Transfer RNA in Protein Synthesis

447 Pages·1992·31.786 MB·English

by  Dolph Hatfield, Byeong J. Lee, Robert M. Pirtle

TRANSFER RNA
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PROTEIN
SYNTHESIS
Edited by
Dolph L. Hatfield, B.A., M.A., Ph.D.
Research Biologist
Laboratory of Experimental Carcinogenesis
National Cancer Institute
National Institutes of Health
Bethesda, Maryland
Byeong J. Lee, B.A., M.A., Ph.D.
Assistant Professor
The Institute for Molecular Biology and Genetics
Seoul National University
Seoul, Korea
Robert M. Pirtle, B.S., Ph.D.
Associate Professor
Department of Biochemistry
University of North Texas(fexas College
of Osteopathic Medicine
Denton, Texas
Boca Raton London New York
CRC Press
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First published 1992 by CRC Press
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Library of Congress Cataloging-in-Publication Data
Transfer RNA in protein synthesis / editors, Dolph L. Hatfield, Byeong J. Lee,
Robert M. Pirtle.
p. cm.
Includes bibliographical references and index.
ISBN 0-8493-5698-9
1. Transfer RNA. 2. Proteins—Synthesis. I. Hatfield, Dolph L.
II. Lee, Byeong J. III. Pirtle, Robert M.
[DNLM: 1. Codon—physiology. 2. Proteins—biosynthesis. 3. RNA,
Transfer—physiology. QU 58 T77112]
QP263.5T73T72 1992
574.87’3283—dc20
DNLM/DLC
for Library of Congress 92-4137
A Library of Congress record exists under LC control number: 92004137
Publisher’s Note
The publisher has gone to great lengths to ensure the quality of this reprint but points out that some imperfections in the
original copies may be apparent.
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The publisher has made every effort to trace copyright holders and welcomes correspondence from those they have been
unable to contact.
ISBN 13: 978-1-315-89829-2 (hbk)
ISBN 13: 978-1-351-07739-2 (ebk)
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DEDICATION
The editors take great pleasure in dedicating this book to their loving wives,
Mary J. Wilson-Hatfield, Hwan Yeon Lee, and Irma Lindsey Pirtle, and to their
loving children, Hugh H. Hatfield and his wife Cherry!, Sandra L. Hatfield,
Michele J. Hatfield, and Hye Jin Lee and Hye Seo Lee.

EDITORS
Dolph L. Hatfield, Ph.D. is a research biologist at the Laboratory of
Experimental Carcinogenesis, National Cancer Institute, National Institutes of
Health, Bethesda, Maryland.
Dr. Hatfield received his B.A., M.A., and Ph.D. degrees in 1958, 1960, and
1962, respectively, in the Genetics Foundation at the University of Texas,
Austin, Texas. After postdoctoral training in the laboratories of Drs. James B.
Wyngaarden, Duke University Medical Center, Durham, NC, Marshall
Nirenberg, National Institutes of Health, Bethesda, MD, and Jacques Monod,
Pasteur Institute, Paris; he joined the National Cancer Institute, National Insti-
tutes of Health, where he has served as a research biologist since 1967. He was
awarded a Robert A. Welsh Foundation Scholarship for studies at the Univer-
sity of Texas, a PHS Postdoctoral Fellowship for studies at Duke University,
an American Cancer society Postdoctoral Fellowship for studies at NIH, and
a National Cancer Institute Postdoctoral Fellowship for studies at the Pasteur
Institute.
Dr. Hatfield has been a member of the American Society for Biochemistry
and Molecular Biology since 1971. His research interests are in the occurrence
and role of nonsense suppressor tRNAs and in the mechanism of expression of
tRNAs in mammalian cells and in the role that specific hypomodified bases in
tRNAs, which occur in cancer tissue, may have in the malignancy process.
Byeong J. Lee, Ph.D. is an assistant professor in the Institute for Molecular
Biology and Genetics and is also associated with the Department of Microbi-
ology at Seoul National University, Seoul, Korea.
