News and Publications
The Skaggs Institute for Chemical Biology
Scientific Report 1998-1999
Decoding Genetic Information in Translation
P. Schimmel, C. Fabrega, M. Farrow, T.A. Hendrickson, S.O. Kelley, A.J. Morales,
B. Nordin, T. Nomanbhoy, L. Ribas de Pouplana, M. Swairjo, K. Tamura, R.J. Turner,
K. Wakasugi, C.-C. Wang, V. de Crecy-Lagard, B. Slike, A. Abraham, L. Nangle,
The genetic code was established more than 2 billion years ago and became
universally part of all living organisms. The rules of the code, which relate
specific nucleotide triplets to specific amino acids, are determined by aminoacylation
reactions catalyzed by aminoacyl tRNA synthetases. In these reactions, an amino
acid is associated with a specific nucleotide triplet of the genetic code by
virtue of being linked to a specific tRNA that harbors the anticodon triplet
cognate to the amino acid. Because of their central role in establishing the
rules of the code, the tRNAs are thought to have arisen quite early, perhaps
in the context of an RNA world. The synthetases may have been among the earliest
proteins to appear, perhaps replacing ribozymes that catalyzed the aminoacylation
of primordial tRNAs.
We wish to understand all aspects of these systems. Areas of research include
detailed studies of molecular recognition of RNA, as represented by the synthetase-tRNA
interactions and by peptide models of those interactions; editing and correction
of potential errors in translation, as represented by the misacylation of tRNAs
and misactivation of amino acids; reconstruction of the assembly of tRNA through
domain-domain interactions of RNA pieces; and dissection of catalytic and RNA-binding
components of tRNA synthetases. We are also interested in evolutionary relationships
between synthetases that can reveal insight into the origins of the code and
protein synthesis; involvement of eukaryotic synthetases in higher order cellular
functions, such as cell signaling pathways and the construction of macromolecular
assemblies; and design and synthesis of systems of tRNA-like molecules that can
be acylated and assemble complexes for peptide synthesis, as examples of the
potential for early systems of protein synthesis that predated the ribosome.
The cloverleaf structure of tRNA is folded into 2 domains (Fig. 1). One domain
contains the anticodon with the template-reading head of the genetic code; the
other, called the minihelix domain, contains the amino acid attachment site.
The minihelix domain itself is a substrate for aminoacylation for at least 10
of the synthetases. Pieces even smaller than the minihelix are active as substrates
(Figs. 1 and 2). Because these pieces lack the anticodon trinucleotides, the
relationship between the sequences and structures of these active pieces (with
as few as 4 bp) and the specific amino acid is distinct from the genetic code.
The relationship between sequences and structures in tRNA acceptor stems and
specific amino acids is referred to as an operational RNA code for amino acids.
The operational RNA code is thought to have predated the genetic code.
A scheme for the assembly of the synthetase-tRNA complex in evolution is given
in Figure 3. Each domain of the synthetase interacts with a separate domain of
the tRNA. The minihelix domain of the tRNA contains the amino acid attachment
site and is thought to be the earliest version of a tRNA molecule. The domain
containing the anticodon was added later in evolution. Similarly, the catalytic
domain of the synthetase, which contains the active site and which interacts
with the minihelix domain of the tRNA, is thought to be the historical enzyme.
Later, a second domain of the synthetase was added; this domain interacts with
the second domain of the tRNA. This model is useful for guiding experiments that
aim at reconstructing the assembly of the synthetase-tRNA complexes in evolution.
Our recent studies expanded on these concepts to elucidate a role for the
tRNA in recognition of the fine structure of amino acids. That is, the ability
to distinguish between 2 closely similar amino acids is greatly enhanced by an
effector function of the tRNA, which causes the rejection of amino acids that
are not exactly matched with the synthetase and its cognate tRNA. This RNA-dependent
fine-structure recognition may have developed first in an RNA world and later
was incorporated into the synthetase system as a critical part of maintaining
the accuracy of the genetic code.
