RNA-Protein Machines Nucleic Acids and Molecular Biology Group Colloquium Organized by M. Hartley (Department of Biological Sciences, University of Warwick), J. McCarthy (Department of Biomolecular Sciences, UMIST) and M. Gait (MRC Laboratory of Molecular Biology, Cambridge), and Edited by M. Gait. 675th Meeting held at the University of York, 17-1 9 December 200 I, Joint with The Physiological Society. Functions and interplay of the tRNA-binding sites of the ribosome V. Marquez, D. N . Wilson and K. H. Nierhaus' Max-Planck-lnstitut fur Molekulare Genetik AG Ribosomen, lhnestrasse 73, D- I 4 I95 Berlin, Germany Abstract signal of the mRNA with the help of specific protein-initiation factors and an initiator tRNA, thus forming an initiation complex. Following the recruitment of the large ribosomal subunit the ribosome is now prepared for the second phase, the elongation cycle. T h e ribosome decodes genetic information as it 'travels' along the mRNA, simultaneously elongating the nascent peptide chain by addition of amino acids. T h e appearance of a stop codon in the A site signals the third phase of protein synthesis, the termination phase, where the nascent peptide chain is cleaved and released from the ribosome. tRNAs play a crucial role during the initiation and elongation phases. These adapter molecules form the connection between the RNA and protein worlds by linking the codon of the mRNA with the corresponding amino acid. There are three tRNA-binding sites on the ribosome. T h e A site, containing the decoding centre, binds an aminoacyl-tRNA corresponding to the codon displayed at this site. T h e P site binds the peptidyltRNA, the tRNA carrying the nascent chain before peptide-bond formation, and the E site binds specifically deacylated tRNAs, tRNAs that have already participated in chain elongation. In the course of two elongation cycles a tRNA moves in succession through the ribosomal A, P and E sites. Figure 1 depicts the elongation cycle in the frame of the CI-E model, a current model that best satisfies the existing structural and biochemical data (see Figure 1 legend and [1,2] for reviews). There are two elongation factors that aid tRNA movement during an elongation cycle. Elongation factor (EF)-Tu delivers the aminoacyl-tRNA to the A site in the form of a ternary complex aminoacyl-tRNA. E F - T u . GTP. EF-G is involved in the translocation reaction, which basically moves the tRNAs into the adjacent binding site on the ribosome, thereby moving the ribo- T h e ribosome translates the genetic information of an mRNA molecule into a sequence of amino acids. T h e ribosome utilizes tRNAs to connect elements of the RNA and protein worlds during protein synthesis, i.e. an anticodon as a unit of genetic information with the corresponding amino acid as a building unit of proteins. Three tRNAbinding sites are located on the ribosome, termed the A, P and E sites. In recent years the tRNAbinding sites have been localized on the ribosome by three different techniques, small-angle neutron scattering, cryo-electron microscopy and X-ray analyses of 70 S crystals. These high-resolution glimpses into various ribosomal states together with a large body of biochemical data reveal an intricate interplay between the tRNAs and the three ribosomal binding sites, providing an explanation for the remarkable features of the ribosome, such as the ability to select the correct ternary complex aminoacyl-tRNA. E F - T u . G T P out of more than 40 extremely similar tRNA complexes, the precise movement of the tRNA, . mRNA complex during translocation and the maintenance of the reading frame. Introduction T h e ribosome translates the genetic information contained within an mRNA in three phases. First, the small ribosomal subunit recognizes the start Key words: A site, E site, P site, protein synthesis. Abbreviations used: EF, elongation factor: PTF, peptidyltransferase; SANS, small-angle neutron scattering; PRE, pretranslational: POST, post translational: cryo-EM, cryo-electron microscopy: SD, Shine-Dalgamo: RF2, release factor 2. 