DOCSLIB.ORG

Structural Basis for the Functional Changes by EGFR Exon 20 Insertion Mutations

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Structural Basis for the Functional Changes by EGFR Exon 20 Insertion Mutations cancers Article Structural Basis for the Functional Changes by EGFR Exon 20 Insertion Mutations Mahlet Z. Tamirat 1, Kari J. Kurppa 2, Klaus Elenius 2,3,4 and Mark S. Johnson 1,* 1 Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland; mahlet.tamirat@abo.fi 2 MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20520 Turku, Finland; kjkurp@utu.fi (K.J.K.); klaus.elenius@utu.fi (K.E.) 3 Department of Oncology, Turku University Hospital, 20521 Turku, Finland 4 Turku Bioscience Center, University of Turku and Åbo Akademi University, 20520 Turku, Finland * Correspondence: mark.s.johnson@abo.fi Simple Summary: Non-small cell lung cancer (NSCLC) is the most common type of lung cancer that claims the lives of many worldwide. Activating mutations occurring on the epidermal growth factor receptor (EGFR) protein have been associated with the pathogenesis of NSCLC, among which exon 20 insertion mutations play a significant role. The objective of this study is to examine the dynamic structural changes occurring on the EGFR protein as a result of two common EGFR exon 20 insertion mutations, V769insASV and D770insNPG. The study further aims to uncover the mechanisms by which the insertion mutations increase kinase activity. Our results suggest that the insertion mutations stabilize structural elements key to maintaining the active EGFR conformation. Furthermore, the insertions disrupt an interaction essential in stabilizing the inactive conformation, which could drive the kinase from an inactive to an active EGFR state. Citation: Tamirat, M.Z.; Kurppa, K.J.; Elenius, K.; Johnson, M.S. Structural Abstract: Activating somatic mutations of the epidermal growth factor receptor (EGFR) are frequently Basis for the Functional Changes by implicated in non-small cell lung cancer (NSCLC). While L858R and exon 19 deletion mutations are EGFR Exon 20 Insertion Mutations. most prevalent, exon 20 insertions are often observed in NSCLC. Here, we investigated the structural Cancers 2021, 13, 1120. https:// implications of two common EGFR exon 20 insertions in NSCLC, V769insASV and D770insNPG. The doi.org/10.3390/cancers13051120 active and inactive conformations of wild-type, D770insNPG and V769insASV EGFRs were probed Academic Editor: Mumtaz V. Rojiani; with molecular dynamics simulations to identify local and global alterations that the mutations exert Srikumar Chellappan; Amyn on the EGFR kinase domain, highlighting mechanisms for increased enzymatic activity. In the active M. Rojiani conformation, the mutations increase interactions that stabilize the αC helix that is essential for EGFR activity. Moreover, the key Lys745–Glu762 salt bridge was more conserved in the insertion mutations. Received: 14 January 2021 The mutants also preserved the state of the structurally critical aspartate–phenylalanine–glycine Accepted: 27 February 2021 (DFG)-motif and regulatory spine (R-spine), which were altered in wild-type EGFR. The insertions Published: 5 March 2021 altered the structure near the ATP-binding pocket, e.g., the P-loop, which may be a factor for the clinically observed tyrosine kinase inhibitor (TKI) insensitivity by the insertion mutants. The inactive Publisher’s Note: MDPI stays neutral state simulations also showed that the insertions disrupt the Ala767–Arg776 interaction that is key with regard to jurisdictional claims in for maintaining the “αC-out” inactive conformation, which could consequently fuel the transition published maps and institutional affil- from the inactive towards the active EGFR state. iations. Keywords: EGFR tyrosine kinase; exon 20 insertion mutations; non-small cell lung cancer; molecular dynamics simulation; structural biology Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article 1. Introduction distributed under the terms and conditions of the Creative Commons Epidermal growth factor receptor (EGFR) is a membrane-bound signaling protein Attribution (CC BY) license (https:// essential for the development of organisms, owing to its role in cell proliferation, differenti- creativecommons.org/licenses/by/ ation, migration and survival [1]. EGFR belongs to the ERBB family of receptor tyrosine 4.0/). kinases (RTK), which additionally includes ERBB2, ERBB3 and ERBB4 [2,3]. As with