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Biochemical Society Transactions (2008) Volume 36, part 4
RNA pseudoknots and the regulation of
protein synthesis
Ian Brierley*1 , Robert J.C. Gilbert† and Simon Pennell‡
*Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, U.K., †Division of Structural Biology, Henry
Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, U.K., ‡Division of Molecular Structure, MRC National
Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, U.K.
Abstract
RNA pseudoknots are structural elements found in almost all classes of RNA. Pseudoknots form when a
single-stranded region in the loop of a hairpin base-pairs with a stretch of complementary nucleotides
elsewhere in the RNA chain. This simple folding strategy is capable of generating a large number of stable
three-dimensional folds that display a diverse range of highly specific functions in a variety of biological
processes. The present review focuses on pseudoknots that act in the regulation of protein synthesis using
cellular and viral examples to illustrate their versatility. Emphasis is placed on structurally well-defined
pseudoknots that play a role in internal ribosome entry, autoregulation of initiation, ribosomal frameshifting
during elongation and trans-translation.
The pseudoknot motif
Pseudoknots were first established as a folding motif in RNA
in the early 1980s by Cornelis Pleij and co-workers [1,2]. As
originally defined [3], a pseudoknot is formed upon basepairing of a single-stranded region of RNA in the loop of a
hairpin to a stretch of complementary nucleotides elsewhere
in the RNA chain (Figure 1). Such pseudoknots, referred to as
H-type pseudoknots (hairpin-type pseudoknots), have two
base-paired stem regions (S1 and S2) and, depending on the
number of loop bases that participate in the pseudoknotting
interaction [4], have two or three single-stranded loops
(L1, L2 and L3). In most H-type pseudoknots (>85 %),
L2 is absent or very short and the base-paired stems can
stack coaxially to form a quasi-continuous helix. In these
structures, L1 spans S2 and crosses the deep groove of the
helix, whereas L3 spans S1 and crosses the shallow groove
(Figure 1). Pseudoknot loops can vary greatly in length,
ranging from a single nucleotide [5] to many thousands
of bases, and can include their own secondary-structure
elements. Pseudoknots are also formed upon pairing of
single-stranded residues in bulge, interior and multibranched
loops with complementary regions elsewhere in the RNA [6].
The biological properties of pseudoknots are intimately
linked to their structural features [4,7–12]. For example, the
geometry of the junction between the stems and the interactions that can occur between the constituent loops
and stems are often of great functional relevance [5,13–16].
Key words: frameshift, internal ribosome entry site (IRES), protein synthesis, ribosome, RNA
pseudoknot, translation.
Abbreviations used: BWYV, beet western yellows virus; CrPV, cricket paralysis virus; cryo-EM,
cryo-electron microscopy; eEF, eukaryotic elongation factor; H-type pseudoknot, hairpin-type
pseudoknot; IGR, intergenic region; IRES, internal ribosome entry site; NCR, non-coding region;
ORF, open reading frame; PK1, pseudoknot 1; PK II, pseudoknot II; PSIV, Plautia stali intestine
virus; SAM, S-adenosylmethionine; tmRNA, transfer-messenger RNA; tRNAAla , alanine tRNA; UTR,
untranslated region.
1
To whom correspondence should be addressed (email [email protected]).
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Authors Journal compilation Indeed, for many pseudoknots, much of the primary sequence
is unimportant to function as long as the conformation and
overall stability of the structure is maintained. Where precise
nucleotide sequence requirements have been identified, this
is likely to reflect a specific structural constraint, although
additional roles may be possible, for example base-specific
recognition by proteins.
This review focuses on viral and cellular pseudoknots
and their role in protein synthesis. Further information is
available in a related review ([12] and references and Supplementary Information therein).
