According to Wobble Rules, What Codons Should Be Recognized by the Anticodon 5ã¢â‚¬â²-gcu-3ã¢â‚¬â²?
Nucleic Acids Res. 2003 Nov 15; 31(22): 6383–6391.
SURVEY AND SUMMARY: Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-catastrophe codons
Kazuyuki Takai
1Cell-Costless Scientific discipline and Engineering Research Heart, 2Section of Applied Chemical science, Faculty of Technology and 3Venture Business concern Laboratory, Ehime Academy, three, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan and 4Section of Biophysics and Biochemistry, School of Science, University of Tokyo, iii-7-ane, Hongo, Bunkyo-ku, Tokyo 113-0033, Nippon, 5Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Nihon and viCellular Signaling Laboratory and Structurome Enquiry Group, RIKEN Harima Institute at Spring-eight, 1-1-1 Kohto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
Shigeyuki Yokoyama
1Jail cell-Free Science and Technology Research Center, 2Department of Applied Chemistry, Faculty of Engineering and threeVenture Concern Laboratory, Ehime Academy, iii, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan and fourDepartment of Biophysics and Biochemistry, School of Science, University of Tokyo, 3-7-one, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, vProtein Research Group, RIKEN Genomic Sciences Center, 1-seven-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan and 6Cellular Signaling Laboratory and Structurome Inquiry Group, RIKEN Harima Institute at Spring-8, 1-i-1 Kohto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
Received 2003 Jul 22; Revised 2003 Sep 10; Accustomed 2003 Sep 20.
Abstruse
Many tRNA molecules that recognize the purine-catastrophe codons but not the pyrimidine-catastrophe codons have a modified uridine at the wobble position, in which a methylene carbon is attached directly to position 5 of the uracil ring. Although several models have been proposed concerning the mechanism past which the v-substituents regulate codon-reading backdrop of the tRNAs, none could explain recent results of the experiments utilizing well-characterized modification-deficient strains of Escherichia coli. Here, nosotros first summarize previous studies on the codon-reading properties of tRNA molecules with a U derivative at the wobble position. Then, we propose a hypothetical mechanism of the reading of the G-ending codons by such tRNA molecules that could explicate the experimental results. The hypothesis supposes unconventional base pairs between a protonated class of the modified uridines and the G at the 3rd position of the codon stabilized by ii direct hydrogen bonds between the bases. The hypothesis too addresses differences between the prokaryotic and eukaryotic decoding systems.
INTRODUCTION
During protein biosynthesis, the ribosomes select correct aminoacyl-tRNA molecules one-by-one by recognizing the anticodon triplet of the tRNA molecule that fits to the A-site codon triplet. According to the wobble hypothesis (1), when a tRNA molecule is recognized as a right ane, the 3rd and 2nd nucleosides of the anticodon (positions 36 and 35, respectively) form Watson–Crick base of operations pairs with the first and 2d nucleosides of the codon, respectively, and the nucleoside at the start position of the anticodon (position 34) forms a Watson–Crick or a wobble base pair with the nucleoside at the third position of the codon (position Iii) (1). The base pairs immune between position 34 and position 3 were assumed to be but those that could form 2 or more than ii directly hydrogen bonds betwixt them with a small deportation from the position for the Watson–Crick base pair. A U-M pair with the U at position 34 could be formed with a small displacement of the uracil base toward the major groove side, while it was known at that time that uridines at position 34 are quite often post-transcriptionally modified.
Modified uridines found at position 34 of naturally occurring tRNA species are classified into two groups (Fig. i) (2). A modified uridine with a methylene carbon directly bonded to the C5 atom (xm5U) (Fig. 1a) is ofttimes found in tRNA species that recognize only the purine-catastrophe codons. The xmfiveU nucleosides are often thiolated at position ii (xmfivedue south2U) or methylated at the ribose 2′-hydroxyl group (xmfiveUm). A modified uridine with an oxygen atom direct bonded to the C5 cantlet of the uracil ring (xo5U) (Fig. aneb) is oft constitute in tRNA species that recognize the U-, A- and Thou-ending codons.
Chemical structures of modified uridines found at position 34 of tRNA species. Symbols of the 5-substituents are shown in parentheses.
In the nowadays paper, we apply an asterisk to stand for whatever substituent. For example, U* represents whatsoever of the naturally occurring modified and unmodified uridines. In the same way, xm5U* stands for any of the xm5U derivatives including xmvU, xm5southwardiiU and xm5Um. Parts of the nucleoside symbols, such as xm5 and s2, may also be used to correspond the substituents, as in Figure 1. 5′-Nucleotides may be symbolized such as pxo5U. The position of a codon nucleoside may exist shown in parentheses in Roman numerals, such as Grand(III), and the position of the anticodon nucleoside may be shown in the aforementioned fashion in Arabic numerals, such equally U(34).