other Cancers 2021, 13, 1120. https://doi.org/10.3390/cancers13051120 https://www.mdpi.com/journal/cancers Cancers 2021, 13, x 2 of 23 1. Introduction Epidermal growth factor receptor (EGFR) is a membrane-bound signaling protein Cancers 2021, 13, 1120 essential for the development of organisms, owing to its role in cell proliferation, differ-2 of 21 entiation, migration and survival [1]. EGFR belongs to the ERBB family of receptor tyro- sine kinases (RTK), which additionally includes ERBB2, ERBB3 and ERBB4 [2,3]. As with otherfamily family members, members, the EGFR the EGFR monomer monomer is composed is composed of an of extracellularan extracellular domain, domain, a single- a sin- gle-passpass transmembrane transmembrane domain domain (TM), (TM), an intracellularan intracellular juxtamembrane juxtamembrane (JM) (JM) segment, segment, a cy- a cytoplasmictoplasmic kinase kinase domain domain and and a a C-terminal C-terminal tail tail (Figure (Figure1 A)1A) [ 3[3].]. ActivationActivation of EGFR is inducedinduced by by binding binding of of growth growth factor factor to to the the ectodomain ectodomain [3], [3], which which triggers triggers a a large large confor- confor- mationalmational change fromfrom aa tethered tethered to to an an extended extended ectodomain ectodomain state state as seenas seen by comparingby comparing the themonomeric monomeric [4] and[4] growth-factorand growth-factor bound bound homodimeric homodimeric [5] X-ray [5] structures.X-ray structures. Consequently, Conse- quently,EGFR monomers EGFR monomers on binding on binding a recognized a recogn growthized growth factor, e.g.,factor, EGF, e.g., form EGF, homodimers form homodi- or mersheterodimers or heterodimers with other with ERBB other familyERBB family monomers, monomers, and the and intracellular the intracellular kinase kinase domains do- mainsassociate associate as the asymmetricas the asymmetric dimer required dimer required for activation. for activation. Activated Activated kinase domains kinase bind do- mainsATP and bind catalyze ATP and the catalyze autophosphorylation the autophosphorylation of tyrosine residuesof tyrosine located residues at the located C-terminal at the C-terminaltail that act tail as dockingthat act as sites docking for various sites for other various proteins, other initiating proteins, intracellularinitiating intracellular signaling signalingpathways pathways [6,7]: in the [6,7]: case ofin EGFRthe case homodimers, of EGFR pathwayshomodimers, such aspathways the MAPK/ERK such as andthe MAPK/ERKPI3K-AKT that and are PI3K-AKT important that in cellare proliferation,important in cell differentiation, proliferation, migration differentiation, and inhibition migra- tionof apoptosis and inhibition [8,9]. of apoptosis [8,9]. Figure 1. EpidermalEpidermal growth growth factor receptor (EGFR) and struct structuralural features of the tyrosine kinase domain. ( A) The The different different domains that make up the EGFR protein and structure of the intracellular kinase domain (Protein Data Bank (PDB) ID 2GS2 [10]); [10]); key structural elements an andd active site-bound ATP are highlighted. ATP was positioned based on AMP-PNP bound EGFR structure (PDB ID 2ITX [[11]).11]). ( B) The active (cyan) and inactive (purple)(purple) conformations of the EGFR kinase domain as seen by comparing PDB ID 2GS2 with PDB ID 2GS7 [[10]:10]: the “αC-in” and “αC-out” conformations of the αC helix, the open and extended state of the activation loop (A-loop), the essential K745–E762 ionic interaction broken in the inactive state, and conformational differences within the aspartate–phenylalanine–glycine (DFG) motif. inactive state, and conformational differences within the aspartate–phenylalanine–glycine (DFG) motif. TheThe EGFR kinase domain exists in an equilibrium between an inactive and active conformationconformation (Figure (Figure 1B)1B) and and the the ATP ATP binding binding pocket pocket lies lies between between the the N-terminal N-terminal and and C- terminalC-terminal lobes lobes (Figure (Figure 1A)1A) [10,12,13]. [ 10,12,13 Both]. Both lobes lobes contribute contribute structural structural units, units, such such as the as αtheC helixαC helix and activation and activation loop loop(A-loop), (A-loop), which which are critical are critical for the for regulation the regulation of EGFR of kinase EGFR activity.kinase activity. On activation, On activation, the αC the helixαC of helix the EGFR of the EGFRkinase kinase domain domain assumes assumes the “α theC-in” “αC-in” con- formation,conformation, where where the α theC helixαC helixlocates locates near where near whereATP binds ATP within binds withinthe active the site active (Figure site 1B).