'To whom correspondence should be addressed (e-mail [email protected]). I33 0 2002 Biochemical Society Biochemical Society Transactions (2002) Volume 30, part 2 codons with a length of l O A each, although a tRNA as an RNA helix measures 20 A in diameter, and at the other end both tRNAs must contact the peptidyl-transferase (PTF) centre. We will see that the simultaneous interaction of both tRNAs with the mRNA is of utmost importance for the accuracy of aminoacyl-tRNA selection, the translocation reaction and the maintenance of the reading frame, i.e. for all the essential features of protein synthesis. some by one codon length towards the 3’-end of the mRNA. Although the ribosome ensures correct codon-anticodon (mRNA-tRNA) interactions, it is actually the synthetases that ensure that each codon in the mRNA is correlated with the correct amino acid. U p to 20 different synthetases exist in a cell, one for each amino acid. T h e synthetases form this link by ensuring that each tRNA species, a tRNA with a unique anticodon, is charged with an amino acid that correlates with the codon that the anticodon recognizes. T h e universal L-shape of the tRNAs is a consequence of the absolute requirement of codon-anticodon interactions of both tRNAs present on the ribosome, which are found in the A and P sites before translocation and in the P and E sites afterwards. T h e reason is that the tRNAs have to make contact, with one end, two adjacent Localization of the tRNA-binding sites on the ribosome T h e first reliable localization of tRNA-binding sites on the ribosome was achieved by means of small-angle neutron scattering (SANS) [3]. T h e two main functional states of the ribosome during elongation were constructed under near-in vivo Figure I The Q-E model of the elongation cycle, according to [ I71 The essential feature is a movable ribosomal a-E domain that connects both subunits through the intenubunit space, binds both tRNAs of an elongating ribosome and carries them from the A and P sites to the P and E sites, respectively, during translocation. The model explains the reciprocal linkage between the A and E sites by the fact that the a-E domain moves out of the A site during translocation, leaving the decoding centre alone at the A site. Yellow and green, the two binding regions of the a-Edomain: blue, the decoding centre at the A site. y3 hk= T EF-TU GTP EF-G GDP + Pi EF-G GTP ar POST l a I E PE Aa u PRE POST PRE 30s 50s POST 0 2002 Biochemical Society I34 RNA-Protein Machines tonated (‘stained’) ligands, in this case tRNAs, within a large deuterated complex like the ribosome. T h e two tRNAs at A and P sites of the PRE state and at P and E sites of the P O S T state could be localized unequivocally between the subunits. An important outcome was that the anticodons of both tRNAs neighbour each other, thus allowing adjacent codon-anticodon interaction in the PRE and P O S T states, and that the ionic conditions, that is the state prior to translocation (pre-translocational or PRE state) and the state after (post-translocational or P O S T state). Ribosomeswerefullydeuteratedand bothmRNA and tRNAs were protonated (their normal state in Nature). Since neutrons are scattered differently by protons and deuterons (protons and deuterons are the atom nuclei of normal and heavy hydrogen, respectively), this allows localization of the pro- Figure 2 tRNA locations on the ribosome (A) tRNAs in the PRE and POST states ofthe E. coli ribosome. Shown are cryo-EM reconstructions oftRNAs bound to the 70 S ribosome [6]. PRE state, tRNAs bound to the A site (pink) and P site (green). POST state, tRNAs bound to the P site (green) and E site (yellow). The small 30 S (yellow) and large (blue) subunit are shown. The 70 S ribosome is presented as a semi-transparent surface to better illustrate the tRNA positions. Abbreviations: CP, central protuberance; ST, L7/LI 2 stalk base; Ib, long bridge (helix 38 of 23 S rRNA); h, head; ch, mRNA channel: sh. shoulder region: sp, spur. (6)Relative positions of the three tRNAs bound at the A, P and E sites. The P and C I ’ atoms The two of the P-site tRNAs are used t o align the molecules of the cryo-EM (brown) [6] with that from the X-ray work (dark green) studies agree on the position of the tRNAs on the ribosome. From this comparison it can be seen that the A-site tRNAs (cryo-EM in olive green, X-ray in cyan) are shifted relative to each other along the anticodon stem axis (vertical arrow), and the E-site-bound tRNAs along the acceptor stem axis (arrow; cryo-EM in red and X-ray in blue). Note that the anticodon regions of all three tRNAs are in close proximity t o each other. Panel (B)is reproduced from [23] with permission. 