AbstractThe crystal structure of a streptomycin binding RNA aptamer displays a novel bipartite fold able to clamp the antibiotic. In view of the recent findings that metabolites directly control mRNA translation, we might expect that similar structures exist in natural RNAs

Piganeau, Nicolas

Schroeder, Renée

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12. Bevitt, D.J., Corte´s, J., Haydock, S.F., and Leadlay, P.F. (1992). 18. Rangan, V.S., Joshi, A.K., and Smith, S. (2001). Biochemistry
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ska, H.E., and Smith, S. (1999). J. Biol. Chem. 274, 11557–11563. Structure 8, 185–195.
a procedure that allowed crystals to develop a few min-
utes [6]. The streptomycin-aptamer complex adopts an
Chemistry & Biology, Vol. 10, February, 2003, 2003 Elsevier Science Ltd. All rights reserved. DOI 10.1016/S1074-5521(03)00028-0
Aptamer Structures: A Preview
into Regulatory Pathways? unusually sophisticated structure characterized by a 90
kink between residues C106 and C107 at the bottom of
the lower asymmetrical loop, giving the complex its L
The crystal structure of a streptomycin binding RNA
aptamer displays a novel bipartite fold able to clamp
the antibiotic. In view of the recent findings that
metabolites directly control mRNA translation, we
might expect that similar structures exist in natural
RNAs.
The notion that RNA molecules are able to fold and build
binding pockets for small molecules first emerged when
it was discovered that self-splicing group I introns have
a cofactor [1]. Guanosine was the first of a list of metabo-
lites that interact with high affinity and specificity with
RNA. The same binding site located in the group I intron
core can accommodate the amino acid arginine and
many antibiotics, among them streptomycin, neomycin,
and viomycin [2]. Today it is clear that RNA is a potent
target for therapeutic drugs. In the past year, a plethora
of high-resolution structures of antibiotic-ribosome
complexes shed light into the binding mode and recog-
nition principles of RNA-antibiotic interactions [3].
With the development of in vitro selection procedures,
it became possible to isolate RNA aptamers for probably
every water-soluble ligand, and the small size of these
aptamers made them perfect tools to explore the rules
that govern recognition of small molecules by RNA.
High-resolution structures of several ligand-aptamer
complexes have been determined, demonstrating the
diversity of structural motifs RNA can fold into [4]. Both
simple noncomposite folds that form tight binding pock-
ets as well as complex composite modular shapes can
be found. One important outcome of these studies will
Secondary Structure of the Streptomycin Aptamerbe a database with an extensive repertoire of RNA struc-
The secondary structure of the streptomycin aptamer with the 90tural modules. The streptomycin binding aptamer pre-
kink between bases C106 and C107 is shown. Solid black linessented by Tereshko et al. in this issue of Chemistry &
represent base pairing. Base triples are indicated with orange lines.Biology represents a novel RNA fold with a distinct way
Bases highlighted in dark blue interact directly with streptomycin,
to encapsulate a small molecule [5]. whereas the interaction of G6 and U112 (highlighted in light blue)
To enhance the crystallization procedure, the original with the antibiotic is mediated by a water molecule. Arrows indicate
binding sites of the three metal ions (labeled M1 to M3).aptamer was split into two strands with dangling 5 ends,
Chemistry & Biology
104
shape (see Figure). Other important features of this loop final fold only after ligand binding, with the ligand being
are the base triple U16-C18-G110 (shown in orange) and an essential part of the structure. In the absence of
the U-turn U16 to C18. The upper asymmetric internal the ligand, the RNA is rather unstructured. This ligand-
loop forms a series of S-turns that span residues C5 to dependent structural stabilization prompted the design
G13. Both of the internal loops zipper up and stack with of a translation regulation system. Aptamers were in-
the central stem, forming a tight structure surrounding serted into the 5 untranslated leader of messenger
the streptomycin binding pocket, which is located in the RNAs without affecting their expression. Only after addi-
elbow of the L shape. The tight interlocking of both tion of the ligand did the RNA fold, leading to repression
the upper and lower internal loops is stabilized by a of translation [7]. Since this discovery, many of us have
magnesium ion interacting with residues U10-11 from wondered why nature did not make use of such a clever