The puckering equilibrium of the ribose band of the nucleosides in RNA molecules is generally biased to the C3′-endo form instead of the C2′-endo form, which is required for the formation of the typical A-form helices. This bias is as well observed in mononucleotides and nucleosides. In xm5U*, the ribose puckering is biased to the C3′-endo conformation to a greater extent than in unmodified U (3–6). On the other hand, the puckering equilibrium of pxofiveU is much shifted to the C2′-endo grade (three). It was also shown that a U in the C2′-endo conformation could basepair with another U through ii direct base–base hydrogen bonds past a model building study (three). Therefore, it was proposed that the modifications in xm5U* restricts, and the xo5 modification promotes, the formation of the U*(34)–U(III) pair (3). Information technology has been shown that the commutation of U(34) of the unmodified grade of Escherichia coli tRNAone Ser by mo5U(34) enhances the in vitro reading of the UCU codon (7).
It is noteworthy that this theory of the regulation of codon recognition at the level of the dynamic conformation of the nucleotides is based on the wobble hypothesis proposed by Crick (ane): ii direct hydrogen bonds are required between the bases at positions 34 and III. A machinery that does non require the two direct base of operations–base hydrogen bonds has also been proposed to contribute to the codon reading and is named as the 'ii out of iii' mechanism (8,9) (see below).
Recently, the physicochemical effects of the mnmv and sii modifications were elucidated in detail by NMR structural analyses of anticodon stalk–loop (ASL) oligonucleotides from E.coli tRNALys (10). The comparison of unlike ASLs with unlike modifications showed that the s2 modification enhances the stacking of the bases in positions 35 and 36 onto the three′ side of the anticodon to elevate the interaction of these bases with the offset and 2d bases of the codon. The mnm5 modification also reduces the flexibility of the anticodon and contributes to 'preorganize' the anticodon into an A-class structure gear up to interact with the codon in collaboration with the due south2 modification. This clearly explained the effects of each modification on the misreading of the AAU/C codons by the tRNA observed in vivo under an Asn starvation condition (11), with the assumption that the misreading primarily depends on the 'ii out of three' mechanism. Therefore, in this case, the 'ii out of iii' mechanism may dominate over the wobble machinery. Information technology is reasonable that, in such cases, the decoding properties of the modification-scarce tRNAs could not be predicted from the conformational properties of the nucleotide at position 34.
On the other mitt, the in vivo effects of the lack of each modification on the reading of the GAA/G codons by E.coli tRNAGlu with an mnm5siiU at position 34 were also measured with the modification mutants (12). Nonetheless, the information could not be explained completely even with the dynamic 3D structures of the ASLs (10), as described in item beneath. This may mean that some unknown mechanism, dissimilar from the conformational regulation, has some contribution to the codon reading by the tRNAs with mnmfives2U(34).
In the nowadays paper, we first summarize the known experimental results and theories on the furnishings of the xmv modification and on other related subjects. Then, nosotros propose a physicochemical model of xm5U(34)–Thou(Iii) pairing that could explain the in vivo furnishings of the mnmv and sii modifications on the reading of the purine-ending codons.
EXPERIMENTAL FACTS AND THEORIES
Views from tRNA limerick
Distribution and backdrop of xm 5 U*(34). In East.coli, mnmvsiiU(34) is institute in tRNALys, tRNAGlu and one of the two tRNAsGln (13). tRNA4 Leu and tRNA4 Arg have cmnm5Um(34) and mnm5U(34), respectively (6,fourteen). Many eubacteria too take the cmnmfive or mnmv modification in Leu (UUA/G), Gln, Lys, Glu and Arg (AGA/Yard) tRNA species (13). At least Due east.coli tRNALys, tRNAGlu and tRNA4 Leu could read the G-catastrophe codons: tRNALys and tRNAGlu are the single tRNA species for the amino acids (15), and a su6 strain in which simply tRNA4 Leu could read the UUG codon grows very well (6,16). tRNA4 Arg was suggested to read the AGG codon merely weakly (17), although the experimental results are not very conclusive: overproduction of tRNA4 Arg might have acquired undermodification, which might take led to overproduction of tRNA molecules that practise not recognize the AGG codon; and the tRNA species that compete with tRNA4 Arg in their frameshifting analysis were dissimilar between the assay of the AGA and AGG codons, which made direct comparison of the activities on the unlike codons difficult. Instead, the above in vivo experiment clearly showed that the tRNAGlu mutant with mnm5U(34) could read the GAG codon efficiently (12). Human mitochondrial tRNALeu (UUA/G) and tRNALys are besides the single tRNAs for the codons and have τm5U(34) and τmvsouthwardtwoU(34), respectively (eighteen).