(Figure Consequently,1B). Consequently, a conserved a conserved ionic interaction ionic interaction between between Glu762 Glu762 of the of α theC helixαC helixand and Lys745 of the β3 strand forms, stabilizing the active conformation. Furthermore, in the activated state, the A-loop attains an extended orientation, opening up space near the binding pocket. The aspartate–phenylalanine–glycine (DFG) motif that is located in the A-loop is placed so that the catalytic
Load more

Recommended publications
  • DNA Insertion Mutations Can Be Predicted by a Periodic Probability
    Research article DNA insertion mutations can be predicted by a periodic probability function Tatsuaki Tsuruyama1 1Department of Pathology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan Running title: Probability prediction of mutation Correspondence to: Tatsuaki Tsuruyama Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan Tel.: +81-75-751-3488; Fax: +81-75-761-9591 E-mail: [email protected] 1 Abstract It is generally difficult to predict the positions of mutations in genomic DNA at the nucleotide level. Retroviral DNA insertion is one mode of mutation, resulting in host infections that are difficult to treat. This mutation process involves the integration of retroviral DNA into the host-infected cellular genomic DNA following the interaction between host DNA and a pre-integration complex consisting of retroviral DNA and integrase. Here, we report that retroviral insertion sites around a hotspot within the Zfp521 and N-myc genes can be predicted by a periodic function that is deduced using the diffraction lattice model. In conclusion, the mutagenesis process is described by a biophysical model for DNA–DNA interactions. Keywords: Insertion, mutagenesis, palindromic sequence, retroviral DNA 2 Text Introduction Extensive research has examined retroviral insertions to further our understanding of DNA mutations. Retrovirus-related diseases, including leukemia/lymphoma and AIDS, develop after retroviral genome insertion into the genomic DNA of the infected host cell. Retroviral DNA insertion is one of the modes of insertional mutation. After reverse-transcription of the retroviral genomic RNA into DNA, the retroviral DNA forms a pre-insertion complex (PIC) with the integrase enzyme, which catalyzes the insertion reaction.
    [Show full text]
  • DNA Sequence Insertion and Evolutionary Variation in Gene Regulation (Mobile Elements/Long Terminal Repeats/Alu Sequences/Factor-Binding Sites) Roy J
    Proc. Natl. Acad. Sci. USA Vol. 93, pp. 9374-9377, September 1996 Colloquium Paper This paper was presented at a colloquium entitled "Biology of Developmental Transcription Control, " organized by Eric H. Davidson, Roy J. Britten, and Gary Felsenfeld, held October 26-28, 1995, at the National Academy of Sciences in Irvine, CA. DNA sequence insertion and evolutionary variation in gene regulation (mobile elements/long terminal repeats/Alu sequences/factor-binding sites) RoY J. BRITrEN Division of Biology, California Institute of Technology, 101 Dahlia Avenue, Corona del Mar, CA 92625 ABSTRACT Current evidence on the long-term evolution- 3 and 4). Sequence change, obscuring the original structure, ary effect of insertion of sequence elements into gene regions has occurred in the long history, and the underlying rate of is reviewed, restricted to cases where a sequence derived from base substitution that is responsible is known (5). a past insertion participates in the regulation of expression of The requirements for a convincing example are: (i) that a useful gene. Ten such examples in eukaryotes demonstrate there be a trace of a known class of elements present in gene that segments of repetitive DNA or mobile elements have been region; (ii) that there is evidence that it has been there long inserted in the past in gene regions, have been preserved, enough to not just be a transient mutation; (iii) that some sometimes modified by selection, and now affect control of sequence residue of the mobile element or repeat participates transcription ofthe adjacent gene. Included are only examples in regulation of expression of the gene; (iv) that the gene have in which transcription control was modified by the insert.
