrons. The marmoset sequence includes 945 nucleotides (nt) of 5' flanking sequence and 1596 nt of 3' flanking sequence that are "unique"; between these are eight repeat units, including the eight GH genes/pseudogenes. The breakpoints between these repeats are very similar, indicating a regular pattern of gene duplication. These breakpoints do not correspond to those found in the much less regular human GH gene cluster. This and phylogenetic analysis of the repeat units within the marmoset gene cluster strongly support the independent origin of these gene clusters, and the idea that the episode of rapid evolution that occurred during GH evolution in primates preceded the gene duplications. The marmoset GH gene cluster also differs from that of human in having fewer and more evenly distributed Alu sequences (a single pair in each repeat unit) and a "P-element" upstream of every gene/pseudogene. In human there is no P-element upstream of the gene encoding pituitary GH, and these elements have been implicated in placental expression of the other genes of the cluster. The GH gene clusters in marmoset and capuchin appear to have arisen as the consequence of a single-gene duplication event, but in capuchin there was then a remarkable expansion of the GH locus, giving at least 40 GH-like genes and pseudogenes. Thus even among NWMs the GH gene cluster is very variable.
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Affiliation(s)
- O Caryl Wallis
- Biochemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
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29
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Ely JJ, Frels WI, Howell S, Izard MK, Keeling ME, Lee DR. Twinning and heteropaternity in chimpanzees (Pan troglodytes). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 130:96-102. [PMID: 16353220 DOI: 10.1002/ajpa.20310] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Unlike monozygotic (MZ) twins, dizygotic (DZ) twins develop from separate ova. The resulting twins can have different sires if the fertilizing sperm comes from different males. Routine paternity testing of a pair of same-sexed chimpanzee twins born to a female housed with two males indicated that the twins were sired by two different males. DNA typing of 22 short-tandem repeat (STR) loci demonstrated that these twins were not MZ twins but heteropaternal DZ twins. Reproductive data from 1926-2002 at five domestic chimpanzee colonies, including 52 twins and two triplets in 1,865 maternities, were used to estimate total twinning rates and the MZ and DZ components. The average chimpanzee MZ twinning rate (0.43%) equaled the average human MZ rate (0.48%). However, the chimpanzee DZ twinning rate (2.36%) was over twice the human average, and higher than all but the fertility-enhanced human populations of Nigeria. Similarly high twinning rates among African chimpanzees indicated that these estimates were not artifacts of captivity. Log-linear analyses of maternal and paternal effects on recurrent twinning indicated that females who twinned previously had recurrence risks five times greater than average, while evidence for a paternal twinning effect was weak. Chimpanzee twinning rates appear to be elevated relative to corresponding estimated human rates, making twinning and possibly heteropaternity more important features of chimpanzee reproductive biology than previously recognized.
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Affiliation(s)
- John J Ely
- Alamogordo Primate Facility, Holloman Air Force Base, New Mexico 88330-0956, USA.
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30
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Poux C, Chevret P, Huchon D, de Jong WW, Douzery EJP. Arrival and diversification of caviomorph rodents and platyrrhine primates in South America. Syst Biol 2006; 55:228-44. [PMID: 16551580 DOI: 10.1080/10635150500481390] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the same molecular data set. Using sequences from three nuclear genes (ADRA2B, vWF, and IRBP, both separate and combined) from 60 species, and eight fossil calibration constraints, we estimated the times of origin and diversification of platyrrhines and caviomorphs via a Bayesian relaxed molecular clock approach. To account for the possible effect of an accelerated rate of evolution of the IRBP gene along the branch leading to the anthropoids, we performed the datings with and without IRBP (3768 sites and 2469 sites, respectively). The time window for the colonization of South America by primates and by rodents is demarcated by the dates of origin (upper bound) and radiation (lower bound) of platyrrhines and caviomorphs. According to this approach, platyrrhine primates colonized South America between 37.0 +/- 3.0 Mya (or 38.9 +/- 4.0 Mya without IRBP) and 16.8 +/- 2.3 (or 20.1 +/- 3.3) Mya, and caviomorph rodents between 45.4 +/- 4.1 (or 43.7 +/- 4.8) Mya and 36.7 +/- 3.7 (or 35.8 +/- 4.3) Mya. Considering both the fossil record and these molecular datings, the favored scenarios are a trans-Atlantic migration of primates from Africa at the end of the Eocene or beginning of the Oligocene, and a colonization of South America by rodents during the Middle or Late Eocene. Based on our nuclear DNA data, we cannot rule out the possibility of a concomitant arrival of primates and rodents in South America. The caviomorphs radiated soon after their arrival, before the Oligocene glaciations, and these early caviomorph lineages persisted until the present. By contrast, few platyrrhine fossils are known in the Oligocene, and the present-day taxa are the result of a quite recent, Early Miocene diversification.
