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How RNA function requires structure
Tao Pan
RNA structure and function edited by Robert W. Simons and Marianne Grunberg-Manago. Published by Cold Spring Harbor Laboratory Press, 10 Skyline Drive,
Plainview, New York, USA; 1998. 726 pages. $145.00.
It is well established that RNA structure
is essential for the function of ribosomal,
transfer, spliceosomal and catalytic
RNAs. Although studying the structures
of these stable RNAs is an exciting area of
research, most molecular biologists deal
only with messenger RNAs, usually considered simply to be the intermediary
from DNA to proteins. The unique aspect
of the book RNA structure and function is
that it goes beyond the required descriptions of the structure and function of stable RNAs, with chapters on structural
requirements of messenger RNAs, in regulating translation and transcription.
This book conveys the message that RNA
structure is relevant for anyone interested
in fully understanding the pathway that
leads from DNA to RNA to protein.
An RNA can form stable structures
with only a small number of nucleotides.
For example, a dozen nucleotides are sufficient to form a stable hairpin loop
under physiological conditions. The
more complex secondary structural
motifs — bulged loops, internal loops
and so forth — involve only a few
nucleotides more. A tertiary structure
such as that of the hammerhead
ribozyme can be constructed with as few
as ~40 nucleotides, and that of a transfer
RNA requires only ~70 nucleotides. On
the basis of this information alone, an
RNA of more >100 nucleotides is expected to contain several structures, some of
which may be stable and some of which
may form only transiently. To make a
protein of 100 amino acids, a messenger
RNA must be longer than 300
nucleotides, and it is therefore not surprising that nature takes advantage of the
enormous structure-forming potential of
RNA. What we know today about RNA
structure may be only the tip of an iceberg.
RNA structure and function begins with
a personal account by J. Fresco of a small
number of crucial experiments, which
required substantial deductive reasoning
and led to the discovery of secondary and
tertiary structures of RNA. This chapter
is enlightening for a modern RNA biolo540
gist armed with tools and techniques not
available in those days. The next six chapters offer a collection of experimental
methods for determining RNA structure.
A chapter by R. Cedergren and F. Major
describes how to model RNA structure
— which is perhaps easier than modeling
protein structure, given the simple base
pairing constraints of nucleic acids —
and provides a summary of models
obtained to date. Following this section,
H. Moine et al. provide a comprehensive
review of chemical probes useful for analyzing RNA structure and function in
solution. Many of these chemical
reagents can yield data at the resolution
of a nucleotide, compensating for the fact
that only a few high resolution RNA
structures have been determined. The
next two chapters present RNA structure
determination using NMR spectroscopy
(described by E. Puglisi and J. Puglisi)
and X-ray crystallography (described by
S. Holbrook). Both chapters explain the
basics such that a first year graduate student could follow the premise of these
complex techniques and evaluate the
structures presented. Surprisingly, these
chapters provide a sense of inadequacy in
RNA structure determination: all known
high-resolution structures can be
described in two short chapters (imagine
trying to do that with proteins). The final
two chapters of this section present the
phylogenetic method used in RNA structure prediction and modeling (unfortunately, the thermodynamic method is not
included here). Phylogenic studies
involve examining the sequences of a set
of RNAs that perform the same function
and comparing the sequence changes at
aligned positions. F. Michel and M. Costa
give an account of the usefulness and
limitations of natural phylogeny and
briefly describe computational methods
to achieve automation. S. Baskerville
et al. describe the use of in vitro selection
to obtain artificial phylogenies in order
to understand structure and function of
natural RNAs, and the authors also provide a thorough pros and cons discussion
of in vitro selection (which should be
useful for scientists considering this technique for their own research).
The next two chapters describe the
structure and dynamics of RNA–RNA
interactions in large biological systems. A
chapter by H. Noller discusses experiments on rRNA–tRNA interactions in
translation — studies which have set the
standard for biochemical work on RNA
(protection against chemical probes,
modification-interference, crosslinking
and so forth). A subsequent review by
T. Nielsen describes RNA–RNA interactions in the spliceosome, which are particularly remarkable in their fluidity and
specificity in directing the splicing reaction. Nevertheless, the author reminds us
that these RNA acrobatics are possible
only in the context of the entire spliceosome and that the roles of protein factors
in splicing have so far been under-investigated.
Topics concerning RNA catalysis are
sampled in the following two chapters.
M. Harris et al. describe modeling the
tertiary structure of the large (~400
nucleotides) catalytic RNA from bacterial RNase P, which has led to the design of
tethered ribozyme–substrate conjugates.