Divergence in prokaryotic and eukaryotic systems. The substituents in the xm5U derivatives in prokaryotes and eukaryotes are different. Prokaryotic tRNAs have derivatives of mnm5U, and eukaryotic tRNAs have those of mcmvU or ncm5U (thirteen). Although many bacteria manipulate with some tRNAs with C(34) that would read the CAG, AAG or GAG codon, all eukaryotes and so far investigated accept the C(34)-containing tRNAs for these codons (19). Therefore, it is possible that the eukaryotic xm5U derivatives do not pair with M(Iii). It has also been suggested that eukaryotes cannot decode G-ending codons with tRNAs having a U derivative at position 34, based on the fact that they have at least a copy of an Ile tRNA cistron with a T at the beginning position of the anticodon (xx), although the postal service-transcriptional modifications of the Us are unknown (the tRNA would insert Ile for the Met codon if it could read the K-ending codon). This difference betwixt prokaryotes and eukaryotes could be ascribed to the difference in the ribosomes also equally the difference in the tRNA modifications. As for prokaryotes, nosotros focus on the modifications in eubacteria, as data on archaebacterial modifications is limited.
Barnyard reading by mitochondria and mycoplasma tRNA species with U(34). In mitochondria and mycoplasmas, many family codon boxes (a codon box is a set of four different codons that have the first two bases in mutual, and if it specifies a single amino acid in the genetic code, it is a family box) are each translated by only 1 tRNA species with unmodified U(34) (21–24). Therefore, information technology was proposed that this kind of undiscriminating codon reading is based on the 'two out of three' mechanism. In some cases, this barnyard codon reading was shown to be less significant in the split codon boxes (a split codon box is a codon box that specifies more than one amino acid) than in family boxes (8,9,25).
Unmodified U
In vitro translation assay and properties of undiscriminating tRNA species with unmodified U(34). It is important to understand the codon-reading backdrop of tRNA species with an unmodified U(34) before discussing the properties of the modified species. Well-nigh studies on such tRNA molecules utilize an in vitro translation system. It is well known that the discrimination of the third bases of the codons volition be ambiguous if only 1 aminoacyl-tRNA species is used in backlog to introduce radiolabeled amino acid into proteins (26). This could be so even in a separate codon box (27). It is besides known that the accuracy of in vitro translation is affected by the reaction atmospheric condition. For instance, pH and the concentrations of magnesium ions and polyamines could bear upon the fidelity of translation (28). Therefore, information technology is necessary to control the experimental conditions carefully. However, such assays accept been used successfully to determine the relative efficiency of a tRNA species in reading a codon as compared with that of some other competing tRNA species.
tRNAGly from Mycoplasma mycoides with U(34) is a single tRNA species for the four Gly codons (29). This tRNA reads all the four Gly codons fifty-fifty in an in vitro translation system from E.coli. It has as well been demonstrated that this barnyard codon reading requires a C at the start position of the anticodon loop (position 32) of the tRNA (30–33). Nevertheless, C(32) is very frequently found in tRNA molecules. Therefore, it likewise seems essential that the interaction of the '2 out of three' is strong enough to back up such ambiguous reading (25). These results also suggested that tRNAs with U(34) acquit differently in unlike situations apropos the bigotry of the third bases of the codons.
On the other hand, Mycoplasma capricolum has two Thr tRNAs with A(34) and U(34) (24). Although the tRNA with U(34) reads all the iv Thr codons, the reading of the ACC codon is weak when the tRNA with A(34) is competing in an in vitro translation organization from Yard.capricolum (34). The readings of the ACU and ACG codons by the tRNA with U(34) are also weaker than those past the tRNA with A(34). Thus, codon preferences could be observed in this case. Therefore, some interaction betwixt U(34) and the third base of operations of the codon contributes to the undiscriminating reading.