0 (2002) Bentham Science Publishers. m. B I Ch . P\sp PRE I35 E P A E P A 0 2002 Biochemical Society Biochemical Society Transactions (2002) Volume 30,part 2 sites at a resolution of 5.5-7.5 A was the next important achievement [7]. T h e crystal structures had a very similar arrangement of the tRNAs when compared with the cryo-EM reconstructions (Figure 2B), even though the complex (i) was obtained from the thermophilic bacterium Thermus thermophilus instead of Escherichia coli, and (ii) does not represent a functional state of the ribosome, since three deacylated tRNAs are never found on the ribosome during protein synthesis. In addition, the tRNA-ribosome contacts could be determined in molecular detail by utilizing the higher-resolution subunit structures (30 S structure [8,9] and 50 S structure [lo]). In particular, the fixation of the anticodon region of the P-site tRNA by a number of ribosomal fingers was revealed. Another interesting observation was that the deacylated tRNA was buried deeply in the ribosomal matrix. This suggests that an active mechanism is necessary to release the E sitebound tRNA. Precisely this point was a topic of intense discussion during the past 15 years. Results obtained with near-in vivo conditions clearly indicated binding of a tRNA at the E-site, invoking an active release mechanism, whereas results gathered under conventional conditions suggested a weak binding and an easy release from the E site (for discussion, see [l]). T h e three tRNA-binding sites differ in their capability to bind tRNAs with different charging states, namely deacylated tRNA, aminoacyltRNA and peptidyl-tRNA. These features are summarized in Table 1 (according to [ l 13). mutual arrangement of both tRNAs was similar in both states. We stress the usage of near-in vivo ionic conditions (Mg’+ at 3-6 mM, 150 m M NH:/Kt, 2 m M spermidine and 0.05 m M spermine), since it has been demonstrated that the usage of conventional buffer systems (10-15 m M Mg2+, z 150 m M N H I / K + and no polyamines) can induce artifacts. During the last two decades these artifacts have provided controversy with regard to the importance of the E site and have given rise to an alternative model for the elongation cycle ([4]; for review, see [l]). However, the resolution power of the SANS method is limited. An estimate of the resolution obtainable with the SANS method would fall within a range of 2 5 4 0 A. In comparison, cryoelectron microscopy (cryo-EM) and X-ray crystallographic analyses of 70 S ribosomes and subunits have produced resolutions of 12-1 8 A and 2.3-5.5 A, respectively. T h e emergence of cryo-EM within the field of ribosome research [5] provided an exciting opportunity to re-analyse functional complexes at near-in vivo conditions in collaboration with the Frank group (Wadsworth Center, Albany, NY, U.S.A.). T h e result was the first clear description of both the PRE and P O S T elongation states in molecular terms [6] (Figure 2A) and the mutual arrangement of the three tRNAs on the ribosome (Figure 2B). T h e tRNA-binding sites can now be seen at higher resolution ( z15 A), generally confirming the positions and the angle between the tRNAs observed in the aforementioned SANS study, but with important improvements. (i) T h e exact tRNA positions could be assessed. A SANS study principally cannot distinguish between a distinct mutual arrangement of the two tRNAs and its mirror arrangement. (ii) T h e anticodon distances of the two adjacent tRNAs could be determined precisely, clearly indicating that a simultaneous codon-anticodon interaction of both tRNAs is possible. (iii) T h e CCA 3’-ends of the two tRNAs in the PRE state are in close proximity to each other, as was expected since both ends must contact the P T F centre on the large subunit. T h e PTF centre is responsible for peptide-bond formation between the peptidyl residue of the peptidyl-tRNA at the P site and the aminoacyl residue of the aminoacyl-tRNA at the A site. In contrast, the CCA ends of the tRNAs in the P O S T in the state are far from each other ( x 17 PRE