Progress in Molecular and Subcellular Biology

194 Pages·1990·4.73 MB·English

by  L. Phi-Van, W. H. Strätling (auth.), Prof. Dr. Philippe Jeanteur, Dr. Yoshiyuki Kuchino, Prof. Dr. Werner E. G. Müller, Prof. Dr. Philip L. Paine (eds.)

Progress
11 in Molecular and
Subcellular Biology
Edited by
P. Jeanteur, Y. Kuchino,
W.E.G. Miiller (Managing Editor),
P.L. Paine
With 13 Figures
Springer-Verlag Berlin Heidelberg New York
London Paris Tokyo Hong Kong
Prof. Dr. WERNERE. G. MULLER Dr. YOSHIYUKI KUCHINO
Physiologisch-Chemisches Institut National Cancer Center
Abt. Angewandte Molekularbiologie Research Institute
Duesbergweg 6 Tsukiji 5-chome
6500 Mainz, FRG Chuo-ku, Tokyo 104, Japan
Prof. Dr. PHILIPPEJEANTEUR Prof. Dr. PHILIP L. PAINE
UACNRS1191 Department of
Laboratoire de Biologie Moleculaire Biological Sciences
Universite des Sciences et Technique St. John's University
du Languedoc Grand Central & Utopia Parkways
34060 Montpellier Cedex, France Jamaica, New York 11439, USA
ISBN-13:978-3-642-75180-6 e-ISBN-13:978-3-642-75178-3
DOl: 10.1007/978-3-642-75178-3
The Library of Congress has catalogued this serial publication as follows:
Library of Congress Catalog Card Number 75-79748
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© Springer-Verlag Berlin Heidelberg 1990