Dr. Lee received his B.A., M.A., and Ph.D. degrees in 1978, 1982, and
1986, respectively, in the Department of Microbiology, at Seoul National
University. He was a visiting fellow from 1986 to 1989 and then a visiting
associate from 1989 to 1991 in the Laboratory of Experimental Carcinogenesis,
National Cancer Institute, National Institutes of Health, Bethesda, MD.
Dr. Lee is a member of the American Society of Biochemistry and Molecu-
lar Biology, the Korean Society of Molecular Biology, and the Microbiological
Society of Korea. His research interests are in the organization, expression, and
function of eukaryotic tRNA genes.
Robert M. Pirtle, Ph.D. is Associate Professor of Biochemistry at the
University of North Texas in Denton, and is also associated with the Depart-
ment of Biochemistry and Molecular Biology at the Texas College of Osteo-
pathic Medicine in Fort Worth.
Dr. Pirtle graduated in 1967 with a B.S. in Applied Psychology from the
Georgia Institute of Technology in Atlanta, where he was supported by a
General Motors Scholarship. After a year of graduate study in psychology at
the University of Louisville in Kentucky, he entered the doctoral program in
biochemistry in the University of Louisville School of Medicine, and received
a Ph.D. in Biochemistry in 1973. His postdoctoral training in nucleic acids
biochemistry and molecular biology was done at the State University of New
York at Stony Brook, where he had an NIH postdoctoral fellowship. From
I 980 to 1987, he was an Assistant Professor of Biochemistry at the University
of North Texas{fexas College of Osteopathic Medicine. There, in 1987, he
became an Associate Professor.
Dr. Pirtle is a member of the American Society of Biochemistry and
Molecular Biology, American Society for Microbiology, American Chemical
Society, American Association for the Advancement of Science, and the
honorary society Sigma Xi. In addition to teaching biochemistry and molecular
biology to graduate, undergraduate, and medical students, he has been the
recipient of research grants from the National Institutes of Health, the National
Science Foundation, the Texas Advanced Research Program, The Robert A.
Welch Foundation, the Research Corporation, and the Samuel Roberts Noble
Foundation. His current major research interests relate to the structure and
chromosomal organization of human transfer RNA genes, the regulation of
tRNA gene expression, and the posttranscriptional modification and process-
ing of tRNA.
CONTRIBUTORS
John Abbotts, Ph.D. Laurence Marechal Drouard,
Research Associate D.Sci.
Laboratory of Biochemistry Charge de Recherches
National Cancer Institute Institut de Biologie Moleculaire
National Institutes of Health des Plantes
Bethesda, Maryland Universite Louis Pasteur
Strasbourg, France
Glenn R. Bjork, Ph.D.
Professor George A. Gutman, Ph.D.
Department of Microbiology
Professor
University of Umea Department of Microbiology and
Umea, Sweden
Molecular Genetics
University of California, Irvine
Conal J. Burgess, B.A.
Irvine, California
Research Student
Department of Genetics
Dolph L. Hatfield, B.A., M.A.,
Trinity College
Ph.D.
Dublin, Ireland
Research Biologist
In Soon Choi, B.A., M.A., Laboratory of Experimental
Ph.D. Carcinogenesis
Visiting Fellow National Cancer Institute
Laboratory of Experimental National Institutes of Health
Carcinogenesis Bethesda, Maryland
National Cancer Institute
National Institutes of Health G. Wesley Hatfield, Ph.D.
Bethesda, Maryland Professor
Department of Microbiology and
Elizabeth Cowe, B.Sc. Molecular Genetics
Research Student University of California, Irvine
Department of Genetics
Irvine, California
Trinity College
Dublin, Ireland
Toshimichi lkemura, D.Sci.
Professor
James F. Curran, Ph.D.
