Table Of ContentNucleic Acids and Molecular Biology
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Nucleic Acids and
Molecular Biology
Volume 9
Edited by
Fritz Eckstein' David M.l. Lilley
With 101 Figures, 12 of Them in Color
Springer
Prof. Dr. FRITZ ECKSTEIN
Max-Planck -Institut
fUr Experimentelle Medizin
Hermann-Rein-StraBe 3
37075 Gottingen, Germany
Prof. Dr. DAVID M.J. LILLEY
University of Dundee
Biochemistry Department
Dundee DDl 4HN
United Kingdom
Cover illustration by kind permission of B. W. Matthews
ISBN-13 :978-3-642-79490-2 e-ISBN-13:978-3-642-79488-9
DOl: 10.1007/978-3-642-79488-9
The Library of Congress has catalogued this serial publication as follows:
Library of Congress Catalog Card Number 90-64/8/7
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© Springer-Verlag Berlin Heidelberg 1995
Softcover reprint of the hardcover 1st edition 1995
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Preface to the Series
From its inception, molecular biology has always been a discipline
of rapid development. Despite this, we are presently experiencing a
period of unprecedented proliferation of information in nucleic
acid studies and molecular biology. These areas are intimately
interwoven, so that each influences the other to their mutual
benefit. This rapid growth in information leads to ever-increasing
specialization, so that it becomes increasingly difficult for a
scientist to keep abreast of developments in all the various aspects
of the field, although an up-to-date knowledge of the field as a
whole is highly desirable.
With this background in mind, we have conceived the present
series Nucleic Acids and Molecular Biology. It comprises focused
review articles by active researchers, who report on the newest
developments in their areas of particular interest. The reviews
are not intended to be exhaustive, but rather to place the most
recent data into context. This format will allow our colleagues to
familiarize themselves with new developments in areas outside
their own immediate speciality, thus facilitating a more global
view of their own work. Moreover, we hope sincerely that this
will convey some of the excitement of the interdisciplinary nature
of the study of nucleic acids and molecular biology.
This series is planned to appear annually. This period will
allow us to return to important topics with sufficient frequency to
cover new developments as they emerge.
FRITZ ECKSTEIN
DAVID M.J. LILLEY
Introduction to Volume 9
Volume 9 contains discussion of two multi-stranded DNA struc
tures. Triplexes may be formed by oligopurine sequences under
certain conditions, and tetraplexes by oligoguanine sequences;
the latter have created interest in view of their possible function
at telomeres and in some recombination reactions. The structure
of the parallel-stranded tetraplex has been solved at high resolu
tion both in solution and in the crystal. In eukaryotes most of the
cellular DNA is complexed with histones to form chromatin, and
this must be taken into account in analysing the function of DNA
in these cells.
DNA undergoes a variety of dynamic genetic processes. In
recombination a junction is formed in the DNA that can exchange
basepairing by branch migration. Kinetic measurements of the
rates of spontaneous branch migration show that this process can
be quite slow, and in Escherichia coli this is catalysed by either
RuvAB or RecG. The topology of DNA is manipulated by
topoisomerases, of which new examples are constantly being
found. The archetypical type II topoisomerase is DNA gyrase of
E. coli, which is finally yielding to structural analysis by crystal
lography. While the role of DNA gyrase appears to be to in
troduce negative supercoiling into the DNA, the role of reverse
gyrase seems to be just the opposite, ie to introduce positive
supercoiling into the DNA of extreme thermophiles. Yet another
topoisomerase, topoisomerase IV of E. coli, has the role
of decatenating the replicated circular chromosome prior to
partitioning.
Ultimately, many of the properties of cells are determined by
the regulation of gene expression by transcription factors. One
of the original transcription factors in eubacteria is the cAMP
receptor protein (CRP or CAP) that activates transcription from
a series of promoters in E. coli. The mechanism of this activation
is gradually emerging thanks to a combination of elegant genetic
studies, biochemistry and structural investigation. The list of
protein structural motifs found in DNA binding proteins continues
to grow, and in this volume the structures of two are presented,
the helix-loop-helix motif found in a variety of oncogene products
VIII Introduction
and other transcnptlOn factors, and the HMG-box motif. The
latter also appears to have been recruited by a range of tran
scription factors and other proteins, including the RNA poly
merase I factor UBF found in Xenopus and other eukaryotes.
Another HMG-box-containing protein has been isolated as one
that selectively binds DNA containing cisplatinum adducts.