state and 60 A in the P O S T state). T h e crystal structure of 70 S ribosomes carrying three deacylated tRNAs at the A, P and E Functional features of the ribosome: selection of the correct aminoacyltRNA at the decoding centre of the A site Two features are of vital importance for the intricate functional spectrum of the ribosome. (i) T h e first and the third tRNA-binding sites, the A and the E sites, are coupled in a reciprocal fashion. This means that a tRNA bound to the E site induces a low-affinity state for an aminoacyltRNA or a ternary complex at the A site and vice versa; occupying the A site promotes a low-affinity state of the E site thus triggering the release of the deacylated tRNA from this site ([12,13]; see also Figure 1). A consequence of this feature is that statistically only two tRNAs are found on the ribosome during protein synthesis, either at the A and P sites (PRE state) or at the P and E sites A 0 2002 Biochemical Society I36 E n 3. n, 85 m h, 0 0 h, 0 +Deacylated tRNA Peptidyl-tRNA at the P site and a deacylated tRNA at the E site +Aminoacyl-tRNA .EF-Tu .GTP +Aminoacyl- or peptidyl-tRNA +Deacylated tRNA +Peptidyl-tRNA +Aminoacyl-tRNA. EF-TU* GTP A peptidyl-tRNA at the P site -6 37 "C: A site induces complete release of E-site-bound tRNA. bound tRNA. 0 "C: binds t o the A site, incomplete release of the E-site- E-site-bound tRNA. 0 "C: no binding t o the A site. 37 " C : binding t o the A site induces quantitative release of the release of the E-site-bound tRNA. 0 "C: no binding. 37 "C: binding t o the A site does not trigger quantitative site without EF-G. 0/37 " C : binds directly t o the E site. 0/37 "C: does not bind t o the A site (exclusion principle [24]). 0 "C: binds directly t o the A site, dipeptide formation. 37 "C: dipeptidyl-tRNA slides within several minutes t o the P site; antibiotic viomycin prevents sliding. 0137 "C: binds directly t o the P site. 0137 "C: binds directly t o the P site. 0 "C: binds directly t o the A site; EF-G promotes translocation t o the P site at 0 "C. 37 " C : binds t o the A site and slides (without EF-G) t o the P +Deacylated tRNA Empty ribosome with mRNA +Peptidyl-tRNA +Aminoacyl-tRNA fEF-TU.GTP Binding event Added tRNA State of the ribosome Binding features of the tRNA-binding sites Table I Biochemical Society Transactions (2002) Volume 30, part 2 more, every one of the 41 ternary complexes would interfere with the selection process and thus could by chance be incorporated erroneously. This is never seen; instead, only three or four ternary complexes can be accepted by the A site, those tRNAs with either the correct (cognate) or similar (near-cognate) anticodon. Thus the majority ( z 90 yo) of the non-cognate ternary complexes that carry an aminoacyl-tRNA with a dissimilar anticodon are never mis-incorporated during protein synthesis. The solution to this selection riddle is the reciprocal coupling between A and E sites. An occupied E site (POST state, see Figure 1) induces a low-affinity state in the A site, and this state mainly allows codon-anticodon interaction but abolishes all interaction outside the anticodon. This ribosomal trick has two consequences. First, equilibrium can be reached in a short time in agreement with that observed in protein synthesis in the cell. Second, after the decoding has been successfully completed, the high-affinity state of the A site has to be adjusted and the aminoacyltRNA adapted at the A site, probably a gross conformational change that lasts significantly longer than the preceding decoding step. A corollary of such a reaction, where the first partial reaction is fast and the second slow, implies that the first reaction reaches equilibrium even under steady-state conditions, thus allowing full exploitation of the discrimination potential of codonanticodon interaction at the A site. This mechanism also explains why non-cognate ternary complexes are never mis-incorporated : at the first step, non-cognate anticodons dissimilar to the cognate one that cannot interact with the A site codon are thus not selected, and the potential contact regions outside of the anticodon are not yet available. (POST state). (ii) As mentioned already, both tRNAs simultaneously undergo codon-anticodon interaction in the PRE and POST