Softcover reprint of the hardcover 1st edition 1990
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Contents
L. PHI-VAN and W.H. STRATLING: Association of DNA with Nuclear Matrix
A. Introduction . . . . . . . . . . . . . 1
B. MAR Elements and Their Properties 1
C. Roles of MAR Elements in DNA Packaging and DNA Replication 5
References ............................... 8
D.O. NEWMEYER: Nuclear Import in Vitro
A. Overview of Nuclear Import ............... 12
I. Nuclear Import Occurs Through the Nuclear Pore 12
II. The Structure and Composition of the Nuclear Pore 14
III. Functional Properties of the Nuclear Pore . . . . . . 16
IV. Signals for Nuclear Accumulation . . . . . . . . . . 18
V. The Effect of Multiple Nuclear Targeting Signals in a Protein . 20
VI. Is There a Role for Intranuclear Binding in Nuclear Import? 21
VII. Nuclear Import is an Active Process. Evidence for a Signal
Sequence Receptor . . . . . . . . . . . . . . . 22
VIII. Is the Signal Sequence Receptor Heterogeneous? . 24
IX. Regulation of Nuclear Import . . . . . . . . . . 26
1. Changes in Nuclear/Cytoplasmic Localization
During Embryogenesis ................... 26
2. Nuclear Import of snRNP Particles ............. 26
3. Nuclear Exclusion of Transcription and Replication Factors:
a Regulatory Mechanism? . . . . . . . . . . . . . . . . . . 27
4. Reversible Nucleocytoplasmic Movement . . . . . . . . . . 28
5. Nuclear Import of Hormone Receptors: Hormone-Dependent? 29
B. In Vitro Systems for Studying Nuclear Import ..... 30
I. In Vitro Systems Based on Xenopus Egg Extracts. 31
1. Rationale for the Use of Egg Extracts . . . . . 31
2. Nuclear Import Activity in Egg Extracts is Authentic 32
VI Contents
3. Nuclear Import is Inhibited by the Lectin, Wheat Germ Agglutinin.
Are Nuclear Pore Glycoproteins Involved in the Transport
Mechanism? . . . . . . . . . . . . . . . . . . . . . . . . .. 33
4. Nuclear Import is Separable Experimentally into Two Steps:
Signal-Mediated Binding and ATP-Dependent Translocation. 33
II. In Vitro Systems Based on Isolated Nuclei in Buffers . . . . . . 34
1. Heparin-Extracted Nuclei . . . . . . . . . . . . . . . . . . 35
2. Systems Involving Whole Isolated Nuclei in Defined Buffers 35
III. Passive Influx into Isolated Nuclei. 39
C. Conclusion 40
References . . 41
G.W. ZIEVE and R.I. FEENEY: Cytoplasmic Assembly and Nuclear Transport
of the snRNP Particles
A. Introduction . . . . 51
B. Maturation of the snRNAs 51
I. snRNAs Appear Transiently in the Cytoplasm 51
II. 3' End Processing of snRNAs . . . . . . . . 57
III. Nucleotide Modification Including the 5' Cap 58
C. snRNP Particle Assembly . . . . . . 59
I. snRNP Proteins . . . . . . . . 59
II. snRNP Core Protein Assembly 63
III. Relationship of B, B', and N snRNP Core Proteins 67
IV. VI and V2 Specific Proteins ........... . 68
V. Independent Synthesis and Assembly of snRNP Proteins
in Xenopus Oocytes . . . . . . . . . . 70
VI. In Vitro Assembly of snRNP Particles . 71
VII. V6 snRNP . . . . . . . . . . . . . . 72
D. Nuclear Accumulation of snRNP Particles 73
I. Interphase......... 73
1. snRNP Core Particles . 73
2. snRNP Specific Proteins 75
II. Mitosis ...... . 76
E. Summary and Perspectives 78
References . . . . . . . . . . 80
M. BORNENS, E. BAILLY, F. GOSTI, and G. KERYER: The Centrosome:
Recent Advances on Structure and Functions
A. Definitions 86
Contents VII
B. Isolation of Centrosomes from Somatic Cells 87
C. The Structure of Isolated Centrosomes . . . 89
D. Centrosomal Proteins ........... . 90
E. The Centrosome and the Nucleation of Microtubules 93
F. The Centrosome Cycle in the Cell Cycle 93
G. Centrosome Continuity . . . . . . . . . . . . . . . 99
H. Centrosome and the Spindle Formation . . . . . . . 101
I. Centrosome and the Spatial Organization of Microtubules in
Terminally Differentiated Cells . . . . . 102
J. Centrosome and Cell Polarity/Movement 103
K. Conclusion 108
References . . . . . . . . . . . . . . . . . 108
D. HATFIELD, B.J. LEE, D.W.E. SMITH, and S. OROSZLAN: Role of Nonsense,
Frameshift, and Missense Suppressor tRNAs in Mammalian Cells
A. Introduction . . . . . . . . . . . . . . . . . . . . . . . 115
B. Suppression of Nonsense Codons . . . . . . . . . . . . 116
I. Naturally Occurring Nonsense Suppressor tRNAs 116
1. Amber Suppressor tRNAs . 116
2. Ochre Suppressor tRNAs . . . . . . . . . . . 121
3. Opal Suppressor tRNAs . . . . . . . . . . . . 121
II. Assays for Nonsense Suppressor tRNAs and Nonsense Mutations 124
III. Introduction of Nonsense Suppressor tRNA Genes into
Intact Cells ..... 126
IV. Other Considerations . . . . . . . . . . 128
C. Ribosomal Frameshifting . . . . . . . . . . . 130
I. Ribosomal Frameshifting in Retroviruses 130
II. tRNAs Involved in Frameshifting . . . . 133
D. Missense Suppression and Misrecognition of Genetic Codewords . 134
E. Conclusion 136
References ........ . . . . . . . . . . . . . . . . . . . . . . 138
Y. KUCHINO, S. NISHIMURA, H.C. SCHRODER, and W.E.G. MULLER: UAG Sup
pressor Glutamine tRNA in Uninfected and Retrovirus-Infected Mammalian Cells
A. Introduction . . . . . . . . . . . . . . . . . . . . . . . . 147
B. Isolation and Sequence Analysis of Glutamine tRNA from
Mammalian Cells . . . . . . . . . . . . . . . . . . . . . 148
C. Analysis of Suppressor Activity of Mammalian Glutamine tRNA . 150
VIII Contents
D. Selective Increase of Suppressor Glutamine tRNA in
Retrovirus-Infected Cells ............. . 151
E. Influence of Increased Amount of Suppressor tRNA on Translation
Reaction of Cellular mRNA . 153
F. Discussion 154
References . 157
W.F. LOOMIS: Essential Genes for Development of Dictyostelium
A. Introduction . . . . . . . . . . . . 159
B. Genetic Analysis in Dictyostelium 160
C. Temporal Sequence of Differentiations 162
D. Initiation of Development . . . . . . . 164
E. Stage 1: Chemotaxis . . . . . . . . . . 165
F. cAMP Regulation of Transcription and Chemotaxis 167
G. Stage 2: Integration . 169
H. Stage 3: Divergence . 171
I. Stage 4: Culmination 175
J. DependentSequence 177
References . . . . . . . 180
Subject Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Contributors
You will find the addresses at the beginning of the respective contribution.