Pseudoknots in the machine
The engine of protein synthesis, the ribosome, harbours
several pseudoknots in its component RNAs [17]. Four
pseudoknots have been documented in the small subunit,
and several more (15 or so) are known or predicted to be
present in the large subunit. The central pseudoknot of
16S rRNA is particularly impressive in that it connects the
three major domains of the molecule and is responsible for
organizing the centre of the 30S subunit. Disruption of this
pseudoknot has been shown to abolish ribosome activity [18]
and, similarly, other pseudoknots of rRNA that have been
examined functionally have been shown to be important or
essential for translation, although their precise role(s) is not
fully understood in each case.
Pseudoknots and translation initiation
Pseudoknots that act in initiation have been described in ribosome recruitment, principally at IRESs (internal ribosome
entry sites), and also in the regulation of initiation frequency.
Pseudoknots have been confirmed in several viral IRESs
and predicted in some cellular IRESs [19]. Their function
Biochem. Soc. Trans. (2008) 36, 684–689; doi:10.1042/BST0360684
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Figure 1 Formation of an H-type RNA pseudoknot
Pseudoknots form when a sequence in the loop of a hairpin (A,
grey) base-pairs to a stretch of complementary bases elsewhere (B).
Pseudoknots are often represented in the literature as shown in
(C). The NMR structure of the VPK pseudoknot [a derivative of the
MMTV (murine-mammary-tumour virus) gag/pro frameshift-promoting
pseudoknot] [48] is shown in (D).
is best understood for the IGR (intergenic region) IRES of
the dicistrovirus CrPV (cricket paralysis virus) [15,16,20]
and its relatives. This remarkable IRES is only ∼200 nt in
length, yet acts as an RNA-based translation factor [21],
recruiting ribosomes and activating translation without the
involvement of initiation factors or even initiator tRNA.
The 40S and 60S subunits bind directly to the IRES, which
interacts with key components of the ribosomal aminoacyl
(A)-, peptidyl (P)- and exit (E)-sites. The three defined
domains of this IRES have distinct functional tasks. Domain
1 contributes to interactions with the 60S subunit in the Eand P-site regions, whereas domain 2 interacts with the 40S
subunit at the E-site. Domain 3 places its most 3 nucleotide
triplet (GCU) into the decoding region of the A-site. Here,
it binds the anticodon of tRNAAla (alanine tRNA), which
is brought to the ribosome as part of the ternary complex
of eEF1A (eukaroytic elongation factor 1A)–GTP–tRNAAla .
Subsequently, tRNAAla is ‘pseudotranslocated’ (without
peptide bond formation) by eEF2 into the P-site, allowing
delivery of the next tRNA into the A-site and authentic elongation to begin. Modelling and structural analysis of the CrPV
IRES and IRESs from related viruses, including PSIV (Plautia
stali intestine virus) [15,16,22–24], has revealed that the RNA
is dominated by three H-type pseudoknots, one per domain
(Figure 2). PK1 (pseudoknot 1), which forms essentially all of
domain 3, acts as a P-site tRNA mimic and nucleotides at the
L3–S2 junction bear similarity to the codon–anticodon helix
[24]. It is believed that the IGR IRES initiates translation by
co-opting the ribosome’s elongation cycle through molecular
mimicry of tRNA [24]. The folding of the rest of the IRES
is dominated by interactions between pseudoknots PK II
(pseudoknot II) and PK III. The pseudoknot of domain 2,
PK III, is a ‘nested’ pseudoknot in that it is entirely contained
within L3 of the pseudoknot of domain 1, PK II. CryoEM (cryo-electron microscopy) and X-ray crystallography
studies [15,16] have indicated a complex folding strategy that
forces two small hairpins present as substructures in L1 and
L3 of PK III to project from a central core and emerge on
the same side of the structure to make interactions with rpS5
at the E-site. Pivotal to this folding strategy are interactions
between the pseudoknot loops and stems. The geometry of
the overall fold is such that S2 of PK II stacks upon S2 of PK
III to create a wedge-shaped section that occupies the mRNA
channel and directs PK1 into the decoding site.