    [Show full text]
  • Insertion Element (IS1 Insertion Sequence/Chloramphenicol Resistance Transposon Tn9/Integrative Recombination) L
    Proc. Nati. Acad. Sci. USA Vol. 75, No. 3, pp. 1490-1494, March 1978 Genetics Chromosomal integration of phage X by means of a DNA insertion element (IS1 insertion sequence/chloramphenicol resistance transposon Tn9/integrative recombination) L. A. MACHATTIE AND J. A. SHAPIRO Department of Microbiology, University of Chicago, Chicago, Illinois 60637 Communicated by Albert Dorfman, January 10, 1978 ABSTRACT Phage Xcamll2, which contains the chlor- carries a deletion of the gal-attB-bio region of the Escherichia amphenicol resistance transposon Tn9 and has a deletion of attP coil chromosome. MGBO is a gal+bio+ transductant of and the int gene, will lysogenize Escherichia coli K-12. Pro- phage integration occurs at different chromosomal sites, in- MADO. MS6 is a galE indicator for detection of XgalE + T- cluding lacYand maiB, but not at attB. All Xcamll2 prophages transducing particles and S1653 is a gal deletion strain for de- are excised from the chromosome after induction but with tection of Xgal + particles (3). Strain 200PS is a thi lacY strain various efficiencies for different locations. Heteroduplex from the Pasteur collection. Strain QL carries a complete lac analysis of XplacZ transducing phages isolated from a lacY:: deletion, strain X9003 carries the nonpolar M15 lacZ deletion, Xcamll2 prophage reveals an insertion sequence 1 (IS1) element and either will serve as indicator for XplacZ phage in a blue at theloint of viral and chromosomal DNA. Two lines of evi- dencekdicate that Xcamll2 encodes an excision activity that plaque assay (8). recognizes the ISI element: (i) prophage derepression increases Media. Our basic minimal medium and complete TYE the frequency of excision from IacYto yield lac+ revertants, and medium have been described (9).
    [Show full text]
  • Gene Therapy Glossary of Terms
    GENE THERAPY GLOSSARY OF TERMS A • Phase 3: A phase of research to describe clinical trials • Allele: one of two or more alternative forms of a gene that that gather more information about a drug’s safety and arise by mutation and are found at the same place on a effectiveness by studying different populations and chromosome. different dosages and by using the drug in combination • Adeno-Associated Virus: A single stranded DNA virus that has with other drugs. These studies typically involve more not been found to cause disease in humans. This type of virus participants.7 is the most frequently used in gene therapy.1 • Phase 4: A phase of research to describe clinical trials • Adenovirus: A member of a family of viruses that can cause occurring after FDA has approved a drug for marketing. infections in the respiratory tract, eye, and gastrointestinal They include post market requirement and commitment tract. studies that are required of or agreed to by the study • Adeno-Associated Virus Vector: Adeno viruses used as sponsor. These trials gather additional information about a vehicles for genes, whose core genetic material has been drug’s safety, efficacy, or optimal use.8 removed and replaced by the FVIII- or FIX-gene • Codon: a sequence of three nucleotides in DNA or RNA • Amino Acids: building block of a protein that gives instructions to add a specific amino acid to an • Antibody: a protein produced by immune cells called B-cells elongating protein in response to a foreign molecule; acts by binding to the • CRISPR: a family of DNA sequences that can be cleaved by molecule and often making it inactive or targeting it for specific enzymes, and therefore serve as a guide to cut out destruction and insert genes.
