Understanding the Introduction of Genetic Variations by Random
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Structural Effects of Point Mutations in Proteins Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier
Structural effects of point mutations in proteins Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier To cite this version: Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier. Structural effects of point muta- tions in proteins. Proteins - Structure, Function and Bioinformatics, Wiley, 2018, 86 (8), pp.853-867. 10.1002/prot.25499. hal-01909365 HAL Id: hal-01909365 https://hal.sorbonne-universite.fr/hal-01909365 Submitted on 31 Oct 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Structural effects of point mutations in proteins Suvethigaa Shanthirabalan1, Jacques Chomilier2, Mathilde Carpentier1,2 1. Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France. 2. Sorbonne Université, CNRS, MNHN, IRD, IMPMC, BiBiP, Paris, France Corresponding author: [email protected] Mail: [email protected]; [email protected]; [email protected] Abstract A structural database of eleven families of chains differing by a single amino acid substitution has been built. Another structural dataset of 5 families with identical sequences has been used for comparison. The RMSD computed after a global superimposition of the mutated protein on each native one is smaller than the RMSD calculated among proteins of identical sequences. -
Population Size and the Rate of Evolution
Review Population size and the rate of evolution 1,2 1 3 Robert Lanfear , Hanna Kokko , and Adam Eyre-Walker 1 Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia 2 National Evolutionary Synthesis Center, Durham, NC, USA 3 School of Life Sciences, University of Sussex, Brighton, UK Does evolution proceed faster in larger or smaller popu- mutations occur and the chance that each mutation lations? The relationship between effective population spreads to fixation. size (Ne) and the rate of evolution has consequences for The purpose of this review is to synthesize theoretical our ability to understand and interpret genomic varia- and empirical knowledge of the relationship between tion, and is central to many aspects of evolution and effective population size (Ne, Box 1) and the substitution ecology. Many factors affect the relationship between Ne rate, which we term the Ne–rate relationship (NeRR). A and the rate of evolution, and recent theoretical and positive NeRR implies faster evolution in larger popula- empirical studies have shown some surprising and tions relative to smaller ones, and a negative NeRR implies sometimes counterintuitive results. Some mechanisms the opposite (Figure 1A,B). Although Ne has long been tend to make the relationship positive, others negative, known to be one of the most important factors determining and they can act simultaneously. The relationship also the substitution rate [5–8], several novel predictions and depends on whether one is interested in the rate of observations have emerged in recent years, causing some neutral, adaptive, or deleterious evolution. Here, we reassessment of earlier theory and highlighting some gaps synthesize theoretical and empirical approaches to un- in our understanding. -
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B. M ü ller, G ü nter P. Wagner, and Werner Callebaut, editors The Evolution of Cognition , edited by Cecilia Heyes and Ludwig Huber, 2000 Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology , edited by Gerd B. M ü ller and Stuart A. Newman, 2003 Environment, Development, and Evolution: Toward a Synthesis , edited by Brian K. Hall, Roy D. Pearson, and Gerd B. M ü ller, 2004 Evolution of Communication Systems: A Comparative Approach , edited by D. Kimbrough Oller and Ulrike Griebel, 2004 Modularity: Understanding the Development and Evolution of Natural Complex Systems , edited by Werner Callebaut and Diego Rasskin-Gutman, 2005 Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution , by Richard A. Watson, 2006 Biological Emergences: Evolution by Natural Experiment , by Robert G. B. Reid, 2007 Modeling Biology: Structure, Behaviors, Evolution , edited by Manfred D. Laubichler and Gerd B. M ü ller, 2007 Evolution of Communicative Flexibility: Complexity, Creativity, and Adaptability in Human and Animal Communication , edited by Kimbrough D. Oller and Ulrike Griebel, 2008 Functions in Biological and Artifi cial Worlds: Comparative Philosophical Perspectives , edited by Ulrich Krohs and Peter Kroes, 2009 Cognitive Biology: Evolutionary and Developmental Perspectives on Mind, Brain, and Behavior , edited by Luca Tommasi, Mary A. Peterson, and Lynn Nadel, 2009 Innovation in Cultural Systems: Contributions from Evolutionary Anthropology , edited by Michael J. O ’ Brien and Stephen J. Shennan, 2010 The Major Transitions in Evolution Revisited , edited by Brett Calcott and Kim Sterelny, 2011 Transformations of Lamarckism: From Subtle Fluids to Molecular Biology , edited by Snait B. -
An Unusually Low Microsatellite Mutation Rate in Dictyostelium Discoideum,An Organism with Unusually Abundant Microsatellites
Copyright Ó 2007 by the Genetics Society of America DOI: 10.1534/genetics.107.076067 An Unusually Low Microsatellite Mutation Rate in Dictyostelium discoideum,an Organism With Unusually Abundant Microsatellites Ryan McConnell, Sara Middlemist, Clea Scala, Joan E. Strassmann and David C. Queller1 Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005 Manuscript received May 18, 2007 Accepted for publication September 4, 2007 ABSTRACT The genome of the social amoeba Dictyostelium discoideum is known to have a very high density of microsatellite repeats, including thousands of triplet microsatellite repeats in coding regions that apparently code for long runs of single amino acids. We used a mutation accumulation study to see if unusually high microsatellite mutation rates contribute to this pattern. There was a modest bias toward mutations that increase repeat number, but because upward mutations were smaller than downward ones, this did not lead to a net average increase in size. Longer microsatellites had higher mutation rates than shorter ones, but did not show greater directional bias. The most striking finding is that the overall mutation rate is the lowest reported for microsatellites: 1 3 10À6 for 10 dinucleotide loci and 6 3 10À6 for 52 trinucleotide loci (which were longer). High microsatellite mutation rates therefore do not explain the high incidence of microsatellites. The causal relation may in fact be reversed, with low mutation rates evolving to protect against deleterious fitness effects of mutation at the numerous microsatellites. ICROSATELLITES, also known as simple se- In humans, certain triplet repeats that occur in or M quence repeats, are long stretches of a short near coding regions are subject to expansions that (1–6 bp), tandemly repeated DNA unit, such as the directly cause genetic diseases (Ashley and Warren motif CAA repeated 20 times. -
Adaptive Tuning of Mutation Rates Allows Fast Response to Lethal Stress In
Manuscript 1 Adaptive tuning of mutation rates allows fast response to lethal stress in 2 Escherichia coli 3 4 a a a a a,b 5 Toon Swings , Bram Van den Bergh , Sander Wuyts , Eline Oeyen , Karin Voordeckers , Kevin J. a,b a,c a a,* 6 Verstrepen , Maarten Fauvart , Natalie Verstraeten , Jan Michiels 7 8 a 9 Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20, 10 3001 Leuven, Belgium b 11 VIB Laboratory for Genetics and Genomics, Vlaams Instituut voor Biotechnologie (VIB) Bioincubator 12 Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium c 13 Smart Systems and Emerging Technologies Unit, imec, Kapeldreef 75, 3001 Leuven, Belgium * 14 To whom correspondence should be addressed: Jan Michiels, Department of Microbial and 2 15 Molecular Systems (M S), Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 16 2460, 3001 Leuven, Belgium, [email protected], Tel: +32 16 32 96 84 1 Manuscript 17 Abstract 18 19 While specific mutations allow organisms to adapt to stressful environments, most changes in an 20 organism's DNA negatively impact fitness. The mutation rate is therefore strictly regulated and often 21 considered a slowly-evolving parameter. In contrast, we demonstrate an unexpected flexibility in 22 cellular mutation rates as a response to changes in selective pressure. We show that hypermutation 23 independently evolves when different Escherichia coli cultures adapt to high ethanol stress. 24 Furthermore, hypermutator states are transitory and repeatedly alternate with decreases in mutation 25 rate. Specifically, population mutation rates rise when cells experience higher stress and decline again 26 once cells are adapted. -
