DOCSLIB.ORG

UC Irvine UC Irvine Electronic Theses and Dissertations

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
UC Irvine UC Irvine Electronic Theses and Dissertations UC Irvine UC Irvine Electronic Theses and Dissertations Title Mitochondrial Metabolism and Morphology in Mitochondrial Disease States Permalink https://escholarship.org/uc/item/7ss5250z Author Simon, Mariella T. Publication Date 2016 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, IRVINE Mitochondrial Metabolism and Morphology in Mitochondrial Disease States DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY In Biological Sciences by Mariella Theresa Simon Dissertation Committee: Professor Susanne Rafelski, Chair Professor Jose Abdenur, Co-Chair Professor Michelle Digman Professor Cristina Kenney Professor Grant MacGregor Professor Ali Mortazavi 2016 Chapter 2 © 2015 Plos BYCC Chapter 3 © 2013 Springer Chapter 4 © 2016 Elsevier All other materials © 2016 Mariella Theresa Simon DEDICATION To those individuals who believe(d) that the suffering of mitochondrial disease patients (young and old) is real and not made up or self-inflicted. For those who did this long before modern science could explain the underlying mechanisms. For all their pain that we cannot see that is real. “Die Elementarkörnchen der Zellen, welche noch heute ihre analogen Vertreter in den primären Mikroorganismen haben und welche seit jenen Perioden in den Zellen existieren, vermögen nicht mehr sebständige Lebewesen zu werden.” “The elementary granules of cells, which still have their analogs in primary micro- organisms and which exist since these time periods inside of cells, are no longer able to exist independently.” Richard Altman 1890 ii TABLE OF CONTENTS LIST OF FIGURES v LIST OF TABLES vii LIST OF ABBREVIATIONS viii ACKNOWLEDGEMENTS xi CURRICULUM VITAE xiv ABSTRACT OF DISSERTATION xix CHAPTER 1: Introduction 1.1 Principles of Mitochondrial Medicine 1 1.2 Age related mitochondrial disease phenotypes 13 1.3 Exercise as treatment for mitochondrial disease 33 CHAPTER 2: Mutations of Human NARS2, Encoding the Mitochondrial 35 Asparaginyl-tRNA Synthetase, Cause Nonsyndromic Deafness and Leigh Syndrome 2.1 Introduction 36 2.2 Results 38 2.3 Discussion 69 2.4 Materials and Methods 76 2.5 Acknowledgements 85 2.6 Contributions 85 CHAPTER 3: Abnormalities in Glycogen Metabolism in a Patient With Alpers’ Syndrome Presenting with Hypoglycemia 86 3.1 Introduction 87 3.2 Results 88 3.3 Discussion 94 3.4 Acknowledgements 98 3.5 Contributions 98 CHAPTER 4 Mutations in TFAM, Encoding Mitochondrial Transcription Factor A, Cause Neonatal Liver Failure Associated with mtDNA Depletion 99 iii 4.1 Introduction 100 4.2 Materials and Methods 103 4.3 Results 108 4.4 Discussion 120 4.5 Acknowledgements 124 4.6 Contributions 125 CHAPTER 5 Activation of a Cryptic Splice Site in the Mitochondrial Elongation Factor GFM1 Causes Combined OXPHOS Deficiency in Two Brothers with Microcephaly, Developmental Delay and Seizure Disorder 126 5.1 Introduction 127 5.2 Materials and Methods 129 5.3 Results 132 5.4 Discussion 139 5.5 Conclusion 143 5.6 Acknowledgements 143 5.7 Contributions 143 CHAPTER 6 Novel Mutations in the Substrate Binding Domain of the Mitochondrial Matrix Protease Lonp1 are a Cause of Mitochondrial Disease 149 6.1 Introduction 150 6.2 Results 155 6.3 Discussion 189 6.4 Materials and Methods 196 6.5 Acknowledgements 200 6.6 Contributions 200 CHAPTER 7 Discussion 200 7.1 The success of the “bedside to bench and back to bedside” 201 paradigm requires collaborative and multidisciplinary approaches 7.2 Emerging methods in mitochondrial medicine 204 7.3 Tissue specificity - a conundrum of mitochondrial disease 209 WEB RESOURCES 227 REFERENCES 228 iv LIST OF FIGURES Figure 1.1 The Cycle of Bedside to Bench and Back Figure 1.2 Electron microscopy of muscle from Luft’s patient Figure 1.3 Cartoon of a mitochondrion with its basic structure of outer and inner membrane, intermembrane space and matrix Figure 2.1 NARS2 mutations identified in two unrelated families Figure