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Affiliation(s)
- Céline Poux
- Laboratoire de Paléontologie, Phylogénie et Paléobiologie, CC064, Institut des Sciences de l'Evolution (UMR 5554/CNRS), Université Montpellier II, Place E., Bataillon, 34 095, Montpellier Cedex 05, France
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31
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Buggiotti L, Primmer CR. Molecular evolution of the avian growth hormone gene and comparison with its mammalian counterpart. J Evol Biol 2006; 19:844-54. [PMID: 16674581 DOI: 10.1111/j.1420-9101.2005.01042.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The molecular evolution of all available avian growth hormone (GH) gene sequences was investigated using both maximum-likelihood and parsimony methods, and the patterns compared to those found in mammals. In contrast to the rapid bursts of evolution observed for mammalian GH, the evolutionary rate of the avian GH mature peptide appears to have been more constant. However several positively selected sites were identified at functionally important positions in the avian signal peptide by the site-specific likelihood method. This implies that sequence variation in the avian GH signal peptide may be adaptive, although more conservative parsimony methods failed to confirm this. Nevertheless, the differing patterns of avian and mammalian GH signal peptide molecular evolution are consistent with the apparently differing roles of GH in controlling growth in these taxonomic groups and support the hypothesis that signal peptide sequence variation may in fact be the basis for increased functional complexity.
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Affiliation(s)
- L Buggiotti
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
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Wallis OC, Bill LJ, Burt EJ, Ellis SA, Wallis M. Polymorphism of the growth hormone gene of red deer (Cervus elaphus). Gen Comp Endocrinol 2006; 146:180-5. [PMID: 16356499 DOI: 10.1016/j.ygcen.2005.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 10/06/2005] [Accepted: 10/09/2005] [Indexed: 11/26/2022]
Abstract
In mammals, pituitary growth hormone (GH) is usually encoded by a single gene, but in some caprine ruminants there are two GH genes, and higher primates have a cluster of at least 5 GH-like genes. We have previously shown that in several artiodactyls (chevrotain, giraffe, and hippopotamus) there are two GH gene sequences, differing by 5-21 nucleotides (nt), but whether these arise from two distinct gene loci is unclear. We report here that in the red deer (Cervus elaphus) also there are two main GH gene sequences (designated A and B) differing at about 23 nt. Investigation of DNA from a number of individual animals demonstrated that this variation was due to allelic polymorphism, with individuals carrying either the A-type or the B-type sequence, or both. A- and B-type sequences showed some variation between individuals. The overall difference between the A and B sequences is substantial-greater than that between the GH gene sequences of three distinct bovine species, Bos taurus (ox), Bos indicus (zebu) and Bos grunniens (yak). The biological significance of the presence of two markedly differing GH gene sequences in red deer is not clear, but it is notable that several of the differences between the A and B sequences occur in the 5' upstream region, which may be associated with differences in gene expression.