Large Accumulation of Mrna and DNA Point Modi¢Cations in a Plant
FEBS Letters 472 (2000) 14^16 FEBS 23560 View metadata, citation and similar papers at core.ac.uk brought to you by CORE Large accumulation of mRNA and DNA point modi¢cationsprovided in by a Elsevier plant - Publisher Connector senescent tissue Maria Plaa;*, Anna Jofre¨a, Maria Martellb, Marisa Molinasa, Jordi Go¨mezb aLaboratori del Suro, Universitat de Girona, Campus Montilivi sn, E-17071 Girona, Spain bLiver Unit, Department of Medicine, Universitat Auto©noma de Barcelona, Hospital General Universitari Vall d'Hebron, E-08035 Barcelona, Spain Received 26 January 2000 Edited by Takashi Gojobori We investigated the frequency of cDNA modi¢cation in Abstract Although nucleic acids are the paradigm of genetic information conservation, they are inherently unstable molecules cork (phellem) compared to a normally growing young tissue that suffer intrinsic and environmental damage. Oxidative stress (root tip) using cork-oak (Quercus suber) as a model system. has been related to senescence and aging and, recently, it has For this purpose, we analyzed a population of Qs_hsp17 been shown that mutations accumulate at high frequency in mRNA sequences (reverse transcription PCR products form mitochondrial DNA with age. We investigated RNA and DNA position 32^401, AC AJ000691) in cork and in root tip tissue modifications in cork, a senescent plant tissue under high [6]. Cork (phellem) is an external layer of protective tissue, endogenous oxidative stress conditions. When compared to consisting of several layers of cells that deposit large amounts normally growing young tissue, cork revealed an unexpected of suberin and undergo programmed cell death. Due to phen- high frequency of point modifications in both cDNA (Pn = oxy radicals generated during suberin synthesis [7,8], cork 1/1784) and nuclear DNA (Pn = 1/1520). -
Estimating Effective Population Size Or Mutation Rate Using the Frequencies of Mutations of Various Classes in a Sample of DNA Sequences
Copyright 0 1994 by the Genetics Society of America Estimating Effective Population Size or Mutation Rate Using the Frequencies of Mutations of Various Classes in a Sample of DNA Sequences Yun-xin FU Center for Demographic and Population Genetics, University of Texas, Houston, Texas 77225 Manuscript received February 18, 1994 Accepted for publication August 27, 1994 ABSTRACT Mutations resulting in segregating sites of a sample of DNA sequences can be classified by size and type and the frequencies of mutations of different sizes and types can be inferred from the sample. A framework for estimating the essential parameter 8 = 4Nu utilizing the frequencies of mutations of various sizes and types is developed in this paper, where N is the effective size of a population and p is mutation rate per sequence per generation.The framework is a combination of coalescent theory, general linear model and Monte-Carlo integration, which leads to two new estimators 6, and 6, as well as a general Watterson’s estimator 6, and a general Tajima’s estimator 6,. The greatest strength of the framework is that it can be used under a variety of population models. The properties of the framework and the four estimators bK, e,,, 6, and 6, are investigated under three important population models: the neutral Wright-Fisher model, the neutral model with recombination and the neutral Wright’s finite-islands model. Under all these models, it is shown that 6, is the best estimator among the four even when recombination rate or migration rate has to be estimated. Under the neutral Wright-Fisher model, it is shown that the new estimator 6,has avariance close to alower bound ofvariances of allunbiased estimators of Owhichsuggests that 6, is a:ery efficient estimator. -
Point Mutations Underlying NF1 and NF2 and Increased Risk of Malignancy