S2.1 Western blot and blue native gel analyses for patient fibroblasts and transmitochondrial cybrids Figure S2.2 Audiograms of individuals V.4 and V.8 from family PKDF406 Figure S2.3 Segregation and Sanger sequencing of mt-tRNACys A5793G Figure S2.4 Sequencing chromatograms Figure 2.2 Expression of Nars2 in mouse inner ear and brain Figure 2.3 NARS2 structure and molecular modeling Figure 2.4 NARS2 homodimerization and RNA level: effect of the p.Val213Phe and p.Asn381Ser mutations Figure S2.5 Interaction between HA- and GFP-tags Figure S2.6 Impact of the p.Val213Phe and p.Asn381Ser mutations on the NARS2 expression level in vitro Figure S2.7 Effect of the p.Val213Phe and p.Asn381Ser mutations on NARS2 localization Figure S2.8 Aminoacylation assays for mitochondrial tRNAAsn Figure S2.9 SDS-PAGE and western blot analysis of lentiviral transduction and expression of NARS2 Figure 2.5 Analysis of the impact of the NARS2 mutations on mitochondrial functions Figure 3.1 Diffusion-weighted images (MRI #2 and #5) Figure 4.1 Molecular analysis confirms segregation with disease of recessive TFAM p.Pro178Leu mutation Figure 4.2 Liver biopsy reveals cirrhosis and cholestasis v Figure 4.3 Skeletal muscle reveals findings consistent with mitochondrial myopathy Figure 4.4 Molecular and biochemical studies in primary fibroblasts Figure 4.5 Characterization of respiratory chain function in fibroblasts Figure 4.6 Nucleoid morphology is disrupted Figure 5.1 Mutations in patient 1 and 2 seggregate with disease Figure 5.2 Mutations in GFM1 are associated with abnormal splicing and result in decreased levels of GFM1 protein and abnormalities in complexes of the ETC Figure 6.1 LonpP1 mutations cluster in the AAA domain Figure 6.2 Modeling of patient mutations onto LonP protein structure Figure 6.3 Seahorse mitostress profile allows for assessment of spare respiratory capacity Figure 6.4 Patient cell lines have decreased spare respiratory capacity depending on availability of pyruvate Figure 6.5 Patient cell lines have decreased spare respiratory capacity depending on carbon source in response to addition of Antibiotic/Antimycotic Figure 6.6 Extracellular Acidification Rate (ECAR) is differently modulated in patient 1 and 2 Figure 6.7 Western blot for LonP1 and it’s targets reveals low levels of LonP1 for patient 1 Figure 6.8 Relative mtDNA copy number is modulated by the use of antibiotics in cell culture Figure 6.9 Large aggregated nucleoids are observed for patient 1 via immunohistochemistry in glucose media without antibiotic Figure 7.1 Overview of functional studies prompted by delineation of novel gene variants Figure 7.2 Impaired astrocytic glycogen metabolism may contribute to basal ganglia disorders Figure 7.3 Immunohistochemistry of Astrocytes shows mitochondria in parts of PAP vi LIST OF TABLES Table S2.1 Abnormal levels of urine organic acids of patient II.1 Table S2.2 Mitochondrial respiratory chain complex activities of muscle homogenate Table 2.1 Clinical findings of affected PKDF406 family members Table S2.3 Summary of Exome sequencing analysis for LS06 Table S2.4a Summary of Exome sequencing analysis for PKDF406 Table S2.4b Primer sequences used to amplify and sequence human NARS2 coding exons Table S2.5 Primer sequences used to amplify mouse Nars2 Table S2.6 Predicted effect of p.Val213Phe and p.Asn381Ser missense mutations on NARS2 Table 2.2 Summary of the known aminoacyl tRNA-synthetase genes associated with deafness Table S2.7 Summary of sequencing statistic for LS06 Table 3.1 Fasting study #1 Table 3.2 Fasting study #2 Table 4.1 Clinical Manifestations of hepatocerebral mitochondrisal DNA depletion syndromes Table 4.2 Mitochondrial respiratory chain enzyme analysis (ETC) - Skeletal muscle Table S5.1 Clinical phenotypes associated with mutations in GFM1 Table 6.1 Electron transport chain studies for muscle homogenate Table 6.2 Oxphos analysis for patient 1 Table 6.3 Comparison of phenotype for patient 1 and 2 vs CODAS syndrome Table 6.4 Insilico pathogenicity prediction for LonP1 variants Table 6.5 