The underlying principles of how an
RNA can catalyze chemical reactions are
also briefly discussed. Ribozymes much
smaller than the RNase P RNA are considered in the following chapter by S.
Siguidsson et al. Small ribozymes such as
the ones described are much easier to
analyze and manipulate (for example,
their catalytic properties have been
exploited to target the destruction of particular mRNAs in vivo). The crystal
structure of the small hammerhead
ribozyme has greatly expanded our
understanding of how RNA structure is
related to RNA catalysis (but, for readers
interested in knowing more about catalysis, it is unfortunate that a discussion of
the well characterized group I ribozyme
is not included in this book).
A block of seven chapters is devoted to
RNA structures that are important in
regulating translation, replication, transcription and mRNA degradation. A
nature structural biology • volume 5 number 7 • july 1998
book review
chapter by M. Springer et al. gives a
detailed description of numerous proteins that bind multiple types of cellular
RNAs. For example, the E. coli threonyltRNA synthetase aminoacylates tRNAThr
and binds its own mRNA to autoregulate
translation (apparently, a segment within
the mRNA mimics the structure of the
threonyl-tRNA). The chapter by
D. Draper et al. provides a quantitative
explanation of translational repression
by proteins. In some cases, not only the
static RNA structures, but also the
dynamic interconversion of structures
can be crucial for function. B. Zeiler and
R. Simons next provide an account of
natural antisense RNAs that regulate
translation and replication. The authors
emphasize that base pairing alone (thermodynamics) in these systems is insufficient; the pathway and speed to the
formation of base pairs (kinetics) are also
critical for function, and natural antisense RNA systems have evolved fast
bimolecular association rates. A section
by M. de Smit provides an account of
mRNA structures that modulate translational initiation in bacteria. In the following chapter T. Platt goes on to
describe the importance of RNA structure in transcription. Although this field
is still in its infancy, RNA structures have
been shown to play intimate roles in
transcriptional elongation (for example
in pausing or arrest) and termination. A
glimmer of what information is to come
regarding the roles of RNA structures in
eukaryotes is exemplified by work on the
iron-responsive element (IRE). The
chapter by J. Harford and T. Rouault
describes how the IRE inhibits translation and regulates mRNA degradation
depending on its location relative to the
protein coding region. Another example
is described in the chapter by
A. Hüttenhofer and A. Böck which shows
that incorporation of the unusual amino
acid selenocysteine into a polypeptide
chain requires a novel tRNA, a welldefined mRNA structure and a specific
protein elongation factor.
The last section of RNA structure and
function describes protein enzymes that
use RNA for substrates or utilize an internal RNA template for DNA synthesis.
The chapter by J. Arnez and D. Moras
provides a detailed description of all 20
aminoacyl-tRNA-synthetases.
Many
crystal structures have been solved in the
past few years, allowing in-depth structural comparison of these enzymes. At
the other end of the spectrum, protein
enzymes involved in RNA editing — in
which the sequence of an mRNA is covalently altered to yield changes in the
translated amino acid sequence — are
just beginning to be isolated. The chapter
by G. Connell and L. Simpson describes
the involvement of RNA structure in
deamidation and insertion/deletion reactions. The protein enzymes in these reactions appear to recognize only secondary
nature structural biology • volume 5 number 7 • july 1998
structural features or even just nucleotide
sequences. A chapter by E. Blackburn
describes the identification of telomerase
RNA, which contains the template for
telomere synthesis and is the site of
assembly for telomerase proteins. The
last chapter by E. Arn and J. Abelson
describes the reaction mechanism of bacterial RNA ligases, a class of enzymes still
without a defined physiological function;
nevertheless, because of their valuable
properties, these enzymes are widely
used for in vitro biochemical experiments.
The editors of RNA structure and function state in the preface that this book
should mark a time in RNA biology with
“. . . a growing appreciation not only of
the importance of RNA structure and
function, but also of the underlying technical and intellectual challenges” (italics
in the original text). The editors also
hope to “. . . attract the best and brightest
to this burgeoning field”. Will they succeed? The answer will undoubtedly be
yes. I was impressed by descriptions of
RNA structure in all aspects of biology —
in particular, how mRNA structures
influence their function. The future for
the RNA field is bright indeed.
Tao Pan is in the Department of
Biochemistry and Molecular Biology,
University of Chicago, 920 E 58th Street,
Chicago, Illinois 60637, USA. email:
[email protected]
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