Central Annals of Otolaryngology and Rhinology Mini Review *Corresponding author Andrea L.O. Hebb, MSc, PhD, RN, Maritime Lateral Skull Base Clinic, Otolaryngology, Neurosurgery and the Point Mutations Underlying NF1 Stereotactic Radiotherapy Group QEII Health Science Centre, Halifax, Canada; Email: [email protected] and NF2 and Increased Risk of Submitted: 12 February 2020 Accepted: 25 February 2020 Published: 27 February 2020 Malignancy ISSN: 2379-948X Copyright 1 2 3,4 3,4 Myles Davidson , Haupt TS , Morris DP , Shoman NM , © 2020 Davidson M, et al. 2,4 1,2,4 Walling SA , and Hebb ALO * OPEN ACCESS 1Department of Psychology, Saint Mary’s University, Canada 2Division of Neurosurgery, Dalhousie University, Canada Keywords 3 Division of Otolaryngology, Dalhousie University, Canada • Neurofibromatosis 4 Maritime Lateral Skull Base Clinic, Otolaryngology, Neurosurgery and the Stereotactic • Missense mutation Radiotherapy Group QEII Health Science Centre, Canada • Frameshift mutation • Nonsense mutation Abstract • KRAS gene • Colorectal cancer Neurofibromatosis Type-1 and Neurofibromatosis Type-2 are autosomal dominant • Acoustic neuroma tumor suppressor disorders that result from inherited or spontaneous mutations in • Vestibular schwannoma their respective genes. Neurofibromatosis Type-1 has been attributed to a non-sense • Meningioma mutation in chromosome 17 and Neurofibromatosis Type-2 a point mutation in its gene on chromosome 22. The following discussion briefly reviews point and frameshift mutations and explores the relationship between point mutations and development of malignancies in patients with Neurofibromatosis Type-1 and Neurofibromatosis Type-2. INTRODUCTION producing phenylalanine hydroxylase, the majority of which are missense mutations [4]. A point mutation is the change of one base for another in the DNA sequence. -
Methods for Detection of Point Mutations: Performance and Quality
Clinical Chemistry 43:7 1114–1128 (1997) Review Methods for detection of point mutations: performance and quality assessment Downloaded from https://academic.oup.com/clinchem/article/43/7/1114/5640834 by guest on 29 September 2021 Peter Nollau and Christoph Wagener*, on behalf of the IFCC Scientific Division, Committee on Molecular Biology Techniques We give an overview of current methods for the detec- 10) What kind of quality assessment can be achieved? tion of point mutations as well as small insertions and Here, different methods for the detection of point muta- deletions in clinical diagnostics. For each method, the tions and small deletions or insertions will be discussed following characteristics are specified: (a) principle, (b) on the basis of the above criteria (for simplification, we major modifications, (c) maximum fragment size that shall refer to point mutations only in the text, though in can be analyzed, (d) ratio and type of mutations that can general, small deletions or insertions are detected equally be detected, (e) minimum ratio of mutant to wild-type well by the methods described). In general, PCR is either alleles at which mutations can be detected, and (f) used for the generation of DNA fragments, or is part of detection methods. Special attention is paid to the the detection method. Screening methods for unknown possibilities of quality assessment and the potential for mutations as well as methods for the detection of known standardization and automation. mutations are included. Though DNA sequencing tech- niques will not be covered, we stress that DNA sequenc- INDEXING TERMS: alleles • electrophoresis • gene insertions ing is considered the gold standard and remains the • gene deletions • polymerase chain reaction definitive procedure for the detection of mutations so far. -
The Mutation Rate and Cancer (Tumorigenesis͞evolution͞selection͞mutator Phenotype͞genomic Instability)
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 14800–14803, December 1996 Medical Sciences The mutation rate and cancer (tumorigenesisyevolutionyselectionymutator phenotypeygenomic instability) I. P. M. TOMLINSON,M.R.NOVELLI, AND W. F. BODMER* Cancer Genetics Laboratory, Imperial Cancer Research Fund, 44, Lincoln’s Inn Fields, London WC2A 3PX, United Kingdom Contributed by W. F. Bodmer, September 9, 1996 ABSTRACT The selection of advantageous mutations un- mutations at loci such as those involved in DNA replication or derlies tumorigenesis. The growth of a tumor is therefore a repair. Thus, p53 mutations might lead to a mutator pheno- form of evolution at the somatic level, in which the population type, because the detection of and response to DNA damage is comprised of individual cells within the tumor. Models of are impaired (11). Many cancers have a mutator phenotype tumorigenesis