Summary of main Seahorse Study findings contrasted with mtDNA copy number vii LIST OF ABBREVIATIONS Auditory brainstem response (AABR) Abnormal carbohydrate deficient transferrin (CDT) Adenosine triphosphate (ATP) Adult onset polyglucosan body disease (APBD) Alanine aminotransferase (ALT) Alzheimer’s disease (AD) Amyloid beta (Aβ) Antibiotic-antimycotic (Anti-Anti) ATPase associated with diverse cellular activities (AAA) Basal respiration (BR) Base pair (bp) Beta-2 microglobulin (B2M) Beta-hydroxybutyrate (b-OH-Butyrate) Biotine-thiamine-responsive basal ganglia disease (BBGD) Blue native gel analysis (BNG) Cerebral spinal fluid (CSF) Charcot Marie Tooth disease (CMT) Clinical exome sequencing (CES) Combined respiratory deficiency (COXPD) Creatine Kinase (CK) Cybrids (cytoplasmic hybrids) Cytochrome C (CYCS) Cytochrome c oxidase subunit IV isoform 1 (COX4-1) Cytochrome oxidase (COX) 2,6-dichlorophenolindophenol (DCPIP) Deoxyguanosine kinase (DGUOK) Detergent compatible (DC) E. coli lon protease (EcLon) Echocardiogram (Echo) Electrocardiogram (EKG) Electroencephalography (EEG) Electron microscopy (EM) Electron transport chain (ETC) Endoplasmic reticulum (ER) Endoplasmic reticulum unfolded protein response (UPR)ER Enzyme carbamoyl phosphate synthetase I (CPS1) Exome aggregation consortium (ExAC) Exome variant server (EVS) Extracellular acidification rate (ECAR) Fibroblast (f) Fluid-attenuated inversion recovery (FLAIR) Free fatty acids (FFA) Fresh frozen plasma (FFP) viii Glutathione
Load more

Recommended publications
  • Proteomic Analysis of the Role of the Quality Control Protease LONP1 in Mitochondrial Protein Aggregation
    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.12.439502; this version posted April 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Proteomic analysis of the role of the quality control protease LONP1 in mitochondrial protein aggregation Karen Pollecker1, Marc Sylvester2 and Wolfgang Voos1,* 1Institute of Biochemistry and Molecular Biology (IBMB), University of Bonn, Faculty of Medicine, Nussallee 11, 53115 Bonn, Germany 2Core facility for mass spectrometry, Institute of Biochemistry and Molecular Biology (IBMB), University of Bonn, Faculty of Medicine, Nussallee 11, 53115 Bonn, Germany *Corresponding author Email: [email protected] Phone: +49-228-732426 Abbreviations: AAA+, ATPases associated with a wide variety of cellular activities; Δψ, mitochondrial membrane potential; gKD, genetic knockdown; HSP, heat shock protein; m, mature form; mt, mitochondrial; p, precursor form; PQC, protein quality control; qMS, quantitative mass spectrometry; ROS, reactive oxygen species; SILAC, stable isotope labeling with amino acids in cell culture; siRNA, small interfering RNA; TIM, preprotein translocase complex of the inner membrane; TMRE, tetramethylrhodamine; TOM, preprotein translocase complex of the outer membrane; UPRmt, mitochondrial unfolded protein response; WT, wild type. bioRxiv preprint doi: https://doi.org/10.1101/2021.04.12.439502; this version posted April 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Segregation and Recombination of Non-Mendelian Genes in Chlamydomonas
    Symposium on Non-chromosomal Inheritance: XIII International Congress of Genetics SEGREGATION AND RECOMBINATION OF NON-MENDELIAN GENES IN CHLAMYDOMONAS NICHOLAS W. GILLHAM, JOHN E. BOYNTON AND ROBERT W. LEE2 Departments of Botany and Zoology, Duke University, Durham, North Carolina 27706 ABSTRACT Non-Mendelian genes in Chamydomonas reinhardfii axe inherited in a uniparental (UP) fashion. Most zygotes and their progeny receive UP genes only from the mt+ or maternal parent. Homwever, a few exceptional zygotes are also found in which tlie mt ur paternal UP genome is transmitted. Most of the exceptional zygotes are biparental in that their progeny segregate UP genes transmitted by bath parents. As a result, biparental zygotes have been extensively used to study the rules governing UP inheritance. The frequency of biparental zygotes can be greatly increased if the maternal parent is irradiated