Histones and Nucleohistones

314 Pages·1995·9.514 MB·English

by  E. W. Johns (auth.), D. M. P. Phillips (eds.)

HISTONES
and
NUCLEOHISTONES
HISTONES
and
NUCLEOHISTONES
Edited by
D. M. P. Phillips
The Chester Beatty Research Institute,
if
Institute Cancer Research, Royal Cancer Hospital,
London S. W.3
9? PLENUM PRESS London and New York·1971
Plenum Publishing Company Ltd.
Davis House
8 Scrubs Lane
Harlesden
London NW 1 0 6SE
U.S. Edition published by
Plenum Publishing Corporation
227 West 17th Street
New York New York 10011
Copyright © 1971 by Plenum Publishing Company Ltd.
Softcover reprint of the hardcover 1st edition 1971
All Rights Reserved
No part of this book may be reproduced in any form by photostat,
microfilm, or any other means without written permission from the
Publisher.
ISBN-13: 978-1-4684-1817-0 e-ISBN-13: 978-1-4684-1815-6
DOl: 10.1007/978-1-4684-1815-6
Library of Congress Catalog Card Number: 71-161306
PREFACE
The histones are now a very well established part of Biochemistry.
The interpretation of all that is known about them, however, is
already too great a burden for a single author to undertake. Indeed, a
survey of the indexed literature shows that the number of
publications on the histones has approximately doubled in every
three years for the past 15 years, and is now several hundred a year.
It is time then to bring together in one publication the major topics
embraced by this great research effort.
This book therefore endeavours to give, in six chapters, a broad
and searching account of the biochemistry and biophysics of these
interesting proteins and their complexes with nucleic acids, the
nucleohistones. Each chapter is written by different authors who are
all active in this research and who have had many years experience
with these proteins and their complexes.
Chapters 1, 2, part of 3, and all of Chapters 5 and 6, cover the
occurrence, preparation, characterization, sequence structure, bio
physical properties and finally, the biosynthesis and functions of the
histones. The other part of Chapter 3, the whole of Chapter 4 and to
a less extent some other chapters, all discuss the properties and
structure of the nucleohistones. The study of these complexes is
undoubtedly of great importance in bridging the gaps in our
knowledge of template activity and differentiation as well as of
chromosomal structure and mechanics. Each chapter is largely
self-contained and altogether reference is made to over one thousand
publications in this field. Where it seemed appropriate, the
protamines have been included in the discussion. Valuable studies in
progress are unravelling the functions of these odd proteins, and
thereby the true connection between them and the histones proper.
I have been most fortunate in finding eight co-authors who would
spare the very considerable time and energy needed for this book. In
all cases the chapters include some unpublished work, and I feel that
they have made a valuable contribution to the understanding of
histone and nucleohistone biochemistry and biophysics. I would like
to thank them all sincerely for their efforts and co-operation.
January 1971 D. M. P. Phillips
v
HISTONE NOMENCLATURE
A wide variety of nomenclatures has evolved in different
laboratories for distinguishing the histone fractions. A table
correlating many of these is given in Chapter 1 (page 34).
However, in order to make this text more intelligible and
consistent, the two most widely adopted nomenclatures are both
used together. For example, when reference is made to the very
lysine-rich histone Fl, which is also histone I, it is designated: Fl (I),
and similarly with the other major histone fractions thus: F2Al (IV),
F2A2(IIbl), F2B(IIb2), F3(III) and F2C(V).
Occasionally, in referring to earlier work, the symbol F2 is used.
This embraces the fractions F2Al(IV), F2A2(IIbl) and F2B(IIb2).
vi
CoNTRIBUTORS
v.
G. Allfrey The Rockefeller University, New York, New
York 10021, U.S.A.
E. M. Bradbury Biophysics Laboratory, Physics Department,
C. Crane-Robinson Portsmouth Polytechnic, Park Road, Ports·
mouth POl 2DZ, U.K.
E. Fredericq Institut de Chimie-Physique, Universite de Liege
au Sart-T£lman, 4000-Liege, Belgium.
L. S. Hnilica Department of Biochemistry, The University of
Texas, M. D. Anderson Hospital and Tumor
Institute at Houston, Texas Medical Center,
Houston, Texas 77025, U.S.A.
E. W.Johns The Chester Beatty Research Institute, Institute
of Cancer Research, Royal Cancer Hospital,
London, S. W.3, U.K.
M. E. McClure Department of Biochemistry, The University of
Texas, M. D. Anderson Hospital and Tumor
Institute at Houston, Texas Medical Center,
Houston, Texas 77025, U.S.A.