    [Show full text]
  • The Origin, Evolution, and Functional Impact of Short Insertion–Deletion Variants Identified in 179 Human Genomes
    Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Research The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes Stephen B. Montgomery,1,2,3,14,16 David L. Goode,3,14,15 Erika Kvikstad,4,13,14 Cornelis A. Albers,5,6 Zhengdong D. Zhang,7 Xinmeng Jasmine Mu,8 Guruprasad Ananda,9 Bryan Howie,10 Konrad J. Karczewski,3 Kevin S. Smith,2 Vanessa Anaya,2 Rhea Richardson,2 Joe Davis,3 The 1000 Genomes Pilot Project Consortium, Daniel G. MacArthur,5,11 Arend Sidow,2,3 Laurent Duret,4 Mark Gerstein,8 Kateryna D. Makova,9 Jonathan Marchini,12 Gil McVean,12,13 and Gerton Lunter13,16 1–13[Author affiliations appear at the end of the paper.] Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our un- derstanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 individuals representing three diverse human populations. We show that rates of indel mutagenesis are highly heterogeneous, with 43%–48% of indels occurring in 4.03% of the genome, whereas in the remaining 96% their prevalence is 16 times lower than SNPs. Polymerase slippage can explain upwards of three-fourths of all indels, with the remainder being mostly simple de- letions in complex sequence. However, insertions do occur and are significantly associated with pseudo-palindromic sequence features compatible with the fork stalling and template switching (FoSTeS) mechanism more commonly as- sociated with large structural variations.
    [Show full text]
  • Glossary of Common Terms in Genetics
    Glossary of Common Terms in Genetics Acquired mutations Gene changes genetic information. DNA is held Multiplexing A sequencing approach that that arise within individual cells and together by weak bonds between base uses several pooled samples simultaneous­ accumulate throughout a person's life pairs of nucleotides: adenine, guanine, ly, greatly increasing sequencing speed. span. cytosine, and thymine. Mutation Any heritable change in DNA Alleles One of a group of genes that Gene The fundamental unit of heredi­ sequence. occur alternatively at a given locus. A ty. A gene is an ordered sequence of single allele is inherited separately from nucleotides located in a particular posi­ Nucleotide A subunit of DNA or RNA each parent (e.g., at a locus for eye tion on a particular chromosome that consisting of a nitrogenous base, a phos­ color, the allele might result in blue or encodes a specific functional product phate molecule, and a sugar molecule. brown eyes). (i.e., a protein or RNA molecule i. Thousands of nucleotides are linked to form a DNA or RNA molecule. Base pair Two nitrogenous bases (ade­ Gene expression The process by which nine and thymine or guanine and cyto- a gene's coded information is converted Oncogene One or more forms of a sine) held together by weak bonds. Two into the structures present and operat­ gene associated with cancer. strands of DNA are held together in the ing in the cell. shape of a double helix by the bonds Polygenic disorders Genetic disorders between base pairs. Gene mapping Determination of the resulting from the combined action of relative positions of genes on a DNA alleles of more than one gene (e.g., Carrier A person who has a recessive molecule and the distance between heart disease, diabetes, and some can­ mutated gene along with its normal them.
    [Show full text]
  • 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.