with ultraviolet light priosr to mating. Based principally on studies with ultraviolet-induced biparental zygotes, SAGERhas argued that a vegetative cell contains two copies of the UP genome and that the progeny of a biparental zygote receive a copy derived from each parent. Results reported in this paper with spontaneous and ultraviolet-induced biparental zygotes do not support the two copy mcdel, but argue for a mulitple copy model with most of the copies normally being transmitted by the maternal parent. A multiple copy model which accolunts for both SAGER’Sresults and ours is presented. ON-MENDELIAN mutations exhibiting uniparental (UP) inheritance in Chla- “zydomonas reinhardtii were first reported by SAGERin 1954. Since that time the UP genetic system has been subject to extensive investigation at both the molecular and genetical levels (see reviews by GILLHAM1969; SAGER1972).
    [Show full text]
  • Neuromuscular Disorders Neurology in Practice: Series Editors: Robert A
    Neuromuscular Disorders neurology in practice: series editors: robert a. gross, department of neurology, university of rochester medical center, rochester, ny, usa jonathan w. mink, department of neurology, university of rochester medical center,rochester, ny, usa Neuromuscular Disorders edited by Rabi N. Tawil, MD Professor of Neurology University of Rochester Medical Center Rochester, NY, USA Shannon Venance, MD, PhD, FRCPCP Associate Professor of Neurology The University of Western Ontario London, Ontario, Canada A John Wiley & Sons, Ltd., Publication This edition fi rst published 2011, ® 2011 by Blackwell Publishing Ltd Blackwell Publishing was acquired by John Wiley & Sons in February 2007. Blackwell’s publishing program has been merged with Wiley’s global Scientifi c, Technical and Medical business to form Wiley-Blackwell. Registered offi ce: John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK Editorial offi ces: 9600 Garsington Road, Oxford, OX4 2DQ, UK The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK 111 River Street, Hoboken, NJ 07030-5774, USA For details of our global editorial offi ces, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell The right of the author to be identifi ed as the author of this work has been asserted in accordance with the UK Copyright, Designs and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher.
    [Show full text]
  • Bzyct-137 Genetics and Evolutionary Biology
    BZYCT-137 GENETICS AND Indira Gandhi EVOLUTIONARY BIOLOGY National Open University School of Sciences VOL 1 GENETICS BLOCK 1 HEREDITY AND PHENOTYPE 7 BLOCK 2 THE PHYSICAL BASIS OF HEREDITY 127 GENETICS AND EVOLUTIONARY BIOLOGY Genetics goes hand in hand with evolution. All traits are inherited whenever we bring up a trait, we should ask when that trait evolved and place in on the appropriate phylogenetic tree. This tree not only shows when certain traits evolved, but can also be used to infer who has them. This tree can be used to show how our genetic traits go back to the universal ancestor that lived 3-5 billion years ago and that all of today’s genomes are product of duplication and divergence. The evidence for the evolution can be read from our genomes. Understanding the connection between Mendel’s principles of heredity and DNA is of paramount importance. There are concrete examples of mutations in DNA that change proteins which in turn, change phenotype is one of the best ways to make these connections we now understand same of the Mendel’s traits at molecular level. Genes code for proteins and proteins determine phenotype. The more vividly you can make this connection, the richer will be their understanding of both genetics and evolution. Looking at the functioning of DNA, RNA and protein in determining phenotype, students can begin to understand that they are guardians of 3.5 billion years of evolution and this provides motivation for taking care of our fragile planet that makes life possible. We welcome you to the study of the first volume of this course which tells you about Genetics.