The structure of the IGR IRESs illustrates how
pseudoknots can be utilized to direct the global folding of an
RNA sequence. The pseudoknot motif provides the potential
for coaxial stacking of component helices and additional
stacking with helices present in loops. This allows longer
helical domains to be generated, a predominant feature in the
organization of global RNA structures. If the pseudoknot
is itself nested within another pseudoknot, additional helical
stacking possibilities are created. Superimposed on this is the
capacity of the single-stranded loops to interact with
constituent stems to add stability, or with other regions of
RNA to promote packing of adjacent helices.
The role of pseudoknots in the regulation of initiation
frequency is illustrated by the autoregulation of gene expression of ribosomal proteins S4, S15 and L35/L20. When these
proteins are synthesized in excess over ribosomal RNA, they
bind close to the translation initiation site of the first cistron
of the relevant mRNA and block its translation. Suppression
is brought about in one of two ways, either entrapment of
ribosomes in a stalled pre-initiation state (S4, S15) [25,26] or
competitive binding of the repressor protein or the ribosome
to overlapping or adjacent mRNA-binding sites [27]. A unifying feature is the presence of a pseudoknot within the regulatory region. The mechanism of autoregulation is perhaps
best understood for the rpsO mRNA, encoding S15. The 5 UTR (5 -untranslated region) of the S15 mRNA can fold into
a mutually exclusive double hairpin or pseudoknot conformation, with S15 binding to and stabilizing the pseudoknot [28].
The default pathway of initiation can be considered as the
docking of the folded 5 -UTR (in pseudoknot conformation
[29]) on to the ribosome, unfolding of the pseudoknot and
accommodation of the mRNA into the mRNA channel.
Recent cryo-EM images of rpsO mRNA–S15–ribosome preinitiation complexes have revealed that the S15 protein stabilizes the pseudoknot, trapping the complex on the ribosome
and preventing unfolding of the structure and accommodation of the mRNA [26]. The S15 pseudoknot is H-type,
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Figure 2 The CrPV IGR IRES pseudoknots
A secondary-structure representation of the CrPV IGR IRES is shown in (A). A model of the CrPV IRES derived from the cryo-EM
study of Schuler et al. [15] is shown in (B). Domains 1 and 2 fold to make essential contacts with each ribosomal subunit.
Domain 3 acts as a tRNA mimic in the P-site, recruiting tRNAAla to the A-site via codon interactions with the 3 -terminal GCU
bases of the IRES (indicated). Crystal structures of domains 1 and 2 of the related IRES of PSIV [16] and domain 3 of CrPV
[24] have also been published.
with L3 containing the Shine–Dalgarno sequence and initiator
AUG. In the stalled, entrapped complex, stabilization of the
pseudoknot redirects the 3 -end of the mRNA away from
the mRNA channel and keeps the initiator tRNA away
from the start codon. When S15 levels fall, the pseudoknot is
no longer stabilized on the ribosome and unfolds [26].
Pseudoknots that act in initiation have also been identified
in riboswitches, cis-acting regulatory elements in the 5 UTR of an mRNA that control gene expression through
their ability to bind small-molecule metabolites. Of the
pseudoknot-containing riboswitches, the most recent structural information comes from an X-ray crystallographic
analysis of the SAM-II riboswitch bound to its ligand, SAM
(S-adenosylmethionine) (Figure 3) [30]. Gilbert et al. [30]
found that the riboswitch is entirely accounted for by a
pseudoknot that bears close resemblance to that present in
C The
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Authors Journal compilation the human telomerase RNA, particularly in the formation of
triplexes at the stem–stem junction [14]. The SAM ligand is
bound along the major groove in an extended configuration
in a binding pocket created by loop–helix interactions. SAM
contacts five successive base-pairs and forms a triplex with
the adenine moiety positioned in the helix. Structure-probing
comparisons of the riboswitch in the presence and absence
of SAM are consistent with the view that SAM stabilizes
the pseudoknot, retaining the Shine–Dalgarno sequence
within the tertiary fold and repressing translation. Other
pseudoknot-containing riboswitches include SAM-I and
glmS, which display a more complex architecture reminiscent
of the self-splicing group I introns. Indeed, the glmS
riboswitch is also a ribozyme; in the presence of its ligand
glucosamine-6-phosphate, it undergoes self-cleavage, regulating the expression of glucosamine-6-phosphate synthase.