states. Interaction in the POST state was a surprise, since decoding does not take place here. Instead, codon-anticodon interaction at the E site is the signal for the ribosome to switch into the POST mode with a low A-site affinity [12]. As will become evident, codon-anticodon interaction of the adjacent tRNAs on the ribosome is a cornerstone for the translocation mechanism as well as for the maintenance of the reading frame (see the next two sections). Here we will discuss the importance of the reciprocal coupling of A and E sites for the accuracy of tRNA selection at the A site. This point has been reviewed extensively ([14,15]), and therefore we only present a brief summary. Enzymes achieve an astonishing precision of substrate recognition and binding (a precision of one error in 103-106 binding events), a precision that is necessary in order to avoid the degeneration of metabolism into complete chaos. Enzymes attain this accuracy mostly or exclusively by binding their substrate using the ‘molecular corner’ that is unique amongst its structural relatives. Therefore, the binding energy is identical to the discrimination energy in the best cases. Since the binding constant describes an equilibrium state, it is clear that the discrimination potential can only be exploited under equilibrium conditions. With this in mind it is evident that the ribosome faces an almost unsolvable selection problem. In E. coli, for example, 41 ternary complexes containing tRNA with different anticodons all compete for the codon displayed at the A site. The discrimination is achieved solely via codon-anticodon interaction, although a tRNA makes many other contacts with the ribosome [7,16,17]. In addition, it is not the aminoacyltRNA but rather the ternary complex of aminoacyl-tRNA . EF-Tu . G T P that is a substrate for the A site. The elongation factor EF-Tu is twice as large as a tRNA molecule and increases the affinity to the A site by at least two orders of magnitude [1 13, indicating additional contacts with the A site. Taken together, this means that the discrimination (or binding) energy due to codon-anticodon interaction is only a tiny fraction of the total binding energy of a ternary complex, and therefore the time to reach equilibrium would take hours rather than milliseconds (in Nature, one elongation cycle lasts % 50-100 ms). Further- 0 2002 Biochemical Society Functional features of the ribosome: the translocation reaction As mentioned already, tRNAs are L-shaped molecules the functional groups of which are located at the tips of the arms and separated by about 75A; the anticodon is at one end and the acyl residue (aminoacyl or peptidyl group) is at the other. The anticodon interacts with the codons on the mRNA at the decoding centre on the small ribosomal subunit and the acyl residues with the P T F centre on the large ribosomal subunit. A tRNA is the size of an average enzyme, and the I38 RNA-Protein Machines problem with the translocation of tRNAs is that both tips of this large molecule have to be moved with high precision. Imprecise movement at the anticodon end would lead to a loss of the reading frame, and at the acyl end would preclude proper placement at the PTF centre, thus preventing peptide-bond formation. T h e analysis of contact patterns of tRNAs in various ribosomal sites has provided an answer to this problem. I n brief, it was found that the contact patterns of both tRNAs at the A and P sites in the PRE state were remarkably different, but that both patterns did not change upon translocation to the P and E sites, respectively, i.e. to the P O S T state. We interpreted this finding to suggest that the microtopography of the tRNA-ribosome interactions does not change during translocation. This implies that a movable ribosomal domain should exist that tightly binds both tRNAs and moves or guides them from one tRNA-binding site to the adjacent one (a-E model for the elongation cycle; Figure 1). Ribosomal components as candidates for the movable domain have been identified with both cryo-EM [18] and X-ray analysis of ribosome crystals [7], It follows that the tRNAs are the handle that is moved actively by the ribosome and that the two associated codon-anticodon interactions are required to concomitantly draw the mRNA through the