As information technology seems that at that place is some confusion in some of the literature concerning the use of the terms 'wobble mechanism' and 'two out of 3' machinery, nosotros define the meanings within this paper equally follows. The wobble machinery is a class of those mechanisms past which two or more direct hydrogen bonds are formed between the bases at positions 34 and III while two Watson–Crick base pairs are formed betwixt the last two positions of the anticodon and the commencement two positions of the codon. The 'two out of 3' mechanism is a class of those mechanisms by which less than two straight base–base hydrogen bonds are formed between positions 34 and III while two Watson–Crick base pairs are formed at the other 2 positions. A '2 out of iii' mechanism is one that satisfies the criteria for this particular mechanism. Therefore, a '2 out of three' machinery may involve some interaction without two direct base–base hydrogen bonds between positions 34 and Iii. A 'base pair' in this newspaper ways a pair of bases with two or more than than 2 direct hydrogen bonds betwixt them, unless mentioned otherwise. Some researchers apply the term '4-way wobble'. However, we exercise non use this term because it is for the machinery of the ambiguous recognition of the four different codons simply is not for the mechanism of recognition of individual codons.
Unexpected inefficiency in the reading of Chiliad-ending codons by unmodified tRNAs with U(34). Artificial unmodified tRNAs with U(34) have also been investigated with an in vitro translation organization. The in vitro transcript of E.coli tRNA1 Ser reads the UCA codon half equally efficiently as the fully modified molecules, but does not read the UCU and UCG codons (the UCU codon may exist recognized weakly) (35). A sample of the same tRNA prepared by chemical synthesis followed by enzymatic ligation had the same codon-reading backdrop, and the substitution of the U(34) past an mo5U enhanced the reading of the UCU and UCG codons (7). The transcripts with base changes at the second and third positions of the anticodon into AA, UC and CU, respectively, likewise read the A-catastrophe codons and did not read the Thou-ending codons (36). Thus, the U(34)–Thousand(Three) interaction is very weak at least with the structural context of the tRNA. As all of these unmodified tRNAs discriminate well the UCX codons, irrespective of C(32) that the tRNAs have, information technology is unlikely that any of the codon readings depends on a 'two out of three' mechanism. Therefore, U(34), which primarily assumes the C3′-endo form, cannot grade a base pair with K(3). Something other than the ribose puckering equilibrium should be different betwixt U(34) and xm5U*(34).
In vitro analyses of the effects of the xm5U* modifications
A-site bounden of ASL. Oligonucleotide-dependent ribosome-bounden experiments accept been used almost conveniently for the determination of codon-specificity of tRNAs. However, researchers should choose an experimental condition that gives reasonable results, equally some tRNAs demark strongly and the others demark weakly. All the same, many researchers have obtained reasonable results. Recently, 17mer ASL oligonucleotides were institute to bind to the ribosomes. Although they mainly bind to the P site in the original techniques, the binding to the A site could as well be measured as the tetracycline-sensitive bounden (37). With this technique, the effects of the mnm5s2U modifications were investigated (37). The results clearly showed that the mnm5 and s2 modifications enhance the A-site binding to the AAA and AAG codons, and that the efficiency of the A-site binding is ever in parallel with that of the P-site binding. The results from the P-site bounden assay showed that the ASLs with U(34) bind simply in the cases where the codon is from a family codon box. It is noteworthy that, although the GUG codon could bind the respective ASL with U(34) with a low analogousness, the GCG, UCG and CCG codons did non bind the ASLs with a measurable analogousness. This is consistent with the inefficiency observed for the reading of the G-ending codons past the unmodified tRNAs with U(34) during the in vitro translation assay mentioned above. Anyhow, the modifications are required for the U*(34)-containing ASLs to bind to the Chiliad-ending codons.
xm 5 U* from eukaryotes. An early piece of work has shown that a yeast tRNAGlu specifically translates the GAA codon in an in vitro translation organization from rabbit reticulocytes (38). This tRNA has mcm5siiU(34), and this may fit to the above idea that eukaryotes practise non use the U*(34)–G(3) wobbling (20). This tRNA was as well investigated by the conventional ribosome-binding method (38). The results were consequent with those from the in vitro translation assay, while the source of the ribosomes was E.coli. Therefore, it may exist the difference in tRNA just not that in the ribosomes that causes the difference in the codon specificity between eukaryotes and eubacteria at to the lowest degree in this case. It was also shown that yeast tRNA3 Arg with mcm5U(34) does not recognize the Chiliad-ending codon either (39). Therefore, the inability to recognize G(Iii) in tRNAGlu may be independent of the s2 modification.