Post-Transcriptional Control
Figure 3 Crystal structure of the SAM-II riboswitch
SAM is bound within an H-type pseudoknot with the adenine moiety
incorporated into the stem 2 helix.
Pseudoknots and translation elongation
RNA pseudoknots in coding regions are principally associated with sites of programmed −1 ribosomal frameshifting,
a translational mechanism employed by many viruses to coordinately express two proteins from a single mRNA at a
defined ratio. In retroviruses, for example, frameshifting at
the overlap of the gag and pol ORFs (open reading frames)
permits expression of the viral Gag-Pol polyprotein and
sets a defined cytoplasmic Gag/Gag-Pol ratio optimized for
virion assembly and packaging of reverse transcriptase. In
other RNA viruses, frameshifting allows expression of RNAdependent RNA polymerases. A number of cellular homologues of viral frameshift signals have also been identified [12].
A typical frameshift signal has two essential elements: a
heptanucleotide ‘slippery’ sequence, where the ribosomebound tRNAs slip into the –1 frame, and an adjacent secondary structure, most often an H-type pseudoknot, which stimulates this process. How the pseudoknot promotes frameshifting is not completely understood, but the mechanism is
probably linked to the helicase activity of the ribosome, with
the pseudoknot presenting an unusual topology that resists
unwinding [31–36]. Takyar et al. [35] have shown that the
prokaryotic 70S ribosome can itself act as a helicase to unwind
mRNA secondary structures before decoding. Prokaryotic
ribosomal proteins S3, S4 and S5 that line the mRNA
entry tunnel are implicated in this activity [35]. Recent
cryo-EM images of mammalian 80S ribosomes, paused at a
coronavirus frameshift-promoting pseudoknot, revealed that
the ribosomes become stalled during the translocation phase
of elongation with eEF2 bound and in the act of transferring
peptidyl-tRNA from the A- to the P-site [36]. Furthermore,
the P-site tRNA is distorted into a ‘spring-like’ conformation.
Consistent with its proposed function, the pseudoknot is
present at the mRNA entry channel in close proximity to
the proteins (rpS3, rpS9 and rpS2) that are likely to form the
mammalian 80S helicase. Namy et al. [36] suggest a mechanical model of frameshifting in which the pseudoknot resists
unwinding by the helicase, compromising translocation by
applying tension on the mRNA, leading to bending of the
tRNA anticodon and, ultimately, repositioning the tRNA on
the slippery sequence in the –1 reading frame. Recent work
has revealed that frameshift pseudoknots possess greater
mechanical stability in comparison with hairpins [37],
supporting the hypothesis that the extent of frameshifting
is related to the difficulty of unfolding the pseudoknot [38].
Structural and functional analyses of frameshift-promoting
pseudoknots have revealed features that could account for
resistance to unwinding by the ribosomal helicase. Chief
among these is the presence of extensive minor groove triplex
interactions between S1 and the crossing L3, first observed
in the pseudoknot of the luteovirus BWYV (beet western
yellows virus) [39]. The S1–L3 RNA triplex is likely to be
the first feature encountered by the elongating ribosome,
and the presence of the ‘third strand’ would conceivably
confound unwinding, at least temporarily. Another feature
of functional importance is the architecture of the junction
between the constituent pseudoknot stems. Several noncanonical interactions have been described in and around
the junction, including base triples, base quadruples and
loop–loop Hoogsteen base-pairing, and distortions such as
over-rotation of the stems, helical displacement and bending
[11,40]. The junction conformation may present a kinetic or
thermodynamic barrier to unwinding [38,40].