ribosome. T h e mRNA follows passively the actively moved tRNAs during translocation. This scenario explains why the number of base pairs during codon-anticodon interactions at the A site can induce frameshifts : tRNAs with modified anticodon loops that allow either 2 or 4 bp instead of the canonical 3 b p provoke a -1 or +1 frameshift during translocation [19,20]. whereas during normal translation the error frequency for frameshifts is not higher than 1 case in 30000 amino acid incorporations [22], i.e. the frameshift on the RF2 mRNA occurs with a frequency that is more than four orders of magnitude larger than normal. What mechanism operates at this recoding site to override the strict maintenance of the reading frame? T h e recoding site has a number of special features; in particular, the presence of a ShineDalgarno (SD)-like sequence upstream of the UGA stop codon. Normally, the SD sequence is associated with initiation in bacteria and is found upstream of the initiation A U G codon. T h e S D sequence is complementary to a sequence of the 3’-end of 16 S rRNA (anti-SD). Duplex formation is a prerequisite for bacterial initiation. What has been overlooked in a number of publications is that here the SD-like sequence would be predicted to extend its interaction into the E site, i.e. basepairing with the first base of the E-site codon. Our hypothesis is that this duplex formation between the anti-SD-like sequence and the E site codon would prevent codon-anticodon interaction and thus trigger the release of the deacylated tRNA from the E site, leaving the ribosome with only a single peptidyl-tRNA at the P site. This situation does not occur during elongation and might facilitate a slip of the ribosome on the mRNA, thus inducing, with high probability, a + 1 frameshift. This hypothesis can be tested and, if true, it not only provides a satisfying explanation for the extremely high frameshift frequency during the translation of the RF2 mRNA, but also suggests that the codon-anticodon interaction at the E site has the important role of maintaining the reading frame during translation. We have already shown in vitro (V. Marquez and K. H. Nierhaus, unpublished work) that the presence of a S D sequence positioned as in the RF2 mRNA in front of an UGA is instrumental for a 1 frameshift with an almost 100% efficiency. Removal of the S D sequence without changing the amino acid sequence of the corresponding peptide lowers the frameshift frequency to background levels. It remains to be seen whether or not removal of the deacylated tRNA from the E site is the essential function of the unusual location of a S D sequence in front of a stop codon (V. Marquez and K. H. Nierhaus, unpublished work). Functional features of the ribosome: maintenance of the reading frame + T h e simple feedback regulation of the synthesis of the termination factor release factor 2 (RF2) might shed some light on this aspect. T h e codon position 26 of the RF2 mRNA is taken by a U G A stop codon that is specifically recognized by RF2. If the concentration of RF2 in the cell is sufficient, the stop codon will be recognized and translation of the RF2 mRNA will abort after the synthesis of a 25-mer peptide that is quickly degraded. However, if there is a shortage of RF2 in the cell, a + 1 frameshift will occur, enabling the translation of the complete RF2 protein. This frameshift can occur with an astonishingly high efficiency of up to 100 yo [21], We thank the Deutsche Forschungsgemeinschaft for support (DFG Ni I74/8-2). D.N.W. would like t o recognizethe support of the Alexander von Humboldt Foundation in awarding a Fellowship that made this work possible. I39 0 2002 Biochemical Society Biochemical Society Transactions (2002) Volume 30, part 2 References I 2 3 4 5 6 7 8 9 10 II Nierhaus, K. H., Spahn, C. M. T., Burkhardt, N.. Dabrowski, M., Diedrich, G., Einfeldt E., Kamp. D., Marquez, V., Patzke, S., Schafer, M. A. et al. (2000) in The Ribosome. Structure, Function, Antibiotics, and Cellular Interactions (Garrett, R A., Douthwaite, S. R., Liljas, A,, Matheson, A. T., Moore, P. B. and Noller, H. F., eds), pp. 3 19-335, American Society for Microbiology Press, Washington D C Blaha. G. and Nierhaus, K. H. (2001) in Ribosome, Cold Spring Harbor Press, Cold Spring