August 13, 2008 -- CHAMPAIGN - A new study of transfer RNA, a molecule that delivers amino
acids to the protein-building machinery of the cell, challenges
long-held ideas about the evolutionary history of protein synthesis.
In
the study, researchers report that the dual functions of transfer RNA
(reading the genetic blueprint for a protein, and adding a specific
amino acid to the protein as it is formed) appear to have originated
independently of one another. The new findings are detailed in the July
30 Public Library of Science (PLoS) ONE.
University of Illinois crop sciences professor Gustavo Caetano-Anollés
and postdoctoral researcher Feng-Jie Sun made the discovery by looking
for clues to the evolution of protein translation in the sequence and
structure of transfer RNA (tRNA).
"Structure is highly
conserved, capturing information that is evolutionarily deep,"
Caetano-Anollés said. "It was only logical to focus on transfer RNA, a
molecule that is believed to be very ancient and is truly central to
the entire protein synthesis machinery." During protein synthesis,
tRNA's dual function is reflected in its unique
L-shaped
structure. One end of the molecule decodes messenger RNA (a molecule
that carries instructions for the sequence of amino acids in a
protein), while the other transfers a specific amino acid to the
growing protein chain.
In previous studies, scientist assumed
that the two functional domains of tRNA had evolved together. Sun and
Caetano-Anollés put this assumption to the test.
They began by
constructing an evolutionary family tree based on the sequence and
two-dimensional structures of tRNA molecules representing every domain
of life (bacteria; the microbes known as archaea; and eucarya, the
domain that includes animals, plants, fungi and many other organisms)
as well as viruses.
There are several dozen tRNAs (each reads a
specific region of the genetic blueprint for a protein and each carries
only one of the 20-plus amino acids found in proteins) so the
researchers looked for clues to their evolutionary histories by
comparing their physical and functional traits.
They converted
the unique features of the individual tRNA cloverleaf structures into
coded characters, a process that allowed a computerized search for the
most parsimonious (the simplest, most probable) tRNA family trees for
different organismal lineages. In this way they were able to test
competing evolutionary hypotheses against the data mined from the
structure of the tRNA itself.
"Our findings uniquely focus on structure, the actual aspect of the molecule that encases its function," Caetano-Anollés said.
The
analysis indicated that the two functions of the tRNA had different
evolutionary histories, Sun said, which suggests that they were
acquired at different points in time.
The study predicted that
the loading of amino acids on tRNA molecules preceded the refinement of
the genetic code into codons, the regions on the messenger RNA that are
read by individual tRNAs.
"For the first time, we believe we
make this distinction between the evolution of the genetic code (codon
discovery) and the evolution of amino acid charging," Sun said.
Source : University of Illinois at Urbana-Champaign
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