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Affiliation(s)
- O Caryl Wallis
- Biochemistry Department, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9QG, UK
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33
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Ryynänen HJ, Primmer CR. Varying signals of the effects of natural selection during teleost growth hormone gene evolution. Genome 2006; 49:42-53. [PMID: 16462900 DOI: 10.1139/g05-079] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The growth hormone (GH) gene of teleost fish exhibits a higher degree of variability compared with other vertebrate groups. However, the different selective constraints at the sequence level are not well understood. In this study, maximum-likelihood (ML) models of codon substitutions were used to investigate Darwinian adaptive evolution of the GH gene in teleost fishes. Complete GH gene sequences of 54 fish species were classified into 4 orders, and the variable nature of GH was examined by determining the dNand dSrate variation and the rates of molecular evolution for each teleost order. The results indicate that although the overall evolution rate for teleost GH is high ((1.15 ± 0.01) × 10–9substitutions/(aa site·y)) compared with the "slow phases" in mammals ((0.21 to 0.28 ± 0.05) × 10–9), the vital structure of this gene has been retained. While the majority of the amino acid changes appear to be due to relaxation of purifying selection, some positively selected sites were detected in regions with no specifically identified role in protein function. The positively selected regions observed in salmoniformes lineage suggests a possible role for positive selection driving functional divergence in paralogous forms of the GH gene after whole-genome duplication in this lineage.Key words: teleost fish, growth hormone, positive selection, synonymous substitution, non-synonymous substitution, molecular evolution.
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Affiliation(s)
- Heikki J Ryynänen
- Department of Biological and Environmental Sciences, University of Helsinki, Finland
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Hughes JF, Coffin JM. Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome. Genetics 2005; 171:1183-94. [PMID: 16157677 PMCID: PMC1456821 DOI: 10.1534/genetics.105.043976] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HERV elements make up a significant fraction of the human genome and, as interspersed repetitive elements, have the capacity to provide substrates for ectopic recombination and gene conversion events. To understand the extent to which these events occur and gain further insight into the complex evolutionary history of these elements in our genome, we undertook a phylogenetic study of the long terminal repeat sequences of 15 HERV-K(HML-2) elements in various primate species. This family of human endogenous retroviruses first entered the primate genome between 35 and 45 million years ago. Throughout primate evolution, these elements have undergone bursts of amplification. From this analysis, which is the largest-scale study of HERV sequence dynamics during primate evolution to date, we were able to detect intraelement gene conversion and recombination at five HERV-K loci. We also found evidence for replacement of an ancient element by another HERV-K provirus, apparently reflecting an occurrence of retroviral integration by homologous recombination. The high frequency of these events casts doubt on the accuracy of integration time estimates based only on divergence between retroelement LTRs.
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Affiliation(s)
- Jennifer F Hughes
- Department of Molecular Microbiology and Program in Genetics, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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Wallis OC, Mac-Kwashie AO, Makri G, Wallis M. Molecular evolution of prolactin in primates. J Mol Evol 2005; 60:606-14. [PMID: 15983870 DOI: 10.1007/s00239-004-0239-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Accepted: 11/22/2004] [Indexed: 10/25/2022]
Abstract
Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked sequence differences between human prolactin and that of nonprimate mammals. We have defined this burst more precisely by sequencing the coding regions of prolactin genes for a prosimian, the slow loris (Nycticebus pygmaeus), and a New World monkey, the marmoset (Callithrix jacchus). Slow loris prolactin is very similar in sequence to pig prolactin, so the episode of rapid change occurred during primate evolution, after the separation of lines leading to prosimians and higher primates. Marmoset prolactin is similar in sequence to human prolactin, so the accelerated evolution occurred before divergence of New World monkeys and Old World monkeys/apes. The burst of change was confined largely to coding sequence (nonsynonymous sites) for mature prolactin and is not marked in other components of the gene sequence. This and the observations that (1) there was no apparent loss of function during the episode of rapid evolution, (2) the rate of evolution slowed toward the basal rate after this burst, and (3) the distribution of substitutions in the prolactin molecule is very uneven support the idea that this episode of rapid change was due to positive adaptive selection. In the slow loris and marmoset there is no evidence for duplication of the prolactin gene, and evidence from another New World monkey (Cebus albifrons) and from the chimpanzee and human genome sequences, suggests that this is the general position in primates, contrasting with the situation for GH genes. The chimpanzee prolactin sequence differs from that of human at two residues and comparison of human and chimpanzee prolactin gene sequences suggests that noncoding regions associated with regulating expression may be evolving differently from other noncoding regions.