Harbor, NY, in the press Nierhaus, K. H., Wadzack J., Burkhardt, N.,Junemann,R, Meerwinck W., Willumek, R and Stuhrmann, H. B. ( I 998) Proc. Natl. Acad. Sci. U.S.A. 95, 945-950 Moazed, D. and Noller, H. F. ( I 989) Nature (London) 342, 142- I 48 Frank I., Verschoor, A.. Wagenknecht, T., Radetmacher, M. and Carazo, J. M. (I988) Trends Biochem. Sci. 13, 123- I27 Agrawal, R K., Spahn, C. M. T., Penczek P., Grassucci, R A,, Nierhaus, K. H. and Frank J. (2000) J. Cell Biol. 150, 447-459 Yusupov, M. M., Yusupova, G. Z., Baucom, A,, Lieberman, K., Earnest, T. N., Cate, J. H. and Noller, H. F. (2001) Science 292, 883-896 Schluenzen, F., Tocilj, A, Zarivach. R. Harms. 1.. Gluehmann, M., Janell. D., Bashan, A,, Bartels, H., Agmon, I., Franceschi, F. and Yonath, A. (2000) Cell 102, 6 15-623 Wimberly, B. T., Brodersen, D. E.,Clemons, W. M., Morgan-Warren, R I., Carter, A. P., Vonrhein, C., Hartsch, T. and Ramakrishnan, V. (2000) Nature (London) 407, 327-339 Ban, N., Nissen, P., Hansen, J., Moore, P. B. and Steitz, T. A. (2000) Science 289,905-920 12 13 14 15 16 17 18 19 20 21 22 23 24 Schilling-Bartetzko, S., Franceschi, F., Sternbach, H. and Nierhaus, K. H. ( I 992) J. Biol. Chem. 267, 4693-4702 Geigenmuller, U. and Nierhaus, K. H. ( I 990) EMBO J. 9, 452745 33 Triana-Alonso, F. J., Chakraburtty, K. and Nierhaus, K H. ( I 995) J. Biol. Chem. 270, 20473-20478 Nierhaus, K. H. ( I 990) Biochemistry 29,4997-5008 Nierhaus, K. H. ( 1993) Mol. Microbiol. 9, 66 1-669 Dabrowski, M., Spahn, C. M. T. and Nierhaus. K. H. ( I 995) EMBO J, 14,48724882 Dabrowski, M., Spahn, C. M. T., Schafer, M. A,, Patzke, S. and Nierhaus, K. H. ( 1998) J. Biol. Chem. 273, 32793-32800 VanLoock M. S., Agrawal, R. K., Gabashvili. I. S., Qi, L., Frank J. and Harvey, S. C. (2000) J. Mol. Biol. 304, 507-5 I5 Culbertson, M., Leeds, P., Sandbaken, M. and Wilson, P. ( 1990) in The Ribosome: Structure, Function, & Evolution (Hill, W. E., Dahlberg, A. E., Garrett, R A,, Moore, P. B., Schlessinger, D. and Warner, J. R., eds), pp. 559-570, American Society for Microbiology Press, Washington D C Atkins. J. F., Weiss, R B., Thompson, S. and Gesteland, R F. ( I 99 I ) Annu. Rev. Genet. 25,20 1-228 Donly, B. C., Edgar, C. D., Adamski, F. M. and Tate, W. P. ( 1990) Nucleic Acids Res. 18, 65 I 7-6522 Jorgensen,F. and Kurland, C. G. ( 1990) J. Mol. Biol. 2 15, 5 I 1-521 Wilson, D. N.. Blaha, G., Connell, S. R, Ivanov, P. V., Jenke, H., Stelzl, U., Teraoka, Y. and Nierhaus, K. H. (2002) Cur. Protein Peptide Sci., 3, 1-53 Rheinbetger, H.-J.,Sternbach. H. and Nierhaus, K. H. ( I 98 I) Proc. Natl. Acad. Sci. U.S.A. 78, 53 I C-53 I 4 Received 22 November 200 I The hepatitis C virus internal ribosome-entry site: a new target for antiviral research J. Gallego' and G. Varan? MRC Laboratoty of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K. Abstract translation-initiationmechanism. The viral RNA contains an internal ribosome-entry site (IRES) that is recognized specifically by the small ribosomal subunit and by eukaryotic initiation factor 3, and these interactions allow cap (7-methylguanine nuc1eotide)-independent initiation of viral protein synthesis. In this article, we review the structure and mechanism of translation initiation of the HCV IRES, and its potential as a target for novel antivirals. The hepatitis C virus (HCV) is the main causative agent of non-A, non-B hepatitis in humans and a major cause of mortality and morbidity in the world. Currently there is no effective treatment available for the infection caused by this virus, whose replication depends on an unusual Key words: elF3, HCV, IRES, translation. Abbreviations used: cap, 7-methyl-guanine nucleotide; elF, eukaryotic initiation factor: EM, electron microscopy: HCV, hepatitis C virus; IRES, internal ribosome-entry Site; UTR untranslated region. 'To whom correspondence should be addressed (e-mail [email protected]). 2Present address: Departments of Biochemistry and Chemistry, University of Washington, Seattle, W A 98 195- 1700, U S A 0 2002 Biochemical Society Introduction The hepatitis C virus (HCV) is the main causative agent of post-transfusion hepatitis. This human pathogen is a positive (messenger) sense singlestranded RNA virus (Figure 1) that relies on an I40
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