Dr. Paul Agris,
News Services, 919/515-3470
the Genomic Code: Gene Decoding Revealed at Atomic
critical decoding structure produced when
modified nucleosides enable tRNA to decode
by wobble recognition. Only the decoding
region of a 50,000+ atom structure of the
ribosome (small subunit) is shown. The modified
nucleoside platform (orange) that stabilizes
the codon-anticodon interaction, and the
modified nucleoside that wobbles (green)
are shown. The structure was determined at
the atomic resolution of -3 angstroms (3
X 10 –10 meters).
A recent finding by a North Carolina State University
biochemist advances the fundamental biology of how
genetic information, encoded in DNA, is decoded for
the production of proteins.
F. Agris, professor of biochemistry at NC State,
and academic colleagues from England and Poland
show concrete evidence in favor of the 1966 “Wobble
Hypothesis” offered by Francis Crick, the co-founder
of the DNA molecule and its double-helix structure,
and Agris’ own “Modified Wobble Hypothesis” posed
used x-ray crystallography of the cell’s
protein-manufacturing unit, the ribosome, to provide
a visual snapshot of the decoding process.
The research is published in the December 2004 edition
of Nature Structural and Molecular Biology.
Hypothesis was Crick’s attempt to
make sense of how the cell decodes the genetic information
of DNA – the molecule that constitutes all the
genetic information in a cell – and then, from
that information, makes biologically active proteins,
61 three-letter codes that are translated by transfer
RNA (tRNA) into amino acids; proteins are
made of amino acids. But there are only 20 natural
amino acids. Squaring the disparity between the number
of codes and the number of amino acids – there
are three times as
many codes as there are amino acids – became
a hurdle for Crick and other early geneticists, Agris
to clear this hurdle with the Wobble Hypothesis.
He based this theory on the first report
of a tRNA molecule’s chemical structure discovered
by Robert Holley in 1963.
RNA molecules are composed of four nucleosides: adenosine,
guanosine, cytosine and uridine (A,G,C,U).
But the tRNA molecule Holley studied included a modified
nucleoside called inosine (I), Agris says. Seeing this
inosine in an important area of the tRNA molecule – an
area that read the three-letter DNA codes when the
cell synthesizes proteins – led Crick to believe
that a single tRNA used inosine to read more than one
code, and that therefore the 61 codes were decoded
by fewer than 61 tRNAs.
As an example,
Agris used the amino acid alanine, which has four
codes. Crick’s hypothesis would
allow that only two tRNA molecules could be capable
to decode all four alanine codes. Using the modified
nucleoside I in place of A, G, C or U, one tRNA may
be able to read three codes, effectively “wobbling” the
Twenty-five years after the Wobble Hypothesis, Agris
proposed his Modified Wobble Hypothesis. It stated
that modified nucleosides other than inosine would
in some cases expand tRNAs ability to translate codes
by wobbling to greater numbers of three-letter codes,
whereas other modified nucleosides would restrict wobble
to only one or two codes.
the recent paper, Agris and colleagues prove Agris’ alteration to Crick’s
hypothesis was correct: Cellular modification of
tRNA alters chemistry
and structure in a manner critical for tRNA to decode
more than one three-letter code.
resolution – in which researchers
can distinguish atom from atom – and working
with a tRNA specific for the amino acid lysine, Agris
and his colleagues show modified nucleosides enabling
tRNA to decode genomic information on the ribosome,
the cell’s protein synthesis machinery.
Specifically, it shows modifications enabling the
decoding of two codes. One modification acts like a
platform on which decoding takes place, and the other
allows a novel chemical and physical interaction to
occur between tRNA and the code, Agris said.
“This is the first visualization that modifications
are critical for decoding the genome through wobble,” he
Agris says that 15 to 20 percent of tRNAs in all
organisms require modified chemistries in order for
codes to be properly read and protein synthesis to
understanding of how modified nucleosides enable
and improve wobble recognition of the three-letter
codes for protein synthesis opens the possibility of
modified nucleosides to expand the cells’ use
of tRNA to make new proteins, or in new ways to target
the protein synthesis machinery in pathogens,” Agris
- kulikowski -
to editors: An abstract of the paper follows.
Role of Modification in Codon Discrimination: tRNALysUUU”
Authors: Paul Agris, North Carolina State University;
Frank V. Murphy IV and V. Ramakrishnan, Medical Research
Council Laboratory of Molecular Biology, Cambridge;
Andrzej Malkiewicz, Institute of Organic Chemistry,
Technical University, Lodz, Poland
Published: December 2004, in Nature Structural and
Abstract: The natural modification of specific nucleosides
in many tRNAs is essential during decoding of mRNA
by the ribosome. For example, tRNALysUUU requires the
modification N-6-threonylcarbomoyladenosine at position
37 (t6A37), 3’-adjacent to the anticodon, to
bind AAA in the A site of the ribosomal 30S subunit.
Moreover, it can only bind both AAA and AAG lysine
codons when doubly modified with t6A37 and either 5-methaylaminomethyluridine
or 2-thiouridine at the wobble position (mnm5U34 or
s2U34). Here we report crystal structures of modified
tRNA anticodon stem-loops (ASLs) bound to the 30S ribosomal
subunit with lysine codons in the A site. These structures
allow the rationalization of how modifications in the
anticodon loop enable decoding of both lysine codons
AAA and AAG.