Old Molecules Yield New Secrets
By Jason Socrates Bardi
Ancient structures can have many lives.
The Tower of London, for instance, was in the 15th, 16th
and 17th centuries an infamous prison where the likes of Thomas
More, Anne Boleyn and the sons of Edward IV were executed.
In the 18th century, it became an innocuous government building,
housing the Royal Mint and pressed silver coins. Today, it
is a tourist destination where travelers can get a glimpse
of the crown jewels and view displays of the building's 1000-year-old
Displays of history exist in biology as well, such as in
the architectures of transfer RNA (tRNA) and aminoacyl-tRNA
synthetase proteins. These ancient tRNA and aminoacyl-tRNA
synthetase molecules are ubiquitous in nature. As we know
them today, they are involved in one of the most fundamental
processes in lifethe culminating step in the expression
of a gene whereby nucleotide bases are translated into amino
In the late 1980s, Professor Paul Schimmel, who is the Ernest
and Jean Hahn Professor and Chair of Molecular Biology and
Chemistry and is a member of The Skaggs Institute for Chemical
Biology at Scripps Research, suggested that these molecules
may have been involved in a "second genetic code" (a term
coined by Nobel prize winner Christian de Duve in a Nature
commentary in 1988). This second genetic code would have acted
as an earlier method of information storage that is perhaps
more appropriately termed the operational RNA code, says Schimmel.
The operational RNA code would have related sequences of
RNA to amino acids, allowing RNA enzymes to grab amino acids
and "borrow" their chemical structures without guidance from
a gene. Amino acids have the ability to catalyze a larger
range of reactions than nucleotides, and perhaps early RNA
life forms evolved ways to use amino acids and their catalytic
abilities. It's also plausible that ancient tRNA-like molecules
would be loaded with amino acids by the action of another
RNA enzyme and these 'loaded' RNAs would condense together
to make peptides.
Now, two back-to-back papers in the latest issue of Molecular
Cell from Schimmel, Senior Staff Scientist Manal A. Swairjo,
Kellogg School of Science and Technology alumna Martha Lovato,
and several of their colleagues at Scripps Research explore
the details of how an ancient, operational genetic code could
High-Resolution Structure and Interdomain Flexibility
The papers provide new insight into how the recognition
of tRNA is achieved.
In the process of attachment of amino acids to tRNA molecules,
one of 20 different synthetases binds to its corresponding
amino acid, a molecule of ATP, and one of 20 different tRNA
molecules. The synthetase then hydrolyzes the ATP, attaches
the amino acid to the end of the tRNA, and lets go. The basic
mechanics of this process have been known for a number of
years, but have not been understood in detail. This is particularly
vexing for the alanyl-tRNA synthetase, the synthetase that
attaches the amino acid alanine to tRNA molecules cognate
for alanine, as it is one of the most well-studied proteins
Until now, there has not been a high-resolution structure
of the alanyl-tRNA synthetase molecule that could give insight
into how the recognition of tRNA is achieved. In the first
paper, applying the technique of x-ray crystallography to
the protein from the ancient marine bacterium Aquifex aeolicus,
Schimmel and Swairjo solved the structure to high resolution2.14
This structure of the alanyl-tRNA synthetase protein docked
to tRNA shows how this 453 amino acid protein reads the identity
of the tRNA molecule so that it can specifically attach alanine
to it. The synthetase reads a single base pair located on
one arm of the L-shaped tRNA called the "acceptor stem."
The acceptor stem is the more ancient part of the tRNA moleculea
remnant of the ancient molecules of the second genetic code.
In fact, in many cases the other arm of the tRNA L (which
carries the information for the amino acid) can be completely
removed and the tRNA will still accept its cognate amino acid.
The second paper describes how the system adapted throughout
evolution to subtle changes in the RNA. In most organisms
the acceptor-stem base pair that is recognized by alanyl-tRNA
synthetase is what is referred to in biology as a "wobble"
base. It has an unusual hydrogen bonding pattern and forms
between a G and a U nucleotide (rather than the standard G-C
or A-U pairs).
This wobble base pair is located three base pairs from the
acceptor end of the tRNA molecule. But occasionally, as in
the mitochondria of the fruit fly Drosophila melanogaster,
the recognition base pair is in another spot, only two base
pairs from the acceptor end.
The unusual thing about a Drosophila mitochondrion
is that its alanyl-tRNA synthetase molecules are not so different
from the canonical ones of Aquifex aeolicus and other
bacteria. One might expect that they would be, since these
molecules are very sensitive to the position of the base pair.
To account for this difference, Drosophila evolved
to use a different mechanism to recognize the pair in its
new location. Lovato, Schimmel, and their colleagues found
that Drosophila alanyl-tRNA synthetase has a 27 amino
acid insertion that allows it to shift its recognition to
the second base pair. The crystal structure demonstrates how
a hinge at the site of the insertion allows the part of the
synthetase molecule, which reads the wobble base pair to move
freely up and down the acceptor stem of the tRNA molecule.
This "interdomain flexibility" is the first example of adaptive
recognition of tRNA identity by synthetases in evolution.
Predating the Tower of London by billions of years, alanyl-tRNA
synthetase yet insisted on preserving the identity of its
cognate tRNA even more rigorously.
The article, "Alanyl-tRNA Synthetase Crystal Structure and
Design for Acceptor-Stem Recognition" was authored by Manal
A. Swairjo, Francella J. Otero, Xiang-Lei Yang, Martha A.
Lovato, Robert J. Skene, Duncan E. McRee, Lluis Ribas de Pouplana,
and Paul Schimmel and appears in the March 26, 2004 issue
of Molecular Cell. See: http://www.molecule.org/content/article/abstract?uid=PIIS1097276504001261
The article, "Positional Recognition of a tRNA Determinant
Dependent on a Peptide Insertion" is authored by Martha A.
Lovato, Manal A. Swairjo, and Paul Schimmel and appears in
the March 26, 2004 issue of Molecular Cell. See: http://www.molecule.org/content/article/abstract?uid=PIIS109727650400125X
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