Bailly, E. .. 86 Miiller, W.E.G .. 147
Bornens, M. 86 Newmeyer, D.D. 12
Feeney, R.J. 51 Nishimura, S. 147
Gosti, F. 86 Oroszlan, S ... 115
Hatfield, D. 115 Phi-Van, L. .. 1
Keryer, G. 86 Schroder, H.C. 147
Kuchino, Y. 147 Smith, D.W.E. 115
Lee, B.J. 115 Striitiing, W.H. 1
Loomis, W.F. 159 Zieve, G.W. 51
Association of DNA with Nuclear Matrix
L. PHI-VAN1,2 and W. H. STRATLING1
A. Introduction
There is increasing evidence that chromosomal DNA is attached to a nuclear
skeleton or matrix. The composition and morphology of the matrix appears to be
highly complex in keeping with the long list of known and postulated functions,
which seems to include nearly all important processes of the nucleus, such as
transcription, RNA processing and transport, replication, and the organization
of interphase chromatin. A significant problem is, however, that nuclear matrices
are operationally defined structures and that results obtained by use of different
methods are not comparable. Depending on various reports, the matrix contains
a more-or-Iess wide spectrum of nonhistone proteins but few of these (mostly
enzymes) have been identified (Razin et al. 1981; Smith and Berezney 1983;
Staufenbiel and Deppert 1983; Berrios et al. 1985; Jackson and Cook 1986;
Lehner et al. 1986; Pieck et al. 1987; Tubo et al. 1987; Tubo and Berezney 1987a, b,
c; Fey and Penman 1988). A class of major structural proteins such as the histones
in chromatin or the lam ins in the nuclear lamina has not yet been found in nuclear
matrix preparations. The matrix, when prepared with 2 M NaCI and DNase I
digestion (Berezney and Coffey 1974), further contains less than 1% o f the nuclear
DNA. Several laboratories have studied the distribution of nuclear DNA in
matrices. Repeatedly, actively transcribed genes and their flanking sequences
were found to be enriched in nuclear matrices (Jackson et al. 1981; Robinson et al.
1982; Ciejek et al. 1983; Hentzen et al. 1984; Jost and Seldran 1984; Rose and
Garrard 1984; Stratling et al. 1986; Stratling 1987). An enrichment of repeated
DNA sequences in nuclear matrix preparations was also reported (Goldberg
et al. 1983; Chimera and Musich 1985).
B. MAR Elements and Their Properties
The structure in metaphase chromosomes thought to be homologous to the
skeleton in interphase nuclei is called the scaffold. Both structures are believed to
lInstitut fur Physioiogische Chemie, Universitats-Krankenhaus Eppendorf, Martinistr. 52,
2000 Hamburg 20, FRG
2 Present address: Kernforschungszentrum Karlsruhe, Institut fUr Genetik und Toxikoiogie,
Postfach 3640, 7500 Karlsruhe, FRG
2 L. Phi-Van and W. H. StriWing
organize chromosomal DNA into domains or loops. While general evidence for
this model has been gathered by biochemical and electron microscopic studies in
the late 1970s and early 1980s (Benyajati and Worcel 1976; Cook and Brazell
1976; Paulson and Laemmli 1977; Igo-Kemenes and Zachau 1978; Lebkowski
and Laemmli 1982), the relationship of the loop organization of chromatin to
specific sequences has become apparent since 1984. In 1984, Mirkovitch et al.
reported that the tandemly repeated histone genes of Drosophila melanogaster are
attached in histone-depleted nuclei to the matrix ( = scaffold) via specific sites
located within a defined fragment of the HI-H3 spacer. Secondly, in two hsp70
heat shock gene loci they found attachment sites upstream of the promoter
regions and of regulatory elements. Since this first report, the matrix attachment
regions (= MARs = SARs = MAR elements) of four other genes and within a
320 kb region around the rosy and Ace loci of Drosophila have been mapped by
Laemmli and co-workers (Gasser and Laemmli 1986b; Mirkovitch et al. 1986;
Mirkovitch et al. 1988) (see Table 1). In Drosophila, MAR elements occur in the
nontranscribed flanking regions and are found in most, but not all, cases in one,
occasionally two, copies upstream as well as downstream of the gene. MAR
elements can bracket one or several transcription units. A surprise was the
Table 1. List of MAR elements
Drosophila melanogaster Reference
Histone-gene repeat
hsp70 (87 A7 locus) } Mirkovitch et al. (1984)
hsp70 (87C1 locus)
Alcohol dehydrogenase
Sgs-4 } Gasser and Laemmli (1986b)
Fushi tarazu
Region of rosy and Ace loci Mirkovitch et al. (1986)
Actin SC Mirkovitch et al. (1988)
Yeast
ARS elements:ARS1, HO ARS,
Histone H4 ARS, HMR-E ARS, 2 JIm
Plasmid ARS
Centromer elements:CENIII, CENIV, CENXI
Chicken
Lysozyme Phi-Van and Strlitling (1988)
Mouse
Immunoglobulin K light chain Cockerill and Garrard (1986)
Immunoglobulin heavy chain locus Cockerill et al. (1987)
Chinese hamster
Dihydrofolate reductase Klis and Chasin (1987)
Human
B-Interferon Bode and MaaB (1988)
B-globin gene locus Jarman and Higgs (1988)
Plants
Soybean leghemoglobin Izaurralde et al. (1988)