    [Show full text]
  • Supplementary Materials
    Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine
    [Show full text]
  • Mitochondrial Lon Protease in Human Disease and Aging: Including an Etiologic Classification of Lon-Related Diseases and Disorders
    UC Irvine UC Irvine Previously Published Works Title Mitochondrial Lon protease in human disease and aging: Including an etiologic classification of Lon-related diseases and disorders. Permalink https://escholarship.org/uc/item/2pw606qk Authors Bota, Daniela A Davies, Kelvin JA Publication Date 2016-11-01 DOI 10.1016/j.freeradbiomed.2016.06.031 Peer reviewed eScholarship.org Powered by the California Digital Library University of California HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Free Radic Manuscript Author Biol Med. Author Manuscript Author manuscript; available in PMC 2016 December 24. Published in final edited form as: Free Radic Biol Med. 2016 November ; 100: 188–198. doi:10.1016/j.freeradbiomed.2016.06.031. Mitochondrial Lon protease in human disease and aging: Including an etiologic classification of Lon-related diseases and disorders Daniela A. Botaa,* and Kelvin J.A. Daviesb,c a Department of Neurology and Chao Family Comprehensive Cancer Center, UC Irvine School of Medicine, 200 S. Manchester Ave., Suite 206, Orange, CA 92868, USA b Leonard Davis School of Gerontology of the Ethel Percy Andrus Gerontology Center, Los Angeles, CA 90089-0191, USA c Division of Molecular & Computational Biology, Department of Biological Sciences, Dornsife College of Letters, Arts, & Sciences, The University of Southern California, Los Angeles, CA 90089-0191, USA Abstract The Mitochondrial Lon protease, also called LonP1 is a product of the nuclear gene LONP1. Lon is a major regulator of mitochondrial metabolism and response to free radical damage, as well as an essential factor for the maintenance and repair of mitochondrial DNA. Lon is an ATP- stimulated protease that cycles between being bound (at the inner surface of the inner mitochondrial membrane) to the mitochondrial genome, and being released into the mitochondrial matrix where it can degrade matrix proteins.
    [Show full text]
  • Uniparental Inheritance of Mitochondrial Genes in Yeast: Dependence on Input Bias of Mitochondrial Dna and Preliminary Investigations of the Mechanism
    UNIPARENTAL INHERITANCE OF MITOCHONDRIAL GENES IN YEAST: DEPENDENCE ON INPUT BIAS OF MITOCHONDRIAL DNA AND PRELIMINARY INVESTIGATIONS OF THE MECHANISM C. WILLIAM BIRICY, JR.*t, CATHERINE A. DEMKO*, PHILIP S. PERLMAN*t, AND ROBERT STRAUSBERwt The Ohio Stale University, Columbus, Ohio 43210 Manuscript received September 26, 1977 Revised copy received March 17, 1978 ABSTRACT In Saccharomyces cerevisiae, previous studies on the inheritance of mito- chondrial genes controlling antibiotic resistance have shown that some crosses produce a substantial number of uniparental zygotes, which transmit to their diploid progeny mitochondrial alleles from only one parent. In this paper, we show that uniparental zygotes are formed especially when one parent (major- ity parent) contributes substantially more mitochondrial DNA molecules to the zygote than does the other (minority) parent. Cellular contents of mito- chondrial DNA (mtDNA) are increased in these experiments by treatment with cycloheximide, alpha-factor, or the uvsp5 nuclear mutation. In such a biased cross, some zygotes are uniparental for mitochondrial alleles from the majority parent, and the frequency of such zygotes increases with increasing bias. In two- and three-factor crosses, the cupl, ery1, and oli1 loci behave coordinately, rather than independently; minority markers tend to be trans- mitted or lost as a unit, suggesting that the uniparental mechanism acts on entire mtDNA molecules rather than on individual loci. This rules out the possibility that uniparental inheritance can be explained by the conversion of minority markers to the majority alleles during recombination. Exceptions to the coordinate behavior of different loci can be explained by marker rescue via recombination. Uniparental inheritance is largely independent of the posi- tion of buds on the zygote.