have considered the relative importance of that results from mutations at loci involved in DNA mismatch mutation and selection. We show that selection is more repair (MMR) (12). In the hereditary nonpolyposis colorectal important than an increased mutation rate in the growth of a cancer (HNPCC) syndrome, one MMR allele is mutant in the tumor. Some cancers may acquire a ‘‘mutator phenotype,’’ germ line and the other allele mutates somatically. In sporadic probably leading to faster growth, but mutator phenotypes are cancers—for example, in up to 15% of all colon cancers— not necessary for carcinogenesis. somatic mutations (including allele loss) inactivate both mis- match repair alleles (13). It is widely accepted that tumorigenesis is a form of somatic Despite this evidence, the role of the mutator phenotype (or evolution, an idea which dates back to the writings of Boveri, ‘‘genomic instability’’) in sporadic cancers remains controver- James Murray, Little, and Tyzzer in the early years of this sial. -
Teacher Materials (PDF)
The Making of the Fittest: LESSON The Birth and Death of Genes TEACHER MATERIALS THE MOLECULAR EVOLUTION OF GENE BIRTH AND DEATH OVERVIEW This advanced lesson describes how mutation is a key element in both the birth and death of genes. Students proceed through a series of presentation slides that include background information, examples, and embedded video, and animation links. Questions challenge students to synthesize information and apply what they learn regarding how genes are gained and lost through evolutionary time. KEY CONCEPTS AND LEARNING OBJECTIVES • Mutations are changes in an organism’s DNA. They occur at random. • Whether or not a mutation has an effect on an organism’s traits depends on the type of mutation and its location. • Mutations can result in both the appearance of new genes and the loss of existing genes. • One way that a new gene can arise is when a gene is duplicated and one copy (or both copies) of the gene accumulates mutations, which change the function of the gene. • One way that a gene can be lost is when one or more mutations accumulate that destroy its function. Students will be able to • analyze gene sequences and transcribe DNA into messenger RNA (mRNA); • translate mRNA into a sequence of amino acids by using a genetic code chart; and • compare wild-type and mutated DNA sequences to determine the type of mutation present. CURRICULUM CONNECTIONS Curriculum Standards NGSS (April 2013) HS-LS1-1, HS-LS3-1, HS-LS3-2, HS-LS4-2, HS-LS4-4, HS-LS4-5 HS.LS1.A, HS.LS3.A, HS.LS3.B, HS.LS4.B, HS.LS4.C Common Core -
The Wayward Dog: Is the Australian Native Dog Or Dingo a Distinct Species?
Zootaxa 4317 (2): 201–224 ISSN 1175-5326 (print edition) http://www.mapress.com/j/zt/ Article ZOOTAXA Copyright © 2017 Magnolia Press ISSN 1175-5334 (online edition) https://doi.org/10.11646/zootaxa.4317.2.1 http://zoobank.org/urn:lsid:zoobank.org:pub:3CD420BC-2AED-4166-85F9-CCA0E4403271 The Wayward Dog: Is the Australian native dog or Dingo a distinct species? STEPHEN M. JACKSON1,2,3,9, COLIN P. GROVES4, PETER J.S. FLEMING5,6, KEN P. APLIN3, MARK D.B. ELDRIDGE7, ANTONIO GONZALEZ4 & KRISTOFER M. HELGEN8 1Animal Biosecurity & Food Safety, NSW Department of Primary Industries, Orange, New South Wales 2800, Australia. 2School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052. 3Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA. E-mail: [email protected] 4School of Archaeology & Anthropology, Australian National University, Canberra, ACT 0200, Australia. E: [email protected]; [email protected] 5Vertebrate Pest Research Unit, Biosecurity NSW, NSW Department of Primary Industries, Orange, New South Wales 2800, Australia. E-mail: [email protected] 6 School of Environmental & Rural Science, University of New England, Armidale, NSW 2351, Australia. 7Australian Museum Research Institute, Australian Museum, 1 William St. Sydney, NSW 2010, Australia. E-mail: [email protected] 8School of Biological Sciences, Environment Institute, and ARC (Australian Research Council) Centre for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia. E-mail: [email protected] 9Corresponding author. E-mail: [email protected] Abstract The taxonomic identity and status of the Australian Dingo has been unsettled and controversial since its initial description in 1792.