News and Publications
The Skaggs Institute for Chemical Biology
Scientific Report 1999-2000
Decoding Genetic Information in Translation
P. Schimmel, A. Abraham, V. de Crécy-Lagard, K. Ewalt, C. Fabrega,
M. Farrow, T.A. Hendrickson, S.O. Kelley, A.J. Morales, L. Nangle, B. Nordin,
T. Nomanbhoy, L. Ribas de Pouplana, B. Slike, M. Swairjo, K. Tamura, R.J. Turner,
C.-C Wang, X. Yang, M. Lovato, A. Bishop, T. Kushiro
The genetic code was established more than 2 billion years ago and became
universally a 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 the 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 eukaryote 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. 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 also active as substrates, as are
special constructs known as pseudoknots (Fig. 1). 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
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.
Recently, we elucidated 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 genetic code.
Our recent investigations forged a link between protein synthesis and signal
transduction pathways in human cells. Specifically, 2 distinct cytokines can
be released from human tyrosyl-tRNA synthetase. The enzyme is secreted during
apoptosis in cell culture (Fig. 2). After secretion, it can be split into 2 fragments
by an extracellular protease such as leukocyte elastase. Each of the 2 fragments
is a distinct cytokine (the unsplit, native enzyme has no cytokine activity).
For example, the C-terminal fragment has potent leukocyte and monocyte chemotaxis
activity and triggers production of tissue factor, myeloperoxidase, and tumor
necrosis factor-α. The N-terminal fragment has the activities of IL-8.
These results suggest applications to medicine in the areas of inflammation and
Chihade, J.W., Brown, J., Schimmel, P., Ribas de Pouplana, L. Origin
of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA
synthetase. Proc. Natl. Acad. Sci. U. S. A. 97:12153, 2000.
Farrow, M.A., Nordin, B.E., Schimmel, P. Nucleotide determinants for
tRNA-dependent amino acid discrimination by a class I tRNA synthetase. Biochemistry
Hendrickson, T.L., Nomanbhoy, T.K., Schimmel, P. Errors from selective
disruption of the editing center in a tRNA synthetase. Biochemistry 39:8180,
Houman, F., Rho, S.B., Zhang, J., Shen. X., Wang, C.-C., Schimmel, P.,
Martinis, S.A. A prokaryote and human tRNA synthetase provide an essential
RNA splicing function in yeast mitochondria. Proc. Natl. Acad. Sci. U. S. A.
Kelley, S.O., Steinberg, S.V., Schimmel, P. Functional defects of
pathogenic human mitochondrial tRNAs related to structural fragility. Nat. Struct.
Biol. 7:862, 2000.
Nomanbhoy, T.K., Schimmel, P. Misactivated amino acids translocate
at similar rates across the surface of a tRNA synthetase. Proc. Natl. Acad. Sci.
U. S. A. 97:5119, 2000.
Ribas de Pouplana, L., Schimmel, P. A view into the origin of life:
Aminoacyl tRNA synthetases. Cell. Mol. Life Sci. 57:865, 2000.
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. II:29, 2000.
Schimmel, P., Kelley, S.O. Exiting an RNA world. Nat. Struct. Biol.
Schimmel, P., Ribas de Pouplana, L. Footprints of aminoacyl tRNA synthetases
are everywhere. Trends Biochem. Sci. 25:207, 2000.
Swairjo, M.A., Morales, A.J., Wang, C.-C., Ortiz, A.R., Schimmel, P. Crystal
structure of Trbp111: A structure-specific tRNA binding protein. EMBO J. 19:6287,
Tao, J., Wendler, P., Connelly, G., Lim, A., Zhang, J., King, M., Li,
T., Silverman, J.A., Schimmel, P., Tally, F.P. Drug target validation: Lethal
infection blocked by inducible peptide. Proc. Natl. Acad. Sci. U. S. A. 97:783,
Wakasugi, K., Schimmel, P. Highly differentiated motifs responsible
for two cytokine activities of a split human tRNA synthetase. J. Biol. Chem.
Wang, C.-C., Morales, A.J., Schimmel, P. Functional redundancy in
the nonspecific RNA binding domain of a class I tRNA synthetase. J. Biol. Chem.