Doyne Lecture Rhodopsin and Autosomal Dominant Retinitis Pigmentosa
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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. -
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). -
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. -
Molecular Biology and Applied Genetics
MOLECULAR BIOLOGY AND APPLIED GENETICS FOR Medical Laboratory Technology Students Upgraded Lecture Note Series Mohammed Awole Adem Jimma University MOLECULAR BIOLOGY AND APPLIED GENETICS For Medical Laboratory Technician Students Lecture Note Series Mohammed Awole Adem Upgraded - 2006 In collaboration with The Carter Center (EPHTI) and The Federal Democratic Republic of Ethiopia Ministry of Education and Ministry of Health Jimma University PREFACE The problem faced today in the learning and teaching of Applied Genetics and Molecular Biology for laboratory technologists in universities, colleges andhealth institutions primarily from the unavailability of textbooks that focus on the needs of Ethiopian students. This lecture note has been prepared with the primary aim of alleviating the problems encountered in the teaching of Medical Applied Genetics and Molecular Biology course and in minimizing discrepancies prevailing among the different teaching and training health institutions. It can also be used in teaching any introductory course on medical Applied Genetics and Molecular Biology and as a reference material. This lecture note is specifically designed for medical laboratory technologists, and includes only those areas of molecular cell biology and Applied Genetics relevant to degree-level understanding of modern laboratory technology. Since genetics is prerequisite course to molecular biology, the lecture note starts with Genetics i followed by Molecular Biology. It provides students with molecular background to enable them to understand and critically analyze recent advances in laboratory sciences. Finally, it contains a glossary, which summarizes important terminologies used in the text. Each chapter begins by specific learning objectives and at the end of each chapter review questions are also included. -
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. -
Increased Transversions in a Novel Mutator Colon Cancer Cell Line
Oncogene (1998) 16, 1125 ± 1130 1998 Stockton Press All rights reserved 0950 ± 9232/98 $12.00 Increased transversions in a novel mutator colon cancer cell line James R Eshleman1,6, P Scott Donover2, Susan J Littman5, Sandra E Swinler2, Guo-Min Li4,7, James D Lutterbaugh2, James KV Willson2, Paul Modrich4, W David Sedwick2, Sanford D Markowitz2 and Martina L Veigl3 1Departments of Pathology; 2Medicine; 3General Medical Sciences and Ireland Cancer Center, University Hospitals of Cleveland and Case Western Reserve University, Suite 200, UCRC II, 11001 Cedar Road, Cleveland, Ohio 44106; 4Department of Biochemistry and Howard Hughes Medical Institute; 5Department of Medicine-Oncology, Duke University Medical Center, Nanaline Duke Building, Durham, North Carolina, 27710 USA We describe a novel mutator phenotype in the Vaco411 In this report we describe the unique speci®city of a colon cancer cell line which increases the spontaneous new mutator defect, which is independent of MMR. mutation rate 10 ± 100-fold over background. This We have previously shown that the Vaco411 colon mutator results primarily in transversion base substitu- cancer cell line displays a moderately (10 ± 100-fold) tions which are found infrequently in repair competent increased spontaneous mutation rate (Eshleman et al., cells. Of the four possible types of transversions, only 1995), and does not exhibit the RER phenotype which three were principally recovered. Spontaneous mutations generally accompanies MMR defects (Eshleman and recovered also included transitions and large deletions, Markowitz, 1995). We now describe the spontaneous but very few frameshifts were recovered. When compared hprt mutations arising in this new colon cancer to known mismatch repair defective colon cancer mutator, and compare these mutations to the repair mutators, the distribution of mutations in Vaco411 is capacity exhibited by cell-free extracts of this cell line. -
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 -
Genetics of Sma
CURE SMA CARE SERIES BOOKLET A SOURCE OF INFORMATION AND SUPPORT FOR INDIVIDUALS LIVING WITH SPINAL MUSCULAR ATROPHY AND THEIR FAMILIES. GENETICS OF SMA 1 SMA AND GENETICS Spinal muscular atrophy (SMA) is often referred to by several terms, including “genetic disease,” ‘’autosomal recessive genetic disorder,” “motor-neuron disease,” or ‘’neuromuscular disease.” SMA is a genetic disease. “Genetic” means it is relating to the genes and is inherited. Genes are responsible for our traits and unique characteristics. In SMA, there is a mutation in a gene responsible for the survival motor neuron (SMN) protein, a protein that is critical to the function of the nerves that control normal muscle movements. SMA is an autosomal recessive genetic disorder. “Autosomal recessive” refers to how the disease is inherited, or passed down, from the parents to the child. In SMA, the individual who is affected by SMA inherits two copies of a non-working gene—one copy from each parent. SMA is a motor-neuron disease. “Motor-neuron” refers to the type of nerve cell that sends messages to and from muscles responsible for movement and control of the head, neck, chest, abdomen, legs, and limbs. In SMA, the motor-neurons in the spinal cord do not have enough SMN protein. As a result, these motor-neurons do not function normally and may die, resulting in muscle weakness and atrophy (shrinkage). SMA is a neuromuscular disease. A “neuromuscular disease” affects the neuromuscular system. This can include problems with the nerves that control muscles, the muscles, and the communication between the nerves and the muscles. -
Understanding the Introduction of Genetic Variations by Random