the upper loop and residue C109 of the lower loop (indi- mechanism. Several years since researchers developed
cated as M1 in the Figure). Residue C109 itself is in- this regulatory concept, it was discovered that this
volved in a noncanonical base pair with G12. mechanism is indeed used by nature. Metabolite binding
The antibiotic binding pocket is an elaborate structure domains in mRNAs, which refold after ligand binding,
in which walls are formed by bases from both interlocked were recently found for cyanocobalamin, thiamine, and
loops. The streptose ring of streptomycin is buried FMN [8]. These recent findings give us a taste of what
deeply in the pocket and makes contacts with multiple is waiting to be discovered and clearly show that metab-
residues, in particular residues at positions U11 and G12 olite-RNA complexes will be used in the future for a
from the upper loop and residues U16 and U17 from the yet unpredictable number of applications. We can now
lower loop. In contrast to the streptomycin-ribosome predict that many biosynthetic pathways will be regu-
structure, most RNA-antibiotic contacts in the aptamer lated by metabolite binding “natural aptamers,” and we
involve base edges and not backbone phosphates. Rec- might even find a structure similar to the streptomycin
ognition between the antibiotic and the RNA is predomi- aptamer in a bacterium producing streptomycin.
nantly achieved through hydrogen bonds, one of which
is mediated through a bridging water molecule. All of
Nicolas Piganeau and Rene´e Schroederthe NH2, NH, and OH groups on the streptose ring are
Institute of Microbiology and Geneticsinvolved in intermolecular contacts, in contrast to the
Vienna Biocentertwo other streptomycin rings, which are positioned out-
Dr. Bohrgasse 9/4side the pocket and contribute to binding only through
A-1030 Viennaone hydrogen bond. The guanidinium group of the strep-
Austriatose ring is buried most deeply in the binding pocket
and is involved in several hydrogen bonds. The substitu-
Selected Readingtion of this group by a carbamino group in bluensomycin
is the reason for the tight aptamer discrimination be-
1. Bass, B.L., and Cech, T.R. (1984). Nature 308, 820–826.tween both antibiotics. 2. Schroeder, R., Wank, H., and Waldsich, C. (2000). EMBO J. 19,
This structure demonstrates once more the diversity 1–9.
of RNA ligand interactions. While aromatic ligands like 3. Schlunzen, F., Zarivach, R., Harms, J., Bashan, A., Tocilj, A.,
ATP, FMN, and theophylline stack between bases, Albrecht, R., Yonath, A., and Franceschi, F. (2001). Nature 413,
814–821.streptomycin lies perpendicular to the base pair planes.
4. Hermann, T., and Patel, D.J. (2000). Science 287, 820–825.Contrary to previously published aminoglycodise-
5. Tereshko, V., Skripkin, E., and Patel, D. (2003). Chem. Biol., thisaptamer structures, neomycin and tobramycin, where
issue, 175–187.
the antibiotics lie in the deep groove of a perturbed 6. Wallace, S.T., and Schroeder, R. (1998). RNA 4, 112–123.
double helix, streptomycin is locked in place via the two 7. Werstuck, G., and Green, M.R. (1998). Science 282, 296–298.
intertwined asymmetric internal loops [4]. 8. Nahvi, A., Sudarsan, N., Ebert, M.S., Zou, X., and Breaker, R.R.
(2002). Chem. Biol. 9, 1043–1049.Many of the in vitro-selected aptamers adopt their
Aminoglycosides are one of the oldest classes of anti-
bacterial natural products [1]. These compounds kill
Chemistry & Biology, Vol. 10, February, 2003, 2003 Elsevier Science Ltd. All rights reserved. DOI 10.1016/S1074-5521(03)00033-4
Resisting Bacterial Drug Resistance
bacteria by binding tightly to the acceptor site (A site)
on the 30S subunit of the ribosome and consequently
inhibit bacterial protein synthesis. As is the case for all
the other compounds classes of antibacterials, resis-
In this issue of Chemistry & Biology, Wright and col- tance to these drugs has increased rapidly with usage.
leagues report an elegant method for inhibiting en- In aminoglycoside-producing organisms, resistance to
zymes critical for rendering bacteria drug resistant. the compound results from the methylation of nucleo-
By using cationic peptides as inhibitors, the authors tides at the A site in the ribosome, preventing the drug
have exploited two antibacterial mechanisms, making from binding due to steric and electrostatic interference.
For the notorious pathogen Mycobacterium tuberculo-it doubly difficult for microbial retaliation.


Aptamer Structures A Preview into Regulatory Pathways?

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Aptamer Structures A Preview into Regulatory Pathways?

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