    [Show full text]
  • Novel GFM2 Variants Associated with Early-Onset Neurological Presentations of Mitochondrial Disease and Impaired Expression of OXPHOS Subunits
    King’s Research Portal DOI: 10.1007/s10048-017-0526-4 Document Version Publisher's PDF, also known as Version of record Link to publication record in King's Research Portal Citation for published version (APA): Glasgow, R. I. C., Thompson, K., Barbosa, I. A., He, L., Alston, C. L., Deshpande, C., Simpson, M. A., Morris, A. A. M., Neu, A., Löbel, U., Hall, J., Prokisch, H., Haack, T. B., Hempel, M., McFarland, R., & Taylor, R. W. (2017). Novel GFM2 variants associated with early-onset neurological presentations of mitochondrial disease and impaired expression of OXPHOS subunits. NEUROGENETICS, 1-9. https://doi.org/10.1007/s10048-017-0526-4 Citing this paper Please note that where the full-text provided on King's Research Portal is the Author Accepted Manuscript or Post-Print version this may differ from the final Published version. If citing, it is advised that you check and use the publisher's definitive version for pagination, volume/issue, and date of publication details. And where the final published version is provided on the Research Portal, if citing you are again advised to check the publisher's website for any subsequent corrections. General rights Copyright and moral rights for the publications made accessible in the Research Portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognize and abide by the legal requirements associated with these rights. •Users may download and print one copy of any publication from the Research Portal for the purpose of private study or research.
    [Show full text]
  • Protection of Scaffold Protein Isu from Degradation by the Lon Protease Pim1 As a Component of Fe–S Cluster Biogenesis Regulation
    M BoC | ARTICLE Protection of scaffold protein Isu from degradation by the Lon protease Pim1 as a component of Fe–S cluster biogenesis regulation Szymon J. Ciesielskia, Brenda Schilkea, Jaroslaw Marszaleka,b, and Elizabeth A. Craiga,* aDepartment of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706; bIntercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk 80307, Poland ABSTRACT Iron–sulfur (Fe–S) clusters, essential protein cofactors, are assembled on the mi- Monitoring Editor tochondrial scaffold protein Isu and then transferred to recipient proteins via a multistep Thomas D. Fox process in which Isu interacts sequentially with multiple protein factors. This pathway is in Cornell University part regulated posttranslationally by modulation of the degradation of Isu, whose abundance Received: Dec 4, 2015 increases >10-fold upon perturbation of the biogenesis process. We tested a model in which Revised: Jan 22, 2016 direct interaction with protein partners protects Isu from degradation by the mitochondrial Accepted: Jan 25, 2016 Lon-type protease. Using purified components, we demonstrated that Isu is indeed a sub- strate of the Lon-type protease and that it is protected from degradation by Nfs1, the sulfur donor for Fe–S cluster assembly, as well as by Jac1, the J-protein Hsp70 cochaperone that functions in cluster transfer from Isu. Nfs1 and Jac1 variants known to be defective in interac- tion with Isu were also defective in protecting Isu from degradation. Furthermore, overpro- duction of Jac1 protected Isu from degradation in vivo, as did Nfs1. Taken together, our re- sults lead to a model of dynamic interplay between a protease and protein factors throughout the Fe–S cluster assembly and transfer process, leading to up-regulation of Isu levels under conditions when Fe–S cluster biogenesis does not meet cellular demands.