Pseudoknots can also promote +1 ribosomal frameshifting
and termination codon suppression. The best-characterized
examples come, respectively, from the cellular gene ornithine
decarboxylase antizyme [41] and the gammaretrovirus
murine leukaemia virus [42], but no high-resolution structural information is available as yet.
Pseudoknots in the 3 -NCR (3 -non-coding
region): translation and replication
Many positive-strand RNA virus genomes harbour
pseudoknots in the 3 -NCR, although none have been described in cellular genes as yet. The best-studied examples
come from plant viruses and include pseudoknots forming
tRNA-like structures [1,2]. Pseudoknots in the 3 -NCR
have been shown to carry out a variety of roles including the
control of virus genome translation, replication, the switch
between translation and replication, and genome packaging.
Further details of the interrelationships between 3 pseudoknot-specific re-activities and virus life cycles can be
found in recent reviews [12,43].
Pseudoknots to the rescue: tmRNA
(transfer-messenger RNA)
Bacterial tmRNA possesses the structural and functional
properties of both tRNA and mRNA. The tmRNA system
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recognizes and rescues ribosomes stalled on aberrant mRNAs
lacking a stop codon. When a translating ribosome reaches
the 3 -end of a non-stop mRNA, alanine-charged tmRNA
enters the A-site of the stalled ribosome (along with two
proteins, SmpB and EF-Tu) where it acts first as a tRNA and
then as an mRNA to direct the addition of a short peptide
tag to the C-terminus of the growing polypeptide [44].
This trans-translation event facilitates release of the tagged
polypeptide and frees the stalled ribosome from the mRNA.
The tmRNA itself contains three major domains, a tRNAlike domain that is aminoacetylated with an alanine residue at
the CCA 3 -terminus and complexed with SmpB and EF-Tu,
an mRNA-like domain that encodes the tagging polypeptide
and a third domain containing four pseudoknots (PK1–PK4)
[45]. Suggested roles for the pseudoknots include aiding
in overall tmRNA folding, slowing tmRNA degradation,
maintaining the correct geometry for efficient translocation
to the tmRNA ORF and serving as binding sites for proteins
that facilitate tmRNA function. While the pseudoknots are
not thought to be essential, they seem to promote biological
fitness. The pseudoknot PK1 shows considerable similarity
to the BWYV family of frameshift-promoting pseudoknots,
including short stems and loops, extensive base stacking,
stabilization of the stem junction by a triplex and exclusion of
a uridine at the junction of the two stems [46]. PK1 functions
at a different site on the ribosome than frameshift-promoting
pseudoknots, however, and its precise role is uncertain. As
detailed above, several pseudoknots have been shown to
interact with the ribosome, and it is clear that they can influence function from different sites.
Pseudoknots: a versatile motif in translation
The prevalence of pseudoknots in translation can be explained
by their functional versatility. Some are extensively stabilized
by both Watson–Crick and non-Watson–Crick interactions
[39] and are more stable than an equivalent hairpin. Thus a
very stable structure can be formed even when space, either
in terms of coding capacity or molecular dimensions, is at a
premium. Other pseudoknots are considerably less stable and
may act as regulatory switches, oscillating between stem–loop
and pseudoknot conformations in response to environmental
signals [26,47]. Pseudoknots also offer binding sites for proteins or single-stranded loops of RNA. The often extensive
intra- and inter-molecular contacts that pseudoknots engage
in provide many targets for such interactions. Pseudoknotting
may also be the most efficient way of folding RNAs in
an active conformation. Long-range interactions are also
possible to organize global folding and to link separate
domains of RNA together. While some or all of the features
of pseudoknots discussed above could be reproduced in other
ways, the pseudoknot fold may be more efficient.