In vivo experiments using modification mutant strains
Rates of translation of the GAA/M codons. The furnishings of the mnm5 and s2 modifications on the rates for the translation of the GAA and GAG codons were measured with the use of well-characterized E.coli mutants of the mnm5s2U modifications (12). The rates at which the GAG codon was translated in the strains with mnm5s2U(34), stwoU(34) and mnm5U(34) were 7.seven, ane.9 and 6.two codons/southward, respectively, and the rates of the reading of the GAA codon were 18, 47 and 4.5 codons/s, respectively. Therefore, the s2 modification of mnmvU elevates the reading of the GAA codon and has only a modest effect on the reading of the GAG codon, and the mnmfive modification of s2U restricts the reading of the GAA codon and enhances the reading of the GAG codon. Although the level of the available undermodified aminoacyl-tRNA species in each mutant was non clear, the elongation rates during the translation of the whole lacZ coding sequence were near the same for these mutants. Therefore, we believe that the results are highly reliable. Yet, these results cannot be explained completely by the 3D structures of the ASL variants as described in item below.
Results from frameshift assays. Brierley et al. (40) besides utilized the modification mutants of E.coli to determine the in vivo correlation betwixt the mnm5s2U modification and frameshifting efficiency at a coronavirus frameshift site. In their analysis, the frameshift efficiencies at the AAA/Thou codons in the modification mutant strains were measured. They tried to translate the results with the assumption that the frameshift efficiency should be negatively correlated with the stability of the codon bounden by the tRNALys species with different modifications. However, the frameshift efficiency may also be affected past the efficiency of the tRNA molecules to shift to the AAA codon in the –ane frame, and, if this was the rate-limiting step of the whole process, the frameshift efficiency should take reflected the relative efficiency to bind to the –1 frame codon as compared to the 0 frame codon. Therefore, interpretation of these results as related to the efficiency of the A-site codon binding is quite difficult, every bit pointed out in other papers (10,12).
Misreading of pyrimidine-ending codons. The same E.coli strains were used to analyze the efficiency of the misreading of the AAU/C Asn codons by the tRNALys modification mutants nether an Asn starvation condition (11). The results indicate that both mnmv and s2 modifications raise the misreading. These results were unexpected, because the modifications were thought to restrict wobbling at that time (iii), but were rationalized when the NMR structures of the wild type and mutant ASLs were revealed in particular (10) (run into below).
Physicochemical aspects
Conformational preferences of uridine derivatives and the expected basepairing pattern. Every bit described above, the conformation of xmfivesouthtwoU is biased to the C3′-endo form (three,4,41). This conformational preference is mainly due to the stwo modification, which would enhance steric repulsion betwixt the O2′ and the atom at position ii in the C2′-endo form. Therefore, 2′-O-methylation was likewise suggested to stabilize the C3′-endo grade. The xmfive modification also contributes to the stabilization of the C3′-endo form (v,10). By dissimilarity, pxo5U is much more in its C2′-endo form than pU. Although the mechanism of the preference is not clear, information technology was suggested to exist due to the interaction between the v′-phosphate and the oxygen atom of the xov substituent (3). With the C2′-endo form, U*(34) could basepair with U(3) if the codon and the second and third positions of the anticodon are in the A form, equally shown by a model building study. Therefore, it was proposed that the conformational restriction into the C3′-endo form in xm5U*(34) should prevent mispairing with U(III) and stabilize the correct pair with A(III) (3).
As long as the A-type RNA is causeless in the other parts of the codon–anticodon duplex, U(34) could not class a base of operations pair with C(Iii) because of steric hindrance (41,42). Therefore, the C2′-endo grade could not explain the reading of the C-catastrophe codons by mitochondrial and mycoplasma tRNAs with U(34). Although the anticodon loop of E.coli tRNALys was recently shown to accept a remarkable flexibility (x), information technology is well known that the 2′-hydroxyl groups of the five nucleosides of the codon–anticodon duplex except the first one of the anticodon are hydrogen-bonded to the ribosome at the A site (43). Thus, it is reasonable to consider that these five nucleosides should exist in the C3′-endo grade on the A site, no matter how flexible the conformation of the unbound anticodon loop is.
In the original hypothesis (3), the U*(34)-M(Iii) was idea to be possible with both of the C2′-endo and C3′-endo forms. However, the above in vitro translation experiments (4,35,36) showed that the U(34)–Thousand(Iii) pair with the C3′-endo form of the U should be weak. Thus, the xm5s2U(34)–G(Three) pair should be very weak, because the C2′-endo form of xm5due southtwoU should exist less stable than that of U and the Southward…H-N hydrogen bond required for the base pair should be weaker than the O…H-N bond required for the U-G pair. Therefore, the reading of the AAG and GAG codons by Due east.coli tRNALys and tRNAGlu, respectively, could non be rationalized by this theory, equally pointed out in an excellent review (44).