D. M. P. Phillips The Chester Beatty Research Institute, Institute
of Cancer Research, Royal Cancer Hospital,
London, S. W.3, U.K.
T. C. Spelsberg Department of Biochemistry, The University of
Texas, M. D. Anderson Hospital and Tumor
Institute at Houston, Texas Medical Center,
Houston, Texas 77025, U.S.A.
vii
CoNTENTS
Preface. v
Histone Nomenclature.
VI
Chapter 1
The Preparation and Characterization of Histones, E. W. Johns
1.1 INTRODUCTION 2
1.1.1 Historical 2
1.2 DEFINITION OF HISTONES 4
1.3 OCCURRENCE OF HISTONES . 6
1.3.1 Multicellular organisms. 6
1.3.2 Unicellular organisms 9
1.4 PREPARATION OF WHOLE HISTONE 9
1.4.1 Isolation of deoxyribonucleoprotein (DNP) 9
1.4.2 Preparation of whole histone from DNP 10
(a) Acid extraction. . 10
(b) Salt dissociation 10
1.5 PREPARATION OF WHOLE PROTAMINE. 11
1.6 FRACTIONATION PROCEDURES FOR WHOLE HISTONE 13
1.6.1 Column chromatography . 13
1.6.2 Other methods 14
1.7 SELECTIVE EXTRACTION PROCEDURES 14
1. 7.1 Selective dissociation with salts . 14
1. 7.2 Selective extraction with acid 15
1. 7.3 Selective extraction using organic solvents 16
1.8 FRACTIONATION PROCEDURES APPLIED TO HISTONES FOR
THEIR FURTHER SUBDIVISION OR PURIFICATION 16
1.8.1 Methods for the separation of specific mixtures of fractions 16
1.8.2 Further purification and subdivision of the five main
histone fractions . 17
1.9 COMPLEXITY AND HETEROGENEITY OF HISTONES 19
1.10 THE FRACTIONATION OF PROTAMINE 21
1.11 HISTONE SPECIFICITY . 22
1.12 CHARACTERIZATION OF HISTONES 23
1.12.1 Amino acid composition 23
1.12.2 Gel electrophoresis . . 26
1.12.3 Other methods 29
1.12.4 Quantitative determination 30
1.13 UNUSUAL HISTONES OR NUCLEAR PROTEINS 30
1.14 A COMPARISON OF HISTONE FRACTIONS AND NOMEN-
CLATURES 33
1.15 THE AGGREGATION OF HISTONES 35
1.16 OTHER GENERAL PROPERTIES OF HISTONES 36
ix
x CONTENTS
Chapter 2
The Primary Structure of Histones and Protamines, D. M. P. Phillips
2.1 INTRODUCTION 47
2.2 METIIODS USED IN AMINO ACID SEQUENCE WORK WITH
HlSTONES 48
2.2.1 Increasing the specificity of trypsin. . 48
2.2.2 The use of other proteolytic enzymes . 49
2.2.3 Chemical methods used for degrading histones for sequence
determination. . 50
2.3 THE PRIMARY STRUCTURE OF HISTONE Fl(I) . 50
2.4 THE PRIMARY STRUCTURE OF HISTONE F2B(IIb2) 55
2.5 THE PRIMARY STRUCTURE OF HISTONE F2A2(IIbl) 58
2.6 THE PRIMARY STRUCTURE OF HISTONE F2Al(IV) 60
2.7 THE PRIMARY STRUCTURE OF HISTONE F3(III) 63
2.8 THE PRIMARY STRUCTURE OF PROTAMINES 65
2.9 HISTONE SEQUENCE AND HISTONE EVOLUTION 67
2.9.1 Internal homology in protamine and histone sequences 67
2.9.2 Comparison of the sequences of different histones. . 72
2.10 THE PRIMARY STRUCTURE OF HISTONES IN RELATION TO
THE STRUCTURE OF DEOXYRIBONUCLEOHISTONE . 76
Chapter 3
Physical and Conformational Studies of Histones
and Nucleohistones, E. M. Bradbury and C. Crane-Robinson
3.1 INTRODUCTION 85
3.2 HISTONES 87
3.2.1 Molecular weights of histones and aggregation 87
3.2.2 Analysis of the primary structure of histones for possible
conformations 89
3.2.3 Physical studies of the conformations of histones . 98
Histones in the solid state. . . . 99
Optical Rotatory Dispersion studies of histones in solution 100
Nuclear Magnetic Resonance Spectroscopic studies of
histones . 103
3.3 THE CONFORMATION OF NUCLEOHISTONE . 110
3.3.1 X-Ray diffraction studies of nucleohistones 110
3.3.2 Evidence for the "supercoiled" form of nucleohistone 112
3.3.3 Factors involved in the "super coiled "structure . 114
3.3.4 Conformation of DNA and histones in nucleohistone 115
Spatial arrangements of histones on DNA. 121