    [Show full text]
  • DNA Mutation Worksheetkey
    Name: ________________________ BIO300/CMPSC300 Mutation - Spring 2016 As you know from lecture, there are several types of mutation: DELETION (a base is lost) INSERTION (an extra base is inserted) Deletion and insertion may cause what’s called a FRAMESHIFT, meaning the reading “frame” changes, changing the amino acid sequence. 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. Complete the boxes below. Classify each as either Deletion, Insertion, or Substitution AND as either frameshift, missense, silent or nonsense (hint: deletion or insertion will always be frameshift). Original DNA Sequence: T A C A C C T T G G C G A C G A C T mRNA Sequence: A U G U G G A A C C G C U G C U G A Amino Acid Sequence: MET -TRP- ASN - ARG- CYS - (STOP) Mutated DNA Sequence #1: T A C A T C T T G G C G A C G A C T What’s the mRNA sequence? A U G U A G A A C C G C U G C U G A What will be the amino acid sequence? MET -(STOP) Will there likely be effects? YES What kind of mutation is this? POINT MUTATION- NONSENSE Mutated DNA Sequence #2: T A C G A C C T T G G C G A C G A C T What’s the mRNA sequence? A U G C U G G A A C C G C U G C U G A What will be the amino acid sequence? MET - LEU -GLU– PRO-LEU-LEU Will there likely be effects? YES What kind of mutation is this? INSERTION - FRAME SHIFT Mutated DNA Sequence
    [Show full text]
  • Basic Molecular Genetics for Epidemiologists F Calafell, N Malats
    398 GLOSSARY Basic molecular genetics for epidemiologists F Calafell, N Malats ............................................................................................................................. J Epidemiol Community Health 2003;57:398–400 This is the first of a series of three glossaries on CHROMOSOME molecular genetics. This article focuses on basic Linear or (in bacteria and organelles) circular DNA molecule that constitutes the basic physical molecular terms. block of heredity. Chromosomes in diploid organ- .......................................................................... isms such as humans come in pairs; each member of a pair is inherited from one of the parents. general increase in the number of epide- Humans carry 23 pairs of chromosomes (22 pairs miological research articles that apply basic of autosomes and two sex chromosomes); chromo- science methods in their studies, resulting somes are distinguished by their length (from 48 A to 257 million base pairs) and by their banding in what is known as both molecular and genetic epidemiology, is evident. Actually, genetics has pattern when stained with appropriate methods. come into the epidemiological scene with plenty Homologous chromosome of new sophisticated concepts and methodologi- cal issues. Each of the chromosomes in a pair with respect to This fact led the editors of the journal to offer the other. Homologous chromosomes carry the you a glossary of terms commonly used in papers same set of genes, and recombine with each other applying genetic methods to health problems to during meiosis. facilitate your “walking” around the journal Sex chromosome issues and enjoying the articles while learning. Sex determining chromosome. In humans, as in Obviously, the topics are so extensive and inno- all other mammals, embryos carrying XX sex vative that a single short glossary would not be chromosomes develop as females, whereas XY sufficient to provide you with the minimum embryos develop as males.
    [Show full text]
  • The Transversion Pathway (Spontaneous Mutation/Acid Mutagenesis/Glycosidic Bond Migration) PAUL M
    Proc. Natl. Acad. Sci. USA Vol. 73, No. 11, pp. 4159-4163, November 1976 Genetics Heat mutagenesis in bacteriophage T4: The transversion pathway (spontaneous mutation/acid mutagenesis/glycosidic bond migration) PAUL M. BINGHAM, RICHARD H. BALTZ*, LYNN S. RIPLEY, AND JOHN W. DRAKEt Department of Microbiology, University of Illinois, Urbana, Ill. 61801 Communicated by Matthew S. Meselson, September 3, 1976 ABSTRACT Heat induces transversions (as well as transi- produce the homologous ochre (UAA) mutant and therefore tions) at GC base pairs in bacteriophage T4. The target base for go undetected, the heat-induced reversion of amber mutants transversions is guanine, which is converted to a product which could occur only by transversions at the G-C base pair (pro- is sometimes replicated and transcribed as a pyrimidine. A model for this process is proposed in which the deoxyguanosine ducing the tyrosine codons UAU or UAC). Table 2 shows that glycosidic bond migrates from N9 to N2: the resulting deoxy- amber mutants readily revert when heated. neoguanosine may pair with normal guanine to produce GC Amber mutants might, however, revert by extracistronic _ CG transversions. suppressors arising by G-C A-T transitions. Hydroxylamine specifically induces this transition, and a considerable number We have previously described the induction by heat of G-C - of amber mutants in the WI region have already been shown A-T transitions in bacteriophage T4 by deamination of cytosine to be refractory to hydroxylamine-induced reversion (3, 4). We to produce uracil (1). Earlier studies of heat mutagenesis in have extended this result by showing that the amber mutants bacteriophage T4 suggested that transversions were also in- described in Table 2 are also insusceptible to hydroxylamine- duced at G-C base pairs (2), and this conjecture is now con- induced reversion even when the treated stocks are grown firmed.
