Ornithine Transcarbamylase

Transcription

1 Ornithine Transcarbamylase

2 Ornithine Transcarbamylase ~ BASIC SCIENCE AND CLINICAL CONSIDERATIONS PHILIP J. SNODGRASS, M.D. Professor of Medicine Emeritus Indiana University School of Medicine.,. ~ KLUWER ACADEMIC PUBLISHERS BostonlDordrecht/London

3 Distributors for North, Central and South America: Kluwer Academic Publishers 101 Philip Drive Assinippi Park Norwell, Massachusetts USA Telephone (781) Fax (781) Distributors for all other countries: Kluwer Academic Publishers Group Post Office Box AH Dordrecht, THE NETHERLANDS Telephone Fax " Electronic Services < Library of Congress Cataloging-in-Publication Data A C.I.P. Catalogue record for this book is available from the Library of Congress. Ornithine Transcarbamylase: Basic Science ami Clinical Considerations by Philip J. Snodgrass ISBN Copyright 2004 by Kluwer Academic Publishers All rights reserved. No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without the written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Pennission for books published in Europe: pennissions@wkap.nl Pennissions for books published in the United States of America: pennissions@wkap.com Printed on acid-free paper. The Publisher offers discounts on this bookfor course use and bulk purchases. For further information, send to<melissaramondetta@wkap.com>.

4 Dedicated to my wife, Marjorie, for her patience and encouragement and to my daughter Jennifer for her editorial advice and guidance

5 Contents Preface Xt1t Acknowledgments xv 1 Gene Structure, Regulation and Function 1 2 Synthesis, Processing and Assembly 7 3 Molecular and Kinetic Characteristics 12 4 Active Site and Other Essential Residues 24 5 Molecular Pathology of OTC Deficiency 49 6 Animal Models of OTC Deficiency and Their Gene Therapy 85 Sparse-fur mutant mouse 85 Sparse-furash mutant mouse 93 Gene therapy of mutant mice 97 7 Clinical and Laboratory Findings in OTC Deficiency 106 OTC deficiency in females 107 OTC deficiency in males 129 Plasma amino acid levels in OTC deficiency 135 Plasma amino acid levels from the literature 137 Case series of OTC deficiency from the literature 138

6 viii Contents Symptoms of OTC deficiency precipitated by valproic acid 145 Rett syndrome and hyperammonemia Diagnosis and Treatment of OTC Deficiency 150 Diagnosis 150 Loading tests 15 6 Neuroimaging, EEG and pathology in liver and brain 158 Treatment 160 Gene replacement therapy Induction and Suppression of OTC and Urea Cycle Enzymes in Bacteria, Fungi and Mammals 165 Development of fetal and neonatal OTC and urea cycle enzymes 179 References 183 Index 239 Biographical Note 243

7 Figures 1-1. Schematic illustration of the structure of the OTC gene Amino acid sequences and secondary structure alignment of human, mouse, Pseudomonas aeruginosa and E. coli ornithine transcarbamylase (OTC) and E. coli aspartate transcarbamylase (ATC) Ribbon diagram of human OTC monomer liganded with the bisubstrate analog PALO Ribbon diagram of the human OTC catalytic trimer Structural model of the human OTC monomer Stereo view and schematic showing the interaction of the bisubstrate analog PALO with active site residues Structure and numbering of the atoms of N-(phosphonacetyl) L-aspartate (PALA) and N-(phosphonacetyl)-L-ornithine (PALO) Catalytic mechanisms of ATC and OTe Algorithm for the diagnosis of OTC deficiency Flow chart for the differential diagnosis of congenital hyperammonemia Organization of arginine, pyrimidine, proline and polyamine metabolism in Neurospora crassa Urea cycle and associated enzymes in the human liver cell, and their inherited defects. 168

8 x. Figures 9-3. Role and regulation of the OTC promoter and enhancer in tissue-selective transcription Factors binding to regulatory regions of the OTC gene. 179

9 Tables 3-1. Molecular weights and subunit weights of OTCs Michaelis constants, specific activities and ph optima ofotcs Invariant, highly conserved and homologous conserved amino acids in the sequence of 33 OTCs Substrate binding and catalytically active residues in E. coli aspartate ATC compared with E. coli and human OTCs Essential structural residues in E. coli ATC compared with E. coli and human OTCs Restriction endonucleases found useful in restriction fragment length polymorphism analysis of OTC deficiency Gene defects in OTC deficiency Polymorph isms detected in the OTC gene that have no functional significance Possible mechanisms for missense mutations that cause neonatal onset of OTC deficiency in males Possible mechanisms for missense mutations that cause late onset of OTC deficiency in males Possible mechanisms for effects of missense mutations in female heterozygotes with OTC deficiency Characteristics of the sparse-fur (spf) mouse model of OTC deficiency 86