NMR structures of the modification variants of the tRNA Lys ASL. As described above, the physicochemical effects of the modifications in mnmfives2U in the tRNALys ASL accept been elucidated by NMR analyses (10). The due southtwo modification enhances the stacking of the 'two out of iii' onto the iii′-side of the anticodon, and the mnm5 modification decreases the flexibility of the loop.
As described above, the stabilization of the A-form construction of the anticodon resulted in the elevated misreading of the AAU/C Asn codons during the Asn starvation. This enhancement of the misreading could non exist predicted from the conformational properties of the nucleotides at position 34 (11). The prediction implied that the misreading should depend primarily on the wobble machinery with the U*(34)–U(III) base pair, instead of the 'two out of 3' mechanism. The fact that the AAC codons were also misread nether the starvation condition indicates that at to the lowest degree the misreading of the AAC codons depended on the 'two out of three' machinery. It is probable that the conformational restriction into the C3′-endo form by the modifications reduced the efficiency of the misreading by the wobble mechanism to the extent that it was lower than that by the 'ii out of iii' mechanism.
The s2 modification could be predicted to enhance the reading of the GAA codon from its structural furnishings, and it did in the in vivo experiment. In the case of the GAG codon, the exchange of O2 with a sulfur atom would destabilize the wobble base pair because the O2…H-N hydrogen bond would be substituted by a weak S2…H-N hydrogen bond, if any, while the stacking enhancement should more or less compensate for the destabilization (though this betoken is non described explicitly in the published material). Therefore, the small result on the reading of the GAG codon observed in the in vivo experiment could be rationalized. On the other hand, the mnmfive modification should stabilize the interaction with A(III), as it should stabilize the 'preorganized' conformation. This contradicts to the in vivo data. As for G(Iii), if the mnm5s2U(34)–G(Three) base pair is formed with the C2′-endo form of the mnm5due south2U, then the mnm5 modification should reduce the reading of the G-ending codon because information technology should destabilize the C2′-endo form, which is again contradictory to the in vivo result. This may mean that the mnm5siiU(34)–One thousand(III) pair with the C3′-endo course of the mnm5siiU is stabilized by the mnmv modification through some unknown mechanism.
Thermodynamic analyses. Stabilities of RNA duplexes could be estimated by measuring the melting profiles of the duplexes. Many oligonucleotides containing modified nucleosides have been studied by this method. Information technology should be noted that the contribution of a single base pair to the stability of the duplex could not be divers because a base of operations pair should affect the neighboring base pair interactions. However, a sum of costless free energy parameters for all the pairs of neighboring ii base pairs in the duplex, plus the parameters for the terminal base pairs and other constants, could exist a good estimation of the stability of the duplex (45,46). Substitution of an A-U pair in the center of an RNA duplex by a G-U pair would usually destabilize the duplex, and the free energy difference could be estimated easily if the neighboring base of operations pairs are known. In the same mode, the effect of the substitution of a terminal A-U pair by a G-U pair could be estimated. Even so, this commutation turns out to exist non-destabilizing or even stabilizing, in general, when the A and G are at the 5′-ends of the duplexes and the Us are at the three′-ends (46). Codon–anticodon duplexes with U(Iii) are in a similar situation to the latter case, as position 34 is at the 5′-stop of the codon–anticodon duplex. It has besides been observed that the substitution of A(34) past a Thousand in a series of unmodified tRNAs raises, or does non change, the efficiencies to read the U-ending codons in an in vitro translation organisation (36). Therefore, the furnishings of a modification of U(34) could not be estimated from the stabilities of RNA duplexes with the modified uridines in the center or at the 3′-end of the duplexes. There have been no experiments in which the effects of the five-substitution of uridines at the 5′-terminate of RNA duplexes are estimated, although even this blazon of experiment would not necessarily be promising in terms of the estimation of the effects of the modification on tRNA codon recognition.
Model-building written report (Lim's model). Lim and coworkers have proposed a model that explains the codon-reading patterns as related to the properties of the nucleosides at position 34 (42,47). In the model, U(34) could interact with U(III) and C(III) through h2o bridges, and a tRNA with U(34) reads all the four bases at position Three. Therefore, the model may be useful to predict codon preferences when the family codons are not fully discriminated. The mnm5 substitution would break some bonds needed for the water-bridged pairs, and this loss of the stabilizing interaction would non be compensated. Therefore, the modification should restrict the germination of the water-bridged pairs. All the same, it is obvious that this model does not take into account that the strength of the interaction between the beginning two codon positions and the terminal two anticodon positions could be changed by the due southii and xmfive modifications (10). Therefore, the model could non predict the in vivo effects of the modification (11,12).