    [Show full text]
  • Genome Imprinting -R-ES-ONANCE
    GENERAL I ARTICLE Genome Imprinting The Silencing of Genes and Genomes H A Ranganath and M T Tanuja Gregor Mendel, the Father of Genetics was, fortunately for us, very lucky in that the characters studied by him presented a very neat pattern of inheritance. This enabled him to generalize from his observations and to give us the basic tenets of inheritance. Genetic investigations in the 20th century have, however, re­ H A Ranganath is a vealed many contradictions to the principles enunciated by Professor of Zoology at Mendel. One of the important challenges facing geneticists is to the University of Mysore. explain the mode of inheritance of traits and conditions that do His interests centre not appear to follow Mendel's laws. One of the principles of around cytogenetics and other aspects of the Mendel is 'The Principle of Equivalence in Reciprocal Crosses': process of race formation no matter which parent contributes a gene to its offspring, the and speciation in gene will behave in the same way in producing the phenotype. Drosophila. Even though this principle holds true most of the time, there are a few exceptions. They are (1) traits linked to genes on the sex chromosomes - X and Y, (2) traits controlled by genes outside the cell nucleus (mitochondrial and chloroplast genomes), and (3) traits governed by a phenomenon called genome imprinting. The term 'imprinting' was probably first used in biology in the M T Tanuja is a CSIR late 1930's in connection with animal behaviour. Helen Crouse Senior Research Fellow, presently working on first used it in cytogenetic context in her study of chromosome hybridization and elimination in Sciara in 1960.
    [Show full text]
  • Phosphorylation of Human TFAM in Mitochondria Impairs DNA Binding and Promotes Degradation by the AAA+ Lon Protease
    Molecular Cell Article Phosphorylation of Human TFAM in Mitochondria Impairs DNA Binding and Promotes Degradation by the AAA+ Lon Protease Bin Lu,1,4,5 Jae Lee,1,5 Xiaobo Nie,1,4,5 Min Li,1 Yaroslav I. Morozov,2 Sundararajan Venkatesh,1 Daniel F. Bogenhagen,3 Dmitry Temiakov,2 and Carolyn K. Suzuki1,* 1Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA 2Department of Cell Biology, School of Osteopathic Medicine, University of Medicine and Dentistry of New Jersey, Stratford, NJ 08084, USA 3Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA 4Present address: Institute of Biophysics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical College, Wenzhou, Zhejiang 325035, PRC 5These authors contributed equally to this work *Correspondence: [email protected] http://dx.doi.org/10.1016/j.molcel.2012.10.023 SUMMARY contrast, TFAM overproduction in transgenic mice increases mtDNA content (Ekstrand et al., 2004; Larsson et al., 1998) Human mitochondrial transcription factor A (TFAM) and also ameliorates cardiac failure (Ikeuchi et al., 2005), neuro- is a high-mobility group (HMG) protein at the nexus degeneration, and age-dependent deficits in brain function of mitochondrial DNA (mtDNA) replication, transcrip- (Hokari et al., 2010). TFAM is the most abundant component tion, and inheritance. Little is known about the mech- of mitochondrial nucleoids, which are protein complexes anisms underlying its posttranslational regulation. associated with mtDNA that orchestrate genome replication, Here, we demonstrate that TFAM is phosphorylated expression, and inheritance (Bogenhagen et al., 2008, 2012; Kukat et al., 2011).
    [Show full text]
  • Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic
    bioRxiv preprint doi: https://doi.org/10.1101/059089; this version posted November 17, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Uniparental inheritance promotes adaptive evolution in 2 cytoplasmic genomes 1,2 1 3 Joshua R. Christie and Madeleine Beekman 1 4 School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006, NSW, 5 Australia 2 6 Corresponding author: [email protected] 7 1 Abstract 8 Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). 9 Lacking recombination, asexual genomes should theoretically suffer from impaired adap- 10 tive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience 11 higher levels of adaptive evolution than predicted by theory. In this study, we use a com- 12 putational model to show that the unique biology of cytoplasmic genomes—specifically 13 their organization into host cells and their uniparental (maternal) inheritance—enable 14 them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic 15 genomes decreases competition between different beneficial substitutions (clonal interfer- 16 ence), promoting the accumulation of beneficial substitutions. Uniparental inheritance 17 also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller’s 18 ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of 19 deleterious substitutions during selective sweeps. Overall, uniparental inheritance pro- 20 motes adaptive evolution by increasing the level of beneficial substitutions relative to 1 bioRxiv preprint doi: https://doi.org/10.1101/059089; this version posted November 17, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
    [Show full text]