10 xii. Tables 6-2. OTC activities, OTC protein and potc mrna in liver and small intestine of sparse-fur (spf) male mice Sparse-fur (spf) mouse as a model of chronic hyperammonemic encephalopathy due to OTC deficiency Characteristics of the sparse-fur-ash mouse model of OTC deficiency OTC activities in sparse-fur-ash vs. normal mice livers Clinical and laboratory findings in reported female probands with OTC deficiency Clinical and laboratory findings in neonatal male probands with OTC deficiency Clinical and laboratory findings in late-onset male probands with OTC deficiency Clinical symptoms in neonatal-onset males, late-onset males and female patients with OTC deficiency Baseline and laboratory data in neonatal-onset males, late-onset males and female patients with OTC deficiency Confirmation testing of female carrier status for OTC deficiency Plasma amino acid levels in neonatal-onset males, late-onset males and female patients with OTC deficiency Nomenclature for Figure

11 Preface Sir Hans Krebs described his discovery in 1932 of the urea/ornithine cycle in his autobiography, Reminiscences and Reflections (1981): "My idea was to use it (the tissue-slice technique) to study other metabolic processes, including synthetic ones, and as a first subject I chose the formation of urea in the liver. I was extraordinarily lucky in this choice because it led within twelve months to a major discovery-that of the ornithine cycle, the first 'metabolic cycle' to be identified"(747). My own interest in this fascinating cycle began in 1964 when I chose ornithine transcarbamylase (OTC), the second enzyme in the cycle, to measure in human serum as a test for liver injury. Background reading led me to appreciate the major role that research on the arginine biosynthetic pathway in bacteria and fungi played in the development of molecular biology and molecular genetics. Part of this pathway evolved into the mammalian urea cycle in liver. Robert Schimke's publications in showed that the rat liver urea cycle enzymes were induced by protein feedings. He demonstrated the role of both synthesis and degradation of the enzymes in the adaptation to the level of protein intake and to starvation, and also showed that glucocorticoids were necessary for maintaining the urea cycle activities. I decided that the problem of induction and suppression of the urea cycle in mammalian liver and the mechanisms by which the enzymes, their messenger-rnas and genes were regulated had long-

12 XIV Preface term possibilities as a research project for my laboratory. My colleagues and I pursued these problems from 1965 to Clinicians, pediatricians and geneticists developed greater interest in the mammalian and human urea cycle because of acquired and genetic causes of hyperammonemia in humans. B. Levin and colleagues first reported OTC deficiency in Other researchers soon reported deficiencies of the other four urea cycle enzymes, of acetylglutamate synthetase and recently of transporters for ornithine/ citrulline and for basic amino acids in liver, all of which caused hyperammonemia of varying severities. Our laboratory collaborated with many pediatricians and geneticists in their studies of urea cycle deficiencies. Our role was to assay the five cycle enzymes in liver, often in needle biopsies, and when possible to carry out kinetic studies on the human enzymes. As a gastroenterologist and hepatologist serving adult patients, I had daily experience with hyperammonemia due to acquired liver diseases but did not care for newborns or children with OTC deficiency. I decided to focus this book on only one enzyme of the cycle, OTC, because I had done more research on it than I had on the other enzymes and genetic OTC deficiency appeared to be the most common defect in the urea cycle. By compiling in one volume the widely scattered information on OTC, both clinical and basic, covering , I hope to help scientists and clinicians find a ready source of useful information about this interesting and important enzyme.

13 Acknowledgments The author acknowledges the contributions of my colleagues, Renee C. Lin, PhD, and Corinne Ulbright, PhD; of my dedicated research fellows; of the many excellent technicians in our laboratory over a 30- year period; of many collaborators in the u.s. from departments of pediatrics, genetics and medicine; and of Patricia Lund, DPhil, of the Metabolic Research Laboratory in Oxford University. The author wishes to thank Thomas D. Hurley, PhD, Professor, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, for his collaboration in preparing Chapter 4 and reviewing Chapters 1-6. The author appreciates the critical reading of Chapters 1-6 by Robert A. Harris, PhD, Showalter Professor and Chairman of the Department of Biochemistry and Molecular Biology, and of Chapters 7 and 8 by Rebecca S. Wappner, MD, Professor of Pediatrics and Director of Metabolism/Genetics,]W Riley Children's Hospital, Indiana University School of Medicine. Any omissions or misinterpretations throughout the text rest entirely with the author.