In this issue of Structure, Sekine et al. (2006) present a splendid example, using glutamyl-tRNA synthetase crystal structures, of the steps potentially taken in the transition from the RNA world to the theater of proteins

Schimmel, Paul

Yang, Xiang-Lei

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Structure 14, 1729–1730, December 2006 ª2006 Elsevier Ltd All rights reserved DOI 10.1016/j.str.2006.11.002PreviewPerfecting the Genetic Code
with an RNP Complex
In this issue of Structure, Sekine et al. (2006) present
a splendid example, using glutamyl-tRNA synthetase
crystal structures, of the steps potentially taken in
the transition from the RNA world to the theater of
proteins.
Since the discovery of ribozymes and the development
of the idea of life first emerging from an RNA world
(Gilbert, 1986), biologists have struggled to imagine the
logical progression of events that led to proteins. At the
same time, regardless of what the imagination can con-
jure, a connection to reality has to be made. That, in turn,
requires experiments to test specific hypotheses or to
provide an opportunity for serendipitous findings.
To go from RNA to proteins requires the genetic
code—triplets of nucleotides representing single amino
acids. The modern code is an algorithm determined by
aminoacylation reactions, whereby each of 20 amino
acids is linked to its cognate tRNA that bears the antico-
don triplet of the code. The 20 aminoacyl tRNA synthe-
tases (one for each amino acid) that catalyze these reac-
tions are ancient proteins that were present in the last
common ancestor of the tree of life (Carter, 1993;
Cusack, 1997). As the eons passed, the tree split into the
three great kingdoms—archaea, bacteria, and eukarya,
which encompass all life forms. Yet, the genetic code re-
mained fixed, with the same 20 aminoacyl tRNA synthe-
tases making the same connections between anticodon
triplets and amino acids. Thus, clues to the history of the
transition from the RNA world to proteins might be im-
bedded in the tRNA synthetases themselves. Sekine
et al. (2006) offer a provocative notion of one such clue.
The earliest aminoacylation reactions are thought to
have been catalyzed by ribozymes, which acted on
primordial tRNAs (Piccirilli et al., 1992; Lee et al., 2000;
Yarus, 2001). These ribozymes may have used nucleo-
tides near the 30-ends of the early tRNAs (where the
amino acids are attached) as determinants that matched
specific amino acids with ‘‘cognate’’ tRNA-like mole-
cules. Peptides spontaneously form if two aminoacyl
RNAs are brought into close proximity. The next step
in evolution of aminoacylation would be development
of catalysts more efficient than ribozymes alone, likely
ribonucleopeptides or ribonucleoproteins (RNPs). As
the code became perfected, proteins could take over
the role of aminoacylation, as contemporary aminoacyl
tRNA synthetases.
The transition from RNP to protein might be facilitated
if the substrate (tRNA) could, in part, take over the role of
the ribozyme moiety that was eventually discarded. This
‘‘takeover’’ would most likely be of a noncatalytic func-
tion, like amino acid recognition, reducing the complex-
ity of the system. This transition would also provide the
opportunity to perfect the specificity of the code (amino
acid-anticodon triplet), strengthening the relationshipbetween the amino acid and tRNA. This specificity is
critical for the accuracy of the genetic code, which has
to be maintained to the highest degree to prevent mis-
translation, that is, incorporation of the wrong amino
acids at specific codons. Here, Sekine et al. (2006) report
a striking set of structures that show how mistranslation
is prevented by the high amino acid specificity coming
from a synthetase-tRNA complex (a kind of RNP), but
not from the synthetase alone.
For most aminoacyl tRNA synthetases (AARSs), the
aminoacylation reaction occurs in two steps. The amino
acid (AA) is first activated by condensation with ATP to
form a tightly bound aminoacyl adenylate (AA-AMP), si-
multaneous with release of pyrophosphate (PPi). The
bound adenylate then reacts with the cognate tRNA to
yield the charged tRNA (AA-tRNA).
AARS + AA + ATP$AARS ðAA2AMPÞ + PPi (1)
AARS ðAA2AMPÞ + tRNA$AA2tRNA + AMP + AARS
(2)
In a few instances (GluRS, GlnRS, ArgRS and an un-
usual LysRS), the amino acid activation reaction (Equa-
tion 1) does not occur in the absence of bound tRNA.
What is known for GluRS is that amino acids similar to
glutamate, like glutamine and aspartate, and even D-
glutamate, can bind to GluRS in the absence of tRNA.
However, in the presence of tRNAGlu, these noncognate
amino acids are excluded from the enzyme (Figure 1).
Thus, specific amino acid recognition is tRNA-depen-
dent, that is, requires the context of an RNP. Although