A MODEL OF THE xm5U(34)–One thousand(III) BASEPAIRING
Here, we propose a model of the xmfiveU*(34)–One thousand(Iii) pairing, by which the in vivo furnishings of each modification on the codon-reading rates and the prokaryote/eukaryote difference of the wobble rule concerning the U*(34)–G(Three) pairing could be rationalized. The xmvU nucleosides from prokaryotes and mitochondria are derivatives of 5-aminomethyluridine (xnm5U*), while those from eukaryotes are not (13). As for xnm5U*, the 5-substituent is probable to lower pK a at the N3 position of the uracil ring, considering the positively charged nitrogen atom of the substituent should withdraw electrons from the uracil ring. Thus, xnm5U* may partially ionize nether the physiological condition. The ionized form of the nucleoside (xnmvU*-) could base pair with Grand(III) in two different configurations (Fig. 2a and b). In the case of the 2-thiolated uridines, the ionization could confer a negative charge on the sulfur atom and catechumen information technology to an efficient proton acceptor. The ionized form would exist able to pair just with G(3), and the neutral form, which may be symbolized here equally xnm5U*0, could pair only with A(III). Both pairs could exist formed with the C3′-endo conformation. Thus, the stabilization of the C3′-endo form by the modifications would stabilize both pairs. We suppose that the ionization should be partial. The relative efficiency in the reading of the G-ending codon to that of the A-catastrophe codon would not merely depend on the caste of the ionization, but would also depend on the difference in the intrinsic stabilities between the xnm5U*-(34)–G(III) and xnm5U*0(34)–A(Iii) pairs. Therefore, an xnm5U* could pair with Thou(Three) more efficiently than with A(Iii) even when the neutral course is the major species. In the example of mnn5s2U, the pairing in the neutral form with A(Three) may be still more efficient, in full, than the pairing in the ionized form with Thou(III). The ionized modified uridine would non pair with U(III) or C(3). As the eukaryotic xm5 substituents do not withdraw electrons every bit xnm5 may do, the eukaryotic tRNAs do non recognize the K-ending codons.
The proposed base pairs between a deprotonated modified U and a G proposed in the present written report (a and b) and the conventional wobble U–G pair (c). (a) The proposed xnmvU*- –One thousand pair with the Watson–Crick configuration; (b) the alternative xnm5U*- –Grand pair with the xnm5U*- displaced toward the pocket-size groove side from the Watson–Crick configuration; (c) the conventional wobble U-M pair. The sulfur atom in (a) and (b) could be substituted with an oxygen cantlet, and the negative accuse could be delocalized within the π-electron system.
HOW THE MODEL FITS TO THE KNOWN FACTS AND THEORIES
Hammett equation and the known pK a values for uridine and uracil derivatives. The pK a values of a series of substituted compounds could exist well predicted using the Hammett equation (48), as described in many organic chemistry textbooks. pK a of a substituted molecule is predicted to be lower than the unsubstituted one by σ times ρ, where σ is a constant specific to the substituent and its position, and ρ is a abiding specific to the core acid. Equally judged from the known pK a values for several uracil derivatives (U, ix.3; m5U, ix.7; and 1-methyl-five-bromouracil, 7.8) (49) and the σ values for the meta position (methyl, –0.07 and bromo, 0.39), ρ for uracil should be positive (and ∼5).
The effects of substitutions at aromatic rings are mainly ascribed to two factors: inductive electron withdrawal and the resonance electron donation by the substituent. In the instance of the xnm5 substituent, the resonance effect may be small because of the methylene grouping directly attached to the uracil ring, and the anterior effect may be large because the nitrogen atom is protonated and is positively charged. Therefore, it is expected that the anterior consequence dominates over the resonance issue, and the pK a of mnm5U should be significantly lower than that of U. In fact, the pYard a values of cmnm5Um and cmnm5U have been measured to be 8.3 and 8.2, respectively (6). As the negative charge of the carboxyl group of the cmnm5 substituent may somewhat neutralize the electron withdrawing effect of the charged nitrogen, it is expected that the pYard a value for mnm5U is non ≤viii.2. Furthermore, as pG a for due south2U (eight.8) is lower than that for U by ∼0.v, information technology is expected that pK a for mnmfivesiiU should be <viii.
pK a values for the uracil N3 position are lower in nucleosides than in the corresponding nucleotides, in general, considering of the negative charge of the phosphate grouping. In fact, the measured values (pU, 9.seven; pm5U, 10.one; 5-bromouridine 5′-monophosphate, 8.1) (50) are higher than those of the corresponding nucleosides by ∼0.4. We have to exist careful when comparison pChiliad a values measured under different weather because the outcome of the charge of the phosphate may depend on the ion strength and probably on the conformational preference of the nucleotide. However, information technology is still reasonable to assume that the pChiliad a value for pmnm5siiU may be higher than that of the nucleoside by ∼0.four.