Understanding the Introduction of Genetic Variations by Random Mutation Lesson Overview The focus of this lesson is on mutations as a source of genetic variability and what it means to say that mutations occur randomly at a particular rate. Students will make predictions about and observe the random mutations in the genomes of Avidians. Big Ideas The basic components of the Darwinian evolutionary mechanism are variation, inheritance, natural selection and time (aka VIST). Genetic variation is produced by mutations—changes in an organism’s genome caused by random replication errors. These errors occur at a relatively constant rate within broad groups of organisms and may be expressed probabilistically in various ways (e.g. mutation rate per base pair or per genome per replication).1 Because each site in the genome is equally susceptible to replication errors, the actual number of mutations occurring during a given replication event is variable, with higher mutation rates increasing the likelihood that mutations will occur. Random mutations produce the raw materials that are shaped by non-random selection into complex adaptive features. Objectives for Student Learning Through engagement in this lesson, students will: • Learn that mutations may occur at random in a genome at various rates • Observe how random mutations introduce genotypic variability in a population • Explain what mutation rates imply about the distribution of genotypic changes • Test hypotheses via a cycle of Hypothesis, Prediction, Testing, and Evaluation. Students’ Prior Knowledge Students should have a basic understanding of probability. However, they may struggle with what is meant by a particular mutation rate. Students may think, for instance, that a 10% mutation rate means that that there will always be a 10% difference between the ancestor and offspring, instead of recognizing that each site in the genome independently has a 10% chance of changing during replication. -
CRISPR-Cas9 DNA Base-Editing and Prime-Editing
International Journal of Molecular Sciences Review CRISPR-Cas9 DNA Base-Editing and Prime-Editing Ariel Kantor 1,2,*, Michelle E. McClements 1,2 and Robert E. MacLaren 1,2 1 Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK 2 Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK * Correspondence: [email protected] Received: 14 July 2020; Accepted: 25 August 2020; Published: 28 August 2020 Abstract: Many genetic diseases and undesirable traits are due to base-pair alterations in genomic DNA. Base-editing, the newest evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas-based technologies, can directly install point-mutations in cellular DNA without inducing a double-strand DNA break (DSB). Two classes of DNA base-editors have been described thus far, cytosine base-editors (CBEs) and adenine base-editors (ABEs). Recently, prime-editing (PE) has further expanded the CRISPR-base-edit toolkit to all twelve possible transition and transversion mutations, as well as small insertion or deletion mutations. Safe and efficient delivery of editing systems to target cells is one of the most paramount and challenging components for the therapeutic success of BEs. Due to its broad tropism, well-studied serotypes, and reduced immunogenicity, adeno-associated vector (AAV) has emerged as the leading platform for viral delivery of genome editing agents, including DNA-base-editors. In this review, we describe the development of various base-editors, assess their technical advantages and limitations, and discuss their therapeutic potential to treat debilitating human diseases. -
Code Cracking Mutation Practice
Name: ___________________________________________ Date: __________________ Period: _____ Code Cracking Mutation Practice Review: Three of the most common types of mutations are: 1. POINT MUTATION (one base is substituted for another) If a point mutation changes the amino acid, it’s called a MISSENSE mutation. If a point mutation does not change the amino acid, it’s called a SILENT mutation. If a point mutation changes the amino acid to a “stop,” it’s called a NONSENSE mutation. 2. INSERTION (an extra base, or bases, is inserted) 3. DELETION (a base, or bases, is lost) Deletion and insertion may cause what’s called a FRAMESHIFT, meaning the reading frame changes. These are typically one of the most serious types of mutations. Directions: 1. Following the same procedure you followed during the decoding activity (DNA to mRNA to Amino Acid), decode the original and mutated sequences and identify them as one of the three types of mutations listed above. If it is a point mutations, include whether it is a missense, silent, or nonsense mutations. The original DNA sequence is: DNA: TGC GTG CTT AAG CGG TGT ACA CGT TGC mRNA: Amino acid: Symbol: Now decode the following mutated sequences: 2. TGC GTG CTT AAG CGA TGT ACA CGT TGC What kind of mutation is this? Do you think it will affect the protein’s function? Why? 3. TGC GTG CTT AAG CGG TGT GCA CGT TGC What kind of mutation is this? Do you think it will affect the protein’s function? Why? 4. TGC GTG CTT AAG TAG TGT ACA CGT TGC What kind of mutation is this? Do you think it will affect the protein’s function? Why? 5. -
A Point Mutation Within Exon 5 of the WT1 Gene of a Sporadic Unilateral Wilms' Tumor Alters Gene Function1
(CANCER RESEARCH 58. 4180-4184. September 15. 1998] A Point Mutation within Exon 5 of the WT1 Gene of a Sporadic Unilateral Wilms' Tumor Alters Gene Function1 Li-Shuang Guan, Jia-jia Liu, Yong-Hua Xu, and Zhao-Yi Wang2 Department of Medicine, Division of Growth Regulation, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215 ¡L-S.C., Z-Y. W.¡.and Shanghai Institute of Cell Biology, Shanghai, People's Republic of China [J-j. L, Y-H. X.¡ ABSTRACT The insertion of three amino acids (+KTS) disrupts the distance between zinc fingers 3 and 4 and thus alters its DNA-binding speci The Wilms' tumor suppressor gene, nil, encodes a zinc-finger tran ficity (6, 7). The NH2 terminus of WT1 contains a proline- and scription factor, WT1, that represses transcription of a number of growth- glutamine-rich domain that exhibited transcription-regulating activity promoting genes and inhibits cell growth. The transcripts of wit undergo in transient cotransfection assays (7, 8) two alternative splicing events, giving rise to four isoforms of mRNA in constant ratios. The first alternative splice introduces an extra exon 5, Consistent with the view that WT1 functions as a tumor suppressor, which encodes 17 amino acid residues inserted between the transcription experimental evidence has demonstrated that WT1 represses tran regulatory domain and the DNA binding domain of WT1. Previously, we scription of a number of growth-related genes. These include, PDGF demonstrated that the 17-amino acid domain functioned as a transcription A-chain, insulin-like growth factor II, epidermal growth factor recep repressor when it was fused with the DNA binding domain of WT1.