Future perspectives
A determination of the true frequency of pseudoknots in
natural RNAs and a better understanding of the thermodynamic parameters that govern pseudoknot formation
are key goals. More information about the structure and
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recently, atomic-resolution structural information has been
restricted to short, often very stable, pseudoknots. The
cryo-EM and crystal structures of the IGR IRESs of CrPV
[15] and PSIV [16] were huge steps forward, but similar
efforts will be required to investigate structures where
pseudoknots orchestrate the folding of long and complex
domains. The field has come a long way since the early work
of Pleij and co-workers, yet there is still much to be
discovered about these fascinating motifs [1,2].
References
1 Rietveld, K., Van Poelgeest, R., Pleij, C.W., Van Boom, J.H. and Bosch, L.
(1982) The tRNA-like structure at the 3 terminus of turnip yellow
mosaic virus RNA: differences and similarities with canonical tRNA.
Nucleic Acids Res. 10, 1929–1946
2 Rietveld, K., Pleij, C.W. and Bosch, L. (1983) Three-dimensional models of
the tRNA-like 3 termini of some plant viral RNAs. EMBO J. 2, 1079–1085
3 Pleij, C.W., Rietveld, K. and Bosch, L. (1985) A new principle of RNA
folding based on pseudoknotting. Nucleic Acids Res. 13, 1717–1731
4 Westhof, E. and Jaeger, L. (1992) RNA pseudoknots. Curr. Opin.
Struct. Biol. 2, 327–333
5 Kolk, M.H., van der Graaf, M., Wijmenga, S.S., Pleij, C.W.A., Heus, H.A.
and Hilbers, C.W. (1998) NMR structure of a classical pseudoknot:
interplay of single- and double-stranded RNA. Science 280, 434–438
6 Mans, R.M., Pleij, C.W. and Bosch, L. (1991) tRNA-like structures:
structure, function and evolutionary significance. Eur. J. Biochem. 201,
303–324
7 Pleij, C.W. (1990) Pseudoknots: a new motif in the RNA game. Trends
Biochem. Sci. 15, 143–147
8 ten Dam, E., Pleij, K. and Draper, D. (1992) Structural and functional
aspects of RNA pseudoknots. Biochemistry 31, 11665–11676
9 Deiman, B.A.L.M. and Pleij, C.W.A. (1997) Pseudoknots: a vital feature in
viral RNA. Semin. Virol. 8, 166–175
10 Hilbers, C.W., Michiels, P.J. and Heus, H.A. (1998) New developments in
structure determination of pseudoknots. Biopolymers 48, 137–153
11 Giedroc, D.P., Theimer, C.A. and Nixon, P.L (2000) Structure, stability and
function of RNA pseudoknots involved in stimulating ribosomal
frameshifting. J. Mol. Biol. 298, 167–185
12 Brierley, I., Pennell, S. and Gilbert, R.J.C. (2007) Viral RNA pseudoknots:
versatile motifs in gene expression and replication. Nat. Rev. Microbiol.
5, 598–610
13 Kim, Y.G., Su, L., Maas, S., O’Neill, A. and Rich, A. (1999) Specific
mutations in a viral RNA pseudoknot drastically change ribosomal
frameshifting efficiency. Proc. Natl. Acad. Sci. U.S.A. 96, 14234–14239
14 Theimer, C.A. and Feigon, J. (2006) Structure and function of telomerase
RNA. Curr. Opin. Struct. Biol. 16, 307–318
15 Schuler, M., Connell, S.R., Lescoute, A., Giesebrecht, J., Dabrowski, M.,
Schroeer, B., Mielke, T., Penczek, P.A., Westhof, E. and Spahn, C.M.T.
(2006) Structure of the ribosome-bound cricket paralysis virus IRES RNA.
