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Web Site Evolution of the Ribosome.

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Angewandte
Web Sites
Chemie
Figure 2. Phylogenetic tree of several species of red algae (rhodophytes).
Evolution of the Ribosome
In the 1830s, Charles Darwin investigated different species of Galapagos finches for common features, which led to his
theory on the origin and evolution of
biological species. 170 years later, advanced techniques in biochemistry and
molecular biology now allow us to carry
out comparative studies on a molecular
level and thus to describe the evolution
of cellular species. In addition to the
primary sequence of DNA as the main
source of genetic information, the development of certain structural features
in biomacromolecules, for example, in
the ribosome, can be used to identify
and explain evolutionary processes.
On “The Comparative RNA Web
Site”, Gutell and co-workers give a very
detailed comparison of the sequences
and structural models of the six most
intensively studied ribonucleic acids: 5S,
16S, and 23S ribosomal RNA (rRNA),
transfer RNA (tRNA), and group I and
group II introns. Most published RNA
sequences have been incorporated in
the extensive data bank. Hence, the
comparisons are based on almost
10 000 16S-like rRNA sequences and
about 1000 23S-like rRNA sequences,
all of which are listed with specific
information, such as the name of the
organism or the entry in the NCBI
GenBank. An unambiguous system has
been introduced for numbering the
bases in each molecule, which allows
the frequency of each base pair to be
determined statistically on various phylogenetic levels. Searches on sequence
homologies and common structural elements in different species can be carried
out with the help of a relational-databank management system. Representative structural models of the molecules
were calculated for all phylogenetic
Angew. Chem. Int. Ed. 2003, 42, 3065
groups based on covariational analysis,
a method developed over the last two
decades, which is described in detail
with its historical refinements. A large
number of figures in postscript and PDF
formats show the structural models with
actual and all possible base pairs, colorcoded secondary and tertiary structural
elements, and labels for the incidence of
introns in the individual phylogenetic
groups. A highlight for structural biologists are diagrams showing the level of
conservation of individual bases, which
can be viewed as a measure of the
importance of certain positions for the
function of the corresponding macromolecule (Figure 1).
several publications by the Gutell
group: Studies concerning the important
U-turn motif or the special role of
unpaired adenosines in rRNA can be
found, as well as thermodynamic studies
on the folding of 16S and 23S rRNA,
and phylogenetic analyses (Figure 2).
In summary, the website contains a
large amount of detailed data, such that
it is difficult for the nonspecialist to keep
an overview of it. Nevertheless, a detailed introduction is given in the publication introducing the website,[1] and
for most functions short explanations
are available, as well as a good documentation system for almost all tables.
The website offers interesting analyses
for all scientists working in the field of
nucleic acids and is of special interest for
structural biologists and phylogeneticists.
Burkhard Luy
Technische Universitt Mnchen (Germany)
[1] J. J. Cannone, S. Subramanian, M. N.
Schnare, J. R. Collett, L. M. D>Souza, Y. Du,
B. Feng, N. Lin, L. V. Madabusi, K. M.
MCller, N. Pande, Z. Shang, N. Yu, R. R.
Gutell, “The comparative RNA web (CRW)
site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs”, BMC
Bioinformatics 2002, 3, 2.
Figure 1. Representative structural model of
the 5S rRNA of Archaea: Through the coding
in uppercase and lowercase letters, dots, and
circles, different levels of base conservation
are visualized in structure diagrams.
For more information visit
http://www.rna.icmb.utexas.edu
or contact
web@www.rna.icmb.utexas.edu
All sequences and structural models
are given in tabular form, but can also be
searched for by using sophisticated
search engines. In addition to the data
bank, which allows direct comparisons
to be made, a collection of material is
accessible that has been the basis for
www.angewandte.org
$ 2003 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
3065
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