Department of Population Genetics
Assistant Professor
National Institute of Genetics
Department of Biology
Mishima, Japan
Wake Forest University
Winston-Salem, North Carolina
Jae-Eon Jung, B.A., M.A., Ph.D.
Andre Dietrich, D.Sci. Visiting Fellow
Directeur de Recherches Laboratory of Experimental
Institut de Biologie Moleculaire Carcinogenesis
des Plantes National Cancer Institute
Universite Louis Pasteur National Institutes of Health
Strasbourg, France Bethesda, Maryland
Ulf Lagerkvist, Ph.D. Irma L. Pirtle, B.S., Ph.D.
Professor Research Assistant Professor
Department of Medical Department of Biochemistry
Biochemistry University of North Texas/
Gothenburg University Texas College of Osteopathic
Medicine
Goteborgs, Sweden
Denton, Texas
Byeong J. Lee, B.A., M.A., Robert M. Pirtle, B.S., Ph.D.
Ph.D. Associate Professor
Assistant Professor Department of Biochemistry
The Institute for Molecular University of North Texas/
Biology and Genetics Texas College of Osteopathic
Seoul National University Medicine
Seoul, Korea Denton, Texas
Andrew T. Lloyd, B.A., Ph.D. LaDonne Schulman, Ph.D.
Research Fellow Professor
Department of Genetics Department of Developmental
Trinity College Biology and Cancer
Dublin, Ireland Albert Einstein College of
Medicine
Bronx, New York
Kevin J. Mitchell, B.A.
Research Student
Paul M. Sharp, B.S., Ph.D.
Department of Genetics
Lecturer
Trinity College
Department of Genetics
Dublin, Ireland Trinity College
Dublin, Ireland
Susumo Ohno, D.V.M., Ph.D.,
D.Sci. Jacques-H. Weil, D.Sci.
Chair Professor
Department of Theoretical Biology Institut de Biologie Moleculaire
Beckman Research Institute of des Plantes
The City of Hope Universite Louis Pasteur
Duarte, California Strasbourg, France
Leo Pallanck, B.S. Samuel H. Wilson, M.D.
Chief, NAE
Graduate Student
Department of Developmental Laboratory of Biochemistry
National Cancer Institute
Biology and Cancer
National Institutes of Health
Albert Einstein College of
Bethesda, Maryland
Medicine
Bronx, New York
Michael Yarns, Ph.D.
Professor
Jack Parker, Ph.D. Department of Molecular, Cellular
Professor and Developmental Biology
Department of Microbiology University of Colorado
Southern Illinois University Boulder, Colorado
Carbondale, Illinois
TABLE OF CONTENTS
Chapter 1
tRNA in the Molecular Biology of Retroviruses ............................................ 1
Samuel H. Wilson and John Abbotts
Chapter 2
The Role of Modified Nucleosides in tRNA Interactions ............................ 23
Glenn R. Bjork
Chapter 3
Correlation Between Codon Usage and tRNA Content in
Microorganisms ............................................................................................. 87
Toshimichi Ikemura
Chapter 4
Aminoacyl-tRNA (Anticodon): Codon Adaptation in
Higher Eucaryotes ....................................................................................... 113
Dolph L. Hatfield, Jae-E. Jung, Byeong J. Lee, and In S. Choi
Chapter 5
Adaptation of tRNA Population to Codon Usage in
Cellular Organelles ...................................................................................... 125
Laurence Marechai-Drouard, Andre Dietrich, and Jacques-H. Weil
Chapter 6
Differential tRNA Gene Expression in Eukaryotes .................................... 141
Robert Pirtle and Irma Pirtle
Chapter 7
Codon Pair Utilization Bias in Bacteria, Yeast, and Mammals ................. 157
G. W. Hatfield and George A. Gutman
Chapter 8
Variations in Reading the Genetic Code .................................................... 191
Jack Parker
Chapter 9
Selenocysteine, a New Addition to the Universal Genetic Code ............... 269
Dolph L. Hatfield, In S. Choi, Byeong J. Lee, and Jae E. Jung