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Affiliation(s)
- O Caryl Wallis
- Biochemistry Department, School of Life Sciences, University of Sussex, Brighton, UK.
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Ye C, Li Y, Shi P, Zhang YP. Molecular evolution of growth hormone gene family in old world monkeys and hominoids. Gene 2005; 350:183-92. [PMID: 15848116 DOI: 10.1016/j.gene.2005.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Revised: 02/07/2005] [Accepted: 03/01/2005] [Indexed: 11/16/2022]
Abstract
Growth hormone is a classic molecule in the study of the molecular clock hypothesis as it exhibits a relatively constant rate of evolution in most mammalian orders except primates and artiodactyls, where dramatically enhanced rate of evolution (25-50-fold) has been reported. The rapid evolution of primate growth hormone occurred after the divergence of tarsiers and simians, but before the separation of old world monkeys (OWM) from new world monkeys (NWM). Interestingly, this event of rapid sequence evolution coincided with multiple duplications of the growth hormone gene, suggesting gene duplication as a possible cause of the accelerated sequence evolution. Here we determined 21 different GH-like sequences from four species of OWM and hominoids. Combining with published sequences from OWM and hominoids, our analysis demonstrates that multiple gene duplications and several gene conversion events both occurred in the evolutionary history of this gene family in OWM/hominoids. The episode of recent duplications of CSH-like genes in gibbon is accompanied with rapid sequence evolution likely resulting from relaxation of purifying selection. GHN genes in both hominoids and OWM are under strong purifying selection. In contrast, CSH genes in both lineages are probably not. GHV genes in OWM and hominoids evolved at different evolutionary rates and underwent different selective constraints. Our results disclosed the complex history of the primate growth hormone gene family and raised intriguing questions on the consequences of these evolutionary events.
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Affiliation(s)
- Chun Ye
- Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Poux C, Douzery EJP. Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; 124:1-16. [PMID: 15085543 DOI: 10.1002/ajpa.10322] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The first third (ca. 1200 bp) of exon 1 of the nuclear gene encoding the interstitial retinoid-binding protein (IRBP) has been sequenced for 12 representative primates belonging to Lemuriformes, Lorisiformes, Tarsiiformes, Platyrrhini, and Catarrhini, and combined with available data (13 other primates, 11 nonprimate placentals, and 2 marsupials). Phylogenetic analyses using maximum likelihood on nucleotides and amino acids robustly support the monophyly of primates, Strepsirrhini, Lemuriformes, Lorisiformes, Anthropoidea, Catarrhini, and Platyrrhini. It is interesting to note that 1) Tarsiidae grouped with Anthropoidea, and the support for this node depends on the molecular characters considered; 2) Cheirogaleidae grouped within Lemuriformes; and 3) Daubentonia was the sister group of all other Lemuriformes. Study of the IRBP evolutionary rate shows a high heterogeneity within placentals and also within primates. Maximum likelihood local molecular clocks were assigned to three clades displaying significantly contrasted evolutionary rates. Paenungulata were shown to evolve 2.5-3 times faster than Perissodactyla and Lemuriformes. Six independent calibration points were used to estimate splitting ages of the main primate clades, and their compatibility was evaluated. Divergence ages were obtained for the following crown groups: 13.8-14.2 MY for Lorisiformes, 26.5-27.2 MY for Lemuroidea, 39.6-40.7 MY for Lemuriformes, 45.4-46.7 MY for Strepsirrhini, and 56.7-58.4 MY for Haplorrhini. The incompatibility between some paleontological and molecular estimates may reflect the incompleteness of the placental fossil record, and/or indicate that the variable IRBP evolutionary rates are not fully accommodated by local molecular clocks.