The significance of the tRNA L-shaped fold in evolution was highlighted by
our recent finding of a structure-specific tRNA-binding protein in the extreme
thermophile Aquifex aeolicus. The role of a structure-specific tRNA-binding
motif in the evolutionary development of the contemporary systems of tRNA recognition
is of great interest.
Alexander, R.W., Schimmel, P. Evidence for breaking domain-domain functional
communication in a synthetase-tRNA complex. Biochemistry 38:16359, 1999.
Chihade, J.W., Schimmel, P. Assembly of a catalytic unit for RNA microhelix
aminoacylation using nonspecific RNA binding domains. Proc. Natl. Acad. Sci.
U. S. A. 96:12316, 1999.
Farrow, M.A., Nordin, B.E., Schimmel, P. Nucleotide determinants for
tRNA-dependent amino acid discrimination by a class I tRNA synthetase. Biochemistry, in
Morales, A.J., Swairjo, M., Schimmel, P. Structure-specific tRNA binding
protein from the extreme thermophile Aquifex aeolicus. EMBO J. 18:3475,
Musier-Forsyth, K., Schimmel, P. Atomic determinants for aminoacylation
of RNA minihelices and relationship to genetic code. Accounts Chem. Res. 32:368,
Nomanbhoy, T.K., Hendrickson, T.L., Schimmel, P. Transfer RNA-dependent
translocation of misactivated amino acids to prevent errors in protein synthesis.
Mol. Cell 4:519, 1999.
Nordin, B., Schimmel, P. RNA determinants for translational editing:
Mischarging a minihelix substrate by a tRNA synthetase. J. Biol. Chem. 274:6835,
Nureki, O., Vassylyev, D.G., Tateno, M., Shimada, A., Nakama, T., Fukai,
S., Konno, M., Hendrickson, T.L., Schimmel, P., Yokoyama, S. Proofreading
by isoleucyl-transfer RNA synthetase: Response. Science 283:459a, 1999.
Sardesai, N.Y., Green, R., Schimmel, P. Efficient 50S ribosome-catalyzed
peptide bond synthesis with an aminoacyl minihelix. Biochemistry 38:12080, 1999.
Sardesai, N.Y., Stagg, S.M., VanLoock, M.S., Harvey, S.C., Schimmel, P. RNA
scaffolds for minihelix-based aminoacyl transfer: Design of transpeptizymes.
J. Biomol. Stereodyn., in press.
Schimmel, P. Aminoacyl tRNA synthetases and decoding of genetic information. In: The
Encyclopedia of Molecular Biology. Creighton, T.E. (Ed.). Wiley, New York, 1999,
Vol. 1, p. 111.
Schimmel, P. Translational editing. In: The Encyclopedia of
Molecular Biology. Creighton, T.E. (Ed.). Wiley, New York, 1999, Vol. 4, p. 2642.
Schimmel, P., Ribas de Pouplana, L.l. Genetic code origins: Experiments
confirm phylogenetic predictions and may explain puzzle. Proc. Natl. Acad. Sci.
U. S. A. 96:327, 1999.
Schimmel, P., Wang, C.-C. Getting tRNA synthetases into the nucleus.
Trends Biochem. Sci. 24:127, 1999.
Steer, B., Schimmel, P. Domain-domain communications in a miniature
archaebacterial tRNA synthetase. Proc. Natl. Acad. Sci. U. S. A. 96:13644, 1999.
Steer, B.A., Schimmel, P. Different adaptations of the same peptide
motif for tRNA functional contacts by closely homologous tRNA synthetases. Biochemistry
Steer, B.A., Schimmel, P. Major anticodon-binding region missing from
an archaebacterial tRNA synthetase. J. Biol. Chem. 274:35601, 1999.
Wakasugi, K., Schimmel, P. Two distinct cytokines released from a human
tRNA synthetase. Science 284:147, 1999.
Wang, C.-C., Schimmel, P. Species barrier to RNA recognition overcome
with nonspecific RNA binding domains. J. Biol. Chem. 274:16508, 1999.