3.4 PARTIAL NUCLEOPROTEINS . 122
3.4.1 Dissociation of histones from nucleohistones 123
3.4.2 Physical studies of partial nucleohistones . 124
3.4.3 Loss of superstructure on histone removal 125
3.5 RECOMBINATION OF HlSTONES WITH DNA 127
3.6 A STRUCTURAL ROLE FOR HISTONES. . . 128
CONTENTS D
Chapter 4
The Chemical and Physical Properties of Nucleohistones,
E. Fredericq
INTRODUCTION 136
4.1 THE PREPARATION AND COMPOSITION OF NUCLEO-
HlSTONES 137
4.1.1 Preparative procedures . 137
4.1.2 The composition of nucleohistones 139
Nucleic acids . 139
Proteins. 140
Acidic proteins 141
Histones 144
4.2 PHYSICO-CHEMICAL PROPERTIES OF NUCLEOHISTONES 144
4.2.1 Solubility. 144
4.2.2 Gel-forming properties 146
4.2.3 Size and shape. 148
4.2.4 Charge and titration. 152
4.2.5 Structural studies on nucleohistones and nucleoprotamines 154
Conformation of nucleohistones 154
Anisotropy and orientation of chromophores. 155
Conformation of nucleoprotamines . 156
Ultraviolet spectra of nucleohistones 157
4.3 INTERACTIONS OF DNA AND NUCLEOHISTONES WITH
OTHER MOLECULES 159
4.3.1 Interactions of DNA with small molecules and polybases 159
DNA-protamine interactions . 161
4.3.2 Interactions of DNA with histones . 162
4.3.3 Dissociation and reassociation of nucleohistones in salt
solu tion . 164
Characteristics of the dissociation process 165
Properties of reassociated nucleohistones . 167
4.3.4 Properties of protein-depleted nucleohistones 168
4.3.5 Interactions of nucleohistones with small cations and
molecules . 170
4.3.6 Interactions of nucleohistones with metal cations . 173
4.4 GENERAL CONCLUSIONS AND STRUCTURAL ASPECTS 174
4.4.1 Nature of the bonds between histones and DNA 175
4.4.2 Structural hypotheses . 178
Chapter 5
Histone Biosynthesis and the Cell Cycle, L. S. Hnilica,
M. E. McClure and T. C. Spelsberg
5.1 INTRODUCTION 187
5.2 HISTONE SYNTHESIS 188
5.2.1 Cellular localization of histone synthesis 188
5.2.2 Rates of biosynthesis of individual histone fractions 196
5.2.3 Histone turnover. 199
5.2.4 Extracellular factors affecting histone synthesis. 204
5.2.5 Histone synthesis during the cell cycle. 205
xii CONTENTS
5.3 HISTONE SYNTHESIS IN GAMETES AND DURING EMBRYO-
GENESIS . 214
5.3.1 Histones in meiosis 214
5.3.2 Arginine-rich proteins of male gametes 215
5.3.3 Histone synthesis in embryos. 221
5.4 THE INTEGRITY OF CHROMATIN 227
Chapter 6
Functional and Metabolic Aspects of DNA-Associated Proteins,
V. C. AUtrey
6.1 INTRODUCTION 241
6.1.1 On the relationship between chromosomal structure and
function 243
6.1.2 The chromosomal localization of histones and protamines 246
6.1.3 The problem of histone specificity 247
6.2 THE EFFECT OF HISTONES IN THE CELL 253
6.2.1 Histone effects on RNA synthesis 253
6.2.2 Histone effects on DNA synthesis 257
6.2.3 Histone effects on cell function-some general observations 258
6.3 ENZYMATIC MODIFICATIONS OF HISTONE STRUCTURE 260
6.3.1 Histone methylation-methylated lysines . 260
w-N-methyl-arginine in histones . 262
Evidence for 3-methyl histidine in histones 263
Methylation of histone carboxyl groups 264
6.3.2 Histone acetylation 264
e. -N-acetyllysine in histones-occurr!'nce and formation 265
Physiological aspects of histone acetylation 267
Correlations between NH2 -terminal acetylation and histone
synthesis 273
6.3.3 Thiol/disulfide conversions in the F3(III) histone fraction 276
6.3.4 Histone phosphorylation 277
6.3.5 Histone structural modifications-some general conclusions. 280
6.4 CHANGES IN ACIDIC CHROMOSOMAL PROTEINS AT TIMES
OF GENE ACTIVATION 281
Index .295