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Affiliation(s)
- Céline Poux
- Laboratoire de Paléontologie, Paléobiologie et Phylogénie-CC064, Institut des Sciences de l'Evolution UMR 5554/CNRS, Université Montpellier II 34095 Montpellier, France
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Maniou Z, Wallis OC, Wallis M. Episodic molecular evolution of pituitary growth hormone in Cetartiodactyla. J Mol Evol 2004; 58:743-53. [PMID: 15461431 DOI: 10.1007/s00239-004-2595-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The sequence of growth hormone (GH) is generally strongly conserved in mammals, but episodes of rapid change occurred during the evolution of primates and artiodactyls, when the rate of GH evolution apparently increased substantially. As a result the sequences of higher primate and ruminant GHs differ markedly from sequences of other mammalian GHs. In order to increase knowledge of GH evolution in Cetartiodactyla (Artiodactyla plus Cetacea) we have cloned and characterized GH genes from camel (Camelus dromedarius), hippopotamus (Hippopotamus amphibius), and giraffe (Giraffa camelopardalis), using genomic DNA and a polymerase chain reaction technique. As in other mammals, these GH genes comprise five exons and four introns. Two very similar GH gene sequences (encoding identical proteins) were found in each of hippopotamus and giraffe. The deduced sequence for the mature hippopotamus GH is identical to that of dolphin, in accord with current ideas of a close relationship between Cetacea and Hippopotamidae. The sequence of camel GH is identical to that reported previously for alpaca GH. The sequence of giraffe GH is very similar to that of other ruminants but differs from that of nonruminant cetartiodactyls at about 18 residues. The results demonstrate that the apparent burst of rapid evolution of GH occurred largely after the separation of the line leading to ruminants from other cetartiodactyls.
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Affiliation(s)
- Zoitsa Maniou
- Biochemistry Department, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex BN1 9QG, UK
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Revol De Mendoza A, Esquivel Escobedo D, Martínez Dávila I, Saldaña H. Expansion and divergence of the GH locus between spider monkey and chimpanzee. Gene 2004; 336:185-93. [PMID: 15246530 DOI: 10.1016/j.gene.2004.03.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2003] [Revised: 02/06/2004] [Accepted: 03/18/2004] [Indexed: 10/26/2022]
Abstract
Growth hormone (GH) has been previously described as showing distinct evolutionary stories between primates and other mammals. A burst of changes and successive amplification events took place in the primate lineage giving rise to a multigene family in the three Anthropoidea lineages. Polymerase chain reaction (PCR) was used to obtain the genes and the intergenic regions comprising the GH loci of the spider monkey (Ateles geoffroyi), a New-World primate, and of the chimpanzee (Pan troglodytes), an ape. The intergenic sequences of both species were screened by hybridization to detect copies of the Alu family, which have been implicated in the formation of the human GH locus. The GH locus of the spider monkey contains at least six GH-related genes, four of them were cloned. Likewise, five short intergenic sequences of approximately 3 kb were amplified and cloned. On the other hand, in the chimpanzee four new placental lactogen (PL) genes as well as four intergenic regions were amplified. Consequently, in this ape, six genes (two GHs, previously obtained, and four PLs) are clustered, separated by intergenic sequences of different lengths (two short ones of about 5 kb, and at least two long ones between 9 and 13 kb). The presence of Alu sequences within the intergenic regions of both GH loci corroborates the current hypothesis that they acted as a driving force for the locus expansion. GH sequence comparisons reveal that several gene-conversion events might have occurred during the formation of this genome region, which has undergone independent evolution in the three Anthropoidea branches. To establish the GH's evolutionary history may prove to be a difficult task due to these gene-conversion events.