A fascinating new class of DNA binding proteins are emerging
that interact with telomeres and other guanine-tetraplex struc
tures. Some, like the yeast RAP1 protein, appear to facilitate the
formation of tetraplex structures. Of course, many proteins
that interact with nucleic acids are enzymes, and these are not
neglected. DNA replication by phage ¢29 DNA polymerase is
discussed, and the structural features of ribonucleotide reductase,
a highly regulated enzyme, are presented in detail. The volume
ends with a review of RNA splicing, a process which increases in
complexity.
We thank all the authors for the high standard of reviews
written for this Volume.
January 1995 DAVID M.J. LILLEY
FRITZ ECKSTEIN
Contents
Triple-Stranded DNA
J. BERNUES and F. AZORIN . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Chromatin Structure and Transcription
J.J. HAYES and A.P. WOLFFE........................ 22
DNA Branch Migration
P. HSIEH and I.G. PANYUTIN .... . . .............. .... 42
The RuvA B and RecG Proteins of Escherichia coli
M.e. WHITBY, G.J. SHARPLES, and R.G. LLOYD 66
Reverse Gyrase
M. DUGUET. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Unlinking of DNA by Topoisomerases
During DNA Replication
C.J. ULLSPERGER, A.V. VOLOGODSKII,
and N.R. COZZARELLI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Structure of Parallel-Stranded Guanine Tetraplexes
A.I.H. MURCHIE, F. ABOUL-ELA, G. LAUGHLAN,
B. LUISI, and D.M.J. LILLEY. . . . . . ... . . . . . . . . . . .... . 143
Structure and Mechanism of DNA Gyrase
D.B. WIGLEY.. . ...... . . . . . . . . . .. . . . . . . . . . . . ... . . . 165
The E. Coli Cyclic AMP Receptor Protein
S. BUSBY, A. KOLB, and H. Buc..... . . . . . . ... .... . .. 177
Structure of Ribonucleotide Reductase
from Escherichia Coli
B.-M. SJOBERG. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
x
Contents
The Structure of the HMG Box and Its Interaction
with DNA
C.M. READ, P.D. CARY, C. CRANE-RoBINSON,
P.C. DRISCOLL, M.O.M. CARRILLO, and D.G. NORMAN 222
UBF, an Architectural Element
for RNA Polymerase I Promoters
R.H. REEDER, C.S. PIKAARD, and B. MCSTAY 251
Consequences of HMG-Domain Protein Binding
to Cisplatin-Modified DNA
M.M. McA'NULTY and S.J. LIPPARD.................. 264
DNA Recognition by Helix-Loop-Helix Proteins
A.R. FERRE-D'AMARE and S.K. BURLEY.. . . . . . . ... . . . 285
Telomere-Binding Proteins of Ciliated Protozoa
C.M. PRICE. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
Repressor Activator Protein 1 and Its Ligands:
Organising Chromatin Domains
E. GILSON and S.M. GASSER. . . . . . . . . . . . . . . . . . . . . . . . 308
Bacteriophage tjJ29 DNA Polymerase
L. BLANCO and M. SALAS. . . . . . . . . . . . . . . . . . . . . . . . . . . 328
Nuclear Pre-mRNA Splicing
c.L. WILL, P. FABRIZIO, and R. LOHRMANN. . . . . ... . . . 342
Subject Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373
Contributors
You will find the addresses at the beginning of the respective contribution.
Aboul-ela, F. 143 Lippard, S.J. 264
Azorin, F. 1 Lloyd, R.G. 66
Bemues, J. 1 Liihrmann, R. 342
Blanco, L. 328 Luisi, B. 143
Buc, H. 177 McA'Nulty, M.M. 264
Burley, S.K. 285 McStay, B. 251
Busby, S. 177 Murchie, A.I.H. 143
Carrillo, M.O.M. 222 Norman, D.G. 222
Cary, P.D. 222 Panyutin, I.G. 42
Cozzarelli, N.R. 115 Pikaard, C. 251
Crane-Robinson, C. 222 Price, C.M. 299
Driscoll, P.C. 222 Read, C.M. 222
Duguet, M. 84 Reeder, R.H. 251
Fabrizio, P. 342 Salas, M. 328
Ferre-D'Amare, A.R. 285 Sharples, G.J. 66
Gasser, S.M. 308 Sjoberg, B.-M. 192
Gilson, E. 308 Ullsperger, C.J. 115
Hayes, J. 22 Vologodskii, A.V. 115
Hsieh, P. 42 Whitby, M.C. 66
Kolb, A. 177 Wigley, D.B. 165
Laughlan, G. 143 Will, C.L. 342
Lilley, D.M.J. 143 Wolffe, A.P. 22