Nat. Struct. Mol. Biol. 13, 1092–1096
16 Pfingsten, J.S., Costantino, D.A. and Kieft, J.S. (2006) Structural basis for
ribosome recruitment and manipulation by a viral IRES RNA. Science
314, 1450–1454
17 Gutell, R,R., Larsen, N. and Woese, C.R. (1994) Lessons from an evolving
rRNA: 16S and 23S rRNA structures from a comparative perspective.
Microbiol. Rev. 58, 10–26
18 Poot, R.A., van den Worm, S.H., Pleij, C.W. and van Duin, J. (1998) Base
complementarity in helix 2 of the central pseudoknot in 16S rRNA is
essential for ribosome functioning. Nucleic Acids Res. 26, 549–553
19 Jopling, C.L., Spriggs, K.A., Mitchell, S.A., Stoneley, M. and Willis, A.E.
(2004) L-Myc protein synthesis is initiated by internal ribosome entry.
RNA 10, 287–298
20 Wilson, J.E., Pestova, T.V., Hellen, C.U. and Sarnow, P. (2000) Initiation of
protein synthesis from the A site of the ribosome. Cell 102, 511–520
21 Spahn, C.M., Jan, E., Mulder, A., Grassucci, R.A., Sarnow, P. and Frank, J.
(2004) Cryo-EM visualization of a viral internal ribosome entry site
bound to human ribosomes: the IRES functions as an RNA-based
translation factor. Cell 118, 465–475
Post-Transcriptional Control
22 Kanamori, Y. and Nakashima, N. (2001) A tertiary structure model of the
internal ribosome entry site (IRES) for methionine-independent initiation
of translation. RNA 7, 266–274
23 Jan, E. and Sarnow, P. (2002) Factorless ribosome assembly on the
internal ribosome entry site of cricket paralysis virus. J. Mol. Biol. 324,
889–902
24 Costantino, D.A., Pfingsten, J.S., Rambo, R.P. and Kieft, J.S. (2008)
tRNA–mRNA mimicry drives translation initiation from a viral IRES.
Nat. Struct. Mol. Biol. 15, 57–64
25 Schlax, P.J., Xavier, K.A., Gluick, T.C. and Draper, D.E. (2001) Translational
repression of the Escherichia coli α operon mRNA: importance of an
mRNA conformational switch and a ternary entrapment complex.
J. Biol. Chem. 276, 38494–38501
26 Marzi, S., Myasnikov, A.G., Serganov, A., Ehresmann, C., Romby, P.,
Yusupov, M. and Klaholz, B.P. (2007) Structured mRNAs regulate
translation initiation by binding to the platform of the ribosome. Cell
130, 1019–1031
27 Haentjens-Sitri, J., Allemand, F., Springer, M. and Chiaruttini, C. (2008) A
competition mechanism regulates the translation of the Escherichia coli
operon encoding ribosomal proteins L35 and L20. J. Mol. Biol. 375,
612–625
28 Ehresmann, C., Ehresmann, B., Ennifar, E., Dumas, P., Garber, M., Mathy,
N., Nikulin, A., Portier, C., Patel, D. and Serganov, A. (2004) Molecular
mimicry in translational regulation: the case of ribosomal protein S15.
RNA Biol. 1, 66–73
29 Philippe, C., Eyermann, F., Bénard, L., Portier, C., Ehresmann, B. and
Ehresmann, C. (1993) Ribosomal protein S15 from Escherichia coli
modulates its own translation by trapping the ribosome on the mRNA
initiation loading site. Proc. Natl. Acad. Sci. U.S.A. 90, 4394–4398
30 Gilbert, S.D., Rambo, R.P., Van Tyne, D. and Batey, R.T. (2008) Structure
of the SAM-II riboswitch bound to S-adenosylmethionine. Nat. Struct.