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Affiliation(s)
- Agnès Revol De Mendoza
- Laboratorio de Biología Molecular, Unidad de Laboratorios de Ingeniería y Expresión Genéticas, Departamento de Bioquímica, Facultad de Medicina, UANL, Av. Madero y Dr. A. Pequeño, Col. Mitras Centro, Monterrey CP64460, Mexico
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Douzery EJP, Delsuc F, Stanhope MJ, Huchon D. Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations. J Mol Evol 2004; 57 Suppl 1:S201-13. [PMID: 15008417 DOI: 10.1007/s00239-003-0028-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.
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Affiliation(s)
- Emmanuel J P Douzery
- Laboratoire de Paléontologie, Paléobiologie et Phylogenie-CC064, Institut des Sciences de l'Evolution UMR 5554/CNRS, Université Montpellier II, Place E. Bataillon, 34 095 Montpellier Cedex 05, France.
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Abstract
Changes in technology in the past decade have had such an impact on the way that molecular evolution research is done that it is difficult now to imagine working in a world without genomics or the Internet. In 1992, GenBank was less than a hundredth of its current size and was updated every three months on a huge spool of tape. Homology searches took 30 minutes and rarely found a hit. Now it is difficult to find sequences with only a few homologs to use as examples for teaching bioinformatics. For molecular evolution researchers, the genomics revolution has showered us with raw data and the information revolution has given us the wherewithal to analyze it. In broad terms, the most significant outcome from these changes has been our newfound ability to examine the evolution of genomes as a whole, enabling us to infer genome-wide evolutionary patterns and to identify subsets of genes whose evolution has been in some way atypical.
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Affiliation(s)
- Kenneth H Wolfe
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland.
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Kondrashov AS, Sunyaev S, Kondrashov FA. Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci U S A 2002; 99:14878-83. [PMID: 12403824 PMCID: PMC137512 DOI: 10.1073/pnas.232565499] [Citation(s) in RCA: 228] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We study fitness landscape in the space of protein sequences by relating sets of human pathogenic missense mutations in 32 proteins to amino acid substitutions that occurred in the course of evolution of these proteins. On average, approximately 10% of deviations of a nonhuman protein from its human ortholog are compensated pathogenic deviations (CPDs), i.e., are caused by an amino acid substitution that, at this site, would be pathogenic to humans. Normal functioning of a CPD-containing protein must be caused by other, compensatory deviations of the nonhuman species from humans. Together, a CPD and the corresponding compensatory deviation form a Dobzhansky-Muller incompatibility that can be visualized as the corner on a fitness ridge. Thus, proteins evolve along fitness ridges which contain only approximately 10 steps between successive corners. The fraction of CPDs among all deviations of a protein from its human ortholog does not increase with the evolutionary distance between the proteins, indicating that substitutions that carry evolving proteins around these corners occur in rapid succession, driven by positive selection. Data on fitness of interspecies hybrids suggest that the compensatory change that makes a CPD fit usually occurs within the same protein. Data on protein structures and on cooccurrence of amino acids at different sites of multiple orthologous proteins often make it possible to provisionally identify the substitution that compensates a particular CPD.
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Affiliation(s)
- Alexey S Kondrashov
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
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Maniou Z, Caryl Wallis O, Wallis M. Cloning and characterisation of the GH gene from the common dolphin (Delphinus delphis). Gen Comp Endocrinol 2002; 127:300-6. [PMID: 12225773 DOI: 10.1016/s0016-6480(02)00058-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The sequence of growth hormone (GH) is generally strongly conserved in mammals, but episodes of rapid change occurred during the evolution of primates and artiodactyls, when the rate of GH evolution apparently increased at least 50-fold. As a result, the sequences of human and ruminant GHs differ substantially from those of other non-primate GHs. Recent molecular studies have suggested that cetaceans are closely related to artiodactyls and may be deeply nested within the artiodactyl phylogenetic tree. To extend the knowledge of GH in Cetartiodactyla (Artiodactyla plus Cetacea), we have cloned and characterised a single GH gene from the common dolphin (Delphinus delphis), using genomic DNA and a polymerase chain reaction technique. As in other mammals, the dolphin GH gene comprises five exons and four introns. The deduced sequence for the mature dolphin GH differs from that of pig at two residues only, showing that the apparent burst of rapid evolution of GH occurred largely after the separation of cetaceans and ruminants.