eight structures of the T. thermophilus enzyme and
enzyme cocrystals were published previously (cited in
Sekine et al., 2006), the key ones were missing.
Four new structures now provide the answers to how
amino acid recognition changes in the context of an
assembled RNP. These structures are of the following
complexes: GluRS-glutamate, GluRS-tRNA-glutamate,
GluRS-tRNA-ATP-glutamate analog, and GluRS-tRNA-
adenylate analog. The structures show how RNA-
dependent amino acid recognition is achieved. In short,
binding of tRNA induces a conformational change in the
amino acid-binding pocket (Figure 1). The pocket is right
next to the 30-end of the tRNA, with the 20-OH of the ri-
bose of A76 binding to the a-carboxylate of glutamate.
In the subtle rearrangement induced by tRNAGlu associ-
ation, the amino acid-binding pocket is squeezed in a
way that excludes glutamine, aspartate, and D-gluta-
mate, and the binding of L-glutamate itself is shifted
(1.3 A˚ for carbon of the a-carboxyl group).
A number of the tRNA synthetases that carry out the
conventional two-step aminoacylation reaction given
above also use tRNA to perfect amino acid recognition.
In these instances, a separate domain for editing is in-
corporated (Hendrickson and Schimmel, 2003). The ed-
iting site hydrolytically clears misactivated amino acids
(as misactivated aminoacyl adenylates or mischarged
tRNAs) and is located typically about 30 A˚ from the site
for amino acid activation and aminoacylation (Equations
Structure
17301 and 2 above). Significantly, the editing activity is
strictly tRNA-dependent, so that the clearance reaction
is in effect carried out by an RNP.
GluRS is not alone in requiring tRNA binding for amino
acid selectivity. GlnRS and ArgRS do as well, and
although less well characterized structurally, there are
hints of mechanistic similarities. In both cases, there is
structural evidence for conformational changes in the
amino acid-binding site upon tRNA binding (Rath et al.,
1998; Delagoutte et al., 2000). Importantly, the structure
of the ternary complex GlnRS-tRNAGln-Gln adenylate
analog shows a contact between the 20-OH of A76 and
the a-carbonyl of the bound glutaminyl adenylate analog
(Rath et al., 1998). While in the ArgRS complex structure
(ArgRS-tRNAArg-Arg), the 20-OH binds to the a-carboxyl-
ate group of arginine (Delagoutte et al., 2000). Thus,
GluRS, and most likely the few other tRNA synthetases
that require tRNA for amino acid activation, appear to
Figure 1. The tRNA-Dependent Amino Acid Recognition for GluRS
Three domains of the monomeric protein are shown as distinct
colors. The holoenzyme can accommodate a variety of substrates
in the amino acid-binding pocket (red circle). Upon tRNA binding,
the pocket undergoes a conformational change (red rectangle)
and gains selectivity for glutamate.have developed an alternative strategy to improve amino
acid recognition; that is, they use the tRNA as a way to
shape the amino acid-binding pocket.
Thus, what is reported in this most recent work on
GluRS—that a synthetase can use tRNA to direct a con-
formational change that perfects amino acid specificity,
using in part a contact with the tRNA itself—may provide
a general mechanism of tRNA-dependent amino acid
specificity. The much bigger implication is that perhaps
this functional interaction is a picture or a ‘‘holdover’’
from an earlier era in the evolution of the genetic code.
Paul Schimmel1 and Xiang-Lei Yang1
1The Skaggs Institute for Chemical Biology
The Scripps Research Institute
Beckman Center, BCC379
10550 North Torrey Pines Road
La Jolla, California 92037
Selected Reading
Carter, C.W., Jr. (1993). Annu. Rev. Biochem. 62, 715–748.
Cusack, S. (1997). Curr. Opin. Struct. Biol. 7, 881–889.
Delagoutte, B., Moras, D., and Cavarelli, J. (2000). EMBO J. 19, 5599–
5610.
Gilbert, W. (1986). Nature 319, 618.
Hendrickson, T.L., and Schimmel, P. (2003). Translational Mecha-
nisms, J. LaPointe and L. Brakier-Gingras, eds. (New York: Eure-
kah.com and Klumer Academic/Plenum Publishers), pp. 34–64.
Lee, N., Bessho, Y., Wei, K., Szostak, J.W., and Suga, H. (2000). Nat.
Struct. Biol. 7, 28–33.
Piccirilli, J.A., McConnell, T.S., Zaug, A.J., Noller, H.F., and Cech,
T.R. (1992). Science 256, 1420–1424.
Rath, V.L., Silvian, L.F., Beijer, B., Sproat, B.S., and Steitz, T.A.
(1998). Structure 6, 439–449.
Sekine, S., Shichiri, M., Bernier, S., Chenevert, R., Lapointe, J., and
Yokoyama, S. (2006). Structure 14, this issue, 1791–1799.
Yarus, M. (2001). Cold Spring Harb. Symp. Quant. Biol. 66, 207–215.


Perfecting the Genetic Code with an RNP Complex 

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Perfecting the Genetic Code with an RNP Complex

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