Mol. Biol. 15, 177–182
31 Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N.,
Cate, J.H. and Noller, H.F. (2001) Crystal structure of the ribosome at
5.5 Å resolution. Science 292, 883–896
32 Yusupova, G.Z., Yusupov, M.M., Cate, J.H. and Noller, H.F. (2001) The
path of messenger RNA through the ribosome. Cell 106, 233–241
33 Plant, E.P., Jacobs, K.L., Harger, J.W., Meskauskas, A., Jacobs, J.L., Baxter,
J.L., Petrov, A.N. and Dinman, J.D. (2003) The 9-Å solution: how mRNA
pseudoknots promote efficient programmed −1 ribosomal
frameshifting. RNA 9, 168–174
34 Plant, E.P. and Dinman, J.D. (2005) Torsional restraint: a new twist on
frameshifting pseudoknots. Nucleic Acids Res. 33, 1825–1833
35 Takyar, S., Hickerson, R.P. and Noller, H.F. (2005) mRNA helicase activity
of the ribosome. Cell 120, 49–58
36 Namy, O., Moran, S.J., Stuart, D.I., Gilbert, R.J. and Brierley, I. (2006) A
mechanical explanation of RNA pseudoknot function in programmed
ribosomal frameshifting. Nature 441, 244–247
37 Green, L., Kim, C.H., Bustamante, C. and Tinoco, Jr, I. (2008)
Characterization of the mechanical unfolding of RNA pseudoknots.
J. Mol. Biol. 375, 511–528
38 Hansen, T.M., Reihani, S.N., Oddershede, L.B. and Sorensen, M.A. (2007)
Correlation between mechanical strength of messenger RNA
pseudoknots and ribosomal frameshifting. Proc. Natl. Acad. Sci. U.S.A.
104, 5830–5835
39 Su, L., Chen, L., Egli, M., Berger, J.M. and Rich, A. (1999) Minor groove
RNA triplex in the crystal structure of a ribosomal frameshifting viral
pseudoknot. Nat. Struct. Biol. 6, 285–292
40 Cornish, P.V., Stammler, S.N. and Giedroc, D.P. (2006) The global
structures of a wild-type and poorly functional plant luteoviral mRNA
pseudoknot are essentially identical. RNA 12, 1959–1969
41 Ivanov, I.P. and Atkins, J.F. (2007) Ribosomal frameshifting in decoding
antizyme mRNAs from yeast and protists to humans: close to 300 cases
reveal remarkable diversity despite underlying conservation. Nucleic
Acids Res. 35, 1842–1858
42 Alam, S.L., Wills, N.M., Ingram, J.A., Atkins, J.F. and Gesteland, R.F. (1999)
Structural studies of the RNA pseudoknot required for readthrough of the
gag-termination codon of murine leukemia virus. J. Mol. Biol. 288,
837–852
43 Dreher, T.W. and Miller, W.A. (2006) Translational control in positive
strand RNA plant viruses. Virology 344, 185–197
44 Keiler, K.C., Waller, P.R. and Sauer, R.T. (1996) Role of a peptide tagging
system in degradation of proteins synthesized from damaged
messenger RNA. Science 271, 990–993
45 Kaur, S., Gillet, R., Li, W., Gursky, R. and Frank, J. (2006) Cryo-EM
visualization of transfer messenger RNA with two SmpBs in a stalled
ribosome. Proc. Natl. Acad. Sci. U.S.A. 103, 16484–16489
46 Nonin-Lecomte, S., Felden, B. and Dardel, F. (2006) NMR structure of the
Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding
event of the ribosomal trans-translation. Nucleic Acids Res. 34,
1847–1853
47 Wyatt, J.R., Puglisi, J.D. and Tinoco, Jr, I. (1990) RNA pseudoknots:
stability and loop size requirements. J. Mol. Biol. 214, 455–470
48 Shen, L.X. and Tinoco, Jr, I. (1995) The structure of an RNA pseudoknot
that causes efficient frameshifting in mouse mammary tumour virus.
J. Mol. Biol. 247, 963–978
Received 11 March 2008
doi:10.1042/BST0360684
C The
C 2008 Biochemical Society
Authors Journal compilation 689