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Affiliation(s)
- Zoitsa Maniou
- Biochemistry Laboratory, School of Biological Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, Sussex, UK.
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Yi S, Bernat B, Pál G, Kossiakoff A, Li WH. Functional promiscuity of squirrel monkey growth hormone receptor toward both primate and nonprimate growth hormones. Mol Biol Evol 2002; 19:1083-92. [PMID: 12082127 DOI: 10.1093/oxfordjournals.molbev.a004166] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Primate growth hormone (GH) has evolved rapidly, having undergone approximately 30% amino acid substitutions from the inferred ancestral eutherian sequence. Nevertheless, human growth hormone (hGH) is physiologically effective when administered to nonprimate mammals. In contrast, its functional counterpart, the human growth hormone receptor (hGHR), has evolved species specificity so that it responds only to Old World primate GHs. It has been proposed that this species specificity of the hGHR is largely caused by the Leu --> Arg change at position 43 after a prior His --> Asp change at position 171 of the GH. Sequence analyses supported this hypothesis and revealed that the transitional phase in the GH:GHR coevolution still persists in New World monkeys. For example, although the GH of the squirrel monkey has the His --> Asp substitution at position 171, residue 43 of its GHR is a Leu, the nonprimate residue. If the squirrel monkey truly represents an intermediate stage of GH:GHR coevolution, its GHR should respond to both hGH and nonprimate GH. Also, if the emergence of species specificity was a result of the selection for a more efficient GH:GHR interaction, then changing residue 43 of the squirrel monkey growth hormone receptor (smGHR) to Arg should increase its binding affinity toward higher primate GH. To test these hypotheses, we performed protein-binding assays between the smGHR and both human and rat GHs, using the surface plasmon resonance methodology. Furthermore, the effects of reciprocal mutations at position 43 of human and squirrel monkey GHRs are measured for their binding affinities toward human and squirrel monkey GHs. The results from the binding kinetic assays clearly demonstrate that the smGHR is in the intermediate state of the evolution of species specificity. Interestingly, the altered residue Arg at position 43 of the smGHR does not lead to an increased binding affinity. The implications of these results on the evolution of the GH:GHR interaction and on functional evolution are discussed.
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Affiliation(s)
- Soojin Yi
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.
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Abstract
The availability of the human genomic sequence is changing the way in which biological questions are addressed. Based on the prediction of genes from nucleotide sequences, homologies among their encoded amino acids can be analyzed and used to place them in distinct families. This serves as a first step in building hypotheses for testing the structural and functional properties of previously uncharacterized paralogous genes. As genomic information from more organisms becomes available, these hypotheses can be refined through comparative genomics and phylogenetic studies. Instead of the traditional single-gene approach in endocrine research, we are beginning to gain an understanding of entire mammalian genomes, thus providing the basis to reveal subfamilies and pathways for genes involved in ligand signaling. The present review provides selective examples of postgenomic approaches in the analysis of novel genes involved in hormonal signaling and their chromosomal locations, polymorphisms, splicing variants, differential expression, and physiological function. In the postgenomic era, scientists will be able to move from a gene-by-gene approach to a reconstructionistic one by reading the encyclopedia of life from a global perspective. Eventually, a community-based approach will yield new insights into the complexity of intercellular communications, thereby offering us an understanding of hormonal physiology and pathophysiology.
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Affiliation(s)
- Chandra P Leo
- Division of Reproductive Biology, Department of Gynecology and Obstetrics, Stanford University School of Medicine, Stanford, California 94305-5317, USA
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46
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Abstract
The Symposium on Evolutionary Genomics was held in Atami, Japan, from 4 to 6 November 2001.
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Affiliation(s)
- Saitou Naruya
- Division of Population Genetics, National Institute of Genetics, Mishima 411-8540, Japan.
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