    [Show full text]
  • Recurrent De Novo Mutations in Neurodevelopmental Disorders: Properties and Clinical Implications Amy B
    Wilfert et al. Genome Medicine (2017) 9:101 DOI 10.1186/s13073-017-0498-x REVIEW Open Access Recurrent de novo mutations in neurodevelopmental disorders: properties and clinical implications Amy B. Wilfert1†, Arvis Sulovari1†, Tychele N. Turner1, Bradley P. Coe1 and Evan E. Eichler1,2* Abstract Next-generation sequencing (NGS) is now more accessible to clinicians and researchers. As a result, our understanding of the genetics of neurodevelopmental disorders (NDDs) has rapidly advanced over the past few years. NGS has led to the discovery of new NDD genes with an excess of recurrent de novo mutations (DNMs) when compared to controls. Development of large-scale databases of normal and disease variation has given rise to metrics exploring the relative tolerance of individual genes to human mutation. Genetic etiology and diagnosis rates have improved, which have led to the discovery of new pathways and tissue types relevant to NDDs. In this review, we highlight several key findings based on the discovery of recurrent DNMs ranging from copy number variants to point mutations. We explore biases and patterns of DNM enrichment and the role of mosaicism and secondary mutations in variable expressivity. We discuss the benefit of whole-genome sequencing (WGS) over whole-exome sequencing (WES) to understand more complex, multifactorial cases of NDD and explain how this improved understanding aids diagnosis and management of these disorders. Comprehensive assessment of the DNM landscape across the genome using WGS and other technologies will lead to the development of novel functional and bioinformatics approaches to interpret DNMs and drive new insights into NDD biology.
    [Show full text]
  • Derived Neural Progenitor Cells Reveal Early Neurodevelopmental Phenotype for Koolen-De Vries Syndrome
    PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. https://hdl.handle.net/2066/226622 Please be advised that this information was generated on 2021-10-05 and may be subject to change. Modeling Neurodevelopmental Disorders Using Human Pluripotent Stem Cells: From Epigenetics Towards New Cellular Mechanisms Katrin Linda 1 Financial Support for printing this thesis was kindly provided by: Radboudumc Nijmegen Donders Institute for Brain, Cognition and Behaviour Cover design: Katrin Linda Lay-Out: Katrin Linda and Ridderprint B.V. (www.ridderprint.nl) Printed by: Ridderprint B.V. (www.ridderprint.nl) Copyright © 2020 by Katrin Linda All rights reserved. No parts of this publication may be reproduced or transmitted in any form or by any means without prior written permission of the author and holder of copyright. 2 Modeling Neurodevelopmental Disorders Using Human Pluripotent Stem Cells: From Epigenetics Towards New Cellular Mechanisms PROEFSCHRIFT ter verkrijging van graad van doctor aan de Radboud Universiteit Nijmegen op gezag van de rector magnificus prof. dr. J.H.J.M. van Krieken, volgens besluit van het college van decanen in het openbaar te verdedigen op woensdag 16 december 2020 om 14:30 uur precies door Katrin Linda geboren op 24 mei 1989 te Goch (Duitsland) 3 Promotoren Prof. dr. ir. J.H.L.M. van Bokhoven Dr. N. Nadif Kasri Copromotor Dr. B.B.A. de Vries Manuscriptcommissie Prof. dr. E.J.M. Storkebaum Dr. V.M. Heine (Amsterdam UMC) Prof. dr. Y.
    [Show full text]