The environment effectually the uracil ring on the decoding site of the ribosome may also bear on the pK a values. However, from the recent results of the X-ray crystallographic analyses of the ribosome (51), we could run into that the charged group nearest to the kickoff base of the anticodon of the A-site-bound tRNA is its 5′-phosphate, and that the altitude of the phosphate from the uracil band may exist almost the same as in the free nucleotide. Therefore, there is no reason now to consider that the pK a values on the ribosome are much college than those in the corresponding nucleotides.
If the pK a value of a molecule is 8.iv, for instance, a 9% fraction of the molecule is ionized nether pH 7.4. Therefore, it is reasonable to assume that a considerable fraction of mnm5south2U in tRNA is ionized under the physiological condition.
Two possible configurations. Two different configurations might be possible for the pair between xnm5U*-(34) and K(III) (Fig. 2a and b). We wait that the one with the Watson–Crick configuration (a) should be more than stable than the i with the wobble configuration in which the xnmvU*- is displaced toward the minor groove side (b). However, it is all the same possible that the latter configuration could contribute significantly. The pair may be possible with the same ribose–phosphate conformation as in the Grand(34)–U(Three) wobble pair, which could exist stabilized by the stacking onto the neighboring base pair (two), and was shown to be no less stable than the A(34)–U(Three) pair in a jail cell-free translation assay (36), as stated above. Thus, the wobble form of the xm5U*-(34)–One thousand(3) pair might be stabilized by the aforementioned mechanism. In addition, as the sulfur atom of the wobble xnm5stwoU*-(34)–Chiliad(Three) pair should not participate in the hydrogen bonding interactions, the pair could be more stable than the pair with the Watson–Crick configuration. The possibility of the dual-manner base pairing itself might also contribute to the enhancement of the reading of the G-catastrophe codon.
Physicochemical and biological furnishings of the mnm five s 2 U(34) modifications. Every bit mentioned above, it is expected that the s2 modification of xnm5U decreases the pK a value. Therefore, the modification should promote the deprotonation. In improver, the s2 modification should promote the stacking of the anticodon as in tRNALys (10) and stabilize the C3′-endo form of the nucleoside. If, for example, the conformational event stabilizes the pair by v-fold and the fraction of the ionized form increased by the thiolation is twenty%, then the full result should exist stabilization by 4-fold (though this may be an oversimplification). Therefore, the xnm5U-to-xnm5south2U modification should enhance the reading of the A-catastrophe codon. This is consistent with the case of E.coli tRNAGlu (12). Equally for the M-catastrophe codon, the xnm5s2U-–Chiliad pair could be weaker in itself than the xmn5U-–M pair, because at least ane of the two possible base pair configurations in the former (Fig. 2) needs a hydrogen bond that involves the sulfur atom. Therefore, it is possible that this outcome cancels the conformational effects. This is not contradictory to the fact that the s2 modification of tRNAGlu had just a pocket-size effect on the reading of the GAG codon in vivo (12). The experimental results also betoken that the reading of the GAG codon past the tRNA with mnm5U(34) is more than efficient than the reading of the GAA codon (12), and this could be reasoned if we assume that the mnm5U-–G pair might be intrinsically much more stable than the mnm5U0–A pair.
The mnm5 modification of s2U would cause the partial ionization, which would destabilize the pair with A(III) and stabilize the pair with G(III), and the restriction of the flexibility of the anticodon, which would stabilize both pairs through stabilizing the C3′-endo form. Therefore, the pair with Chiliad(Iii) should be stabilized, while the prediction of the furnishings on the pair with A(Iii) is more difficult. The conformational outcome might be smaller for the s2U-to-mnm5southward2U modification than for the U-to-mnm5U modification, equally the s2U-containing anticodon is already much biased to the preorganized conformation (10). On the other paw, the subtract in the fraction of the neutral form required for the pairing with A(Three) by the lowering of pK a should be larger in the presence of the stwo modification, as s2U has a lower pK a value than U. Thus, the mnmv modification might exist more destabilizing equally for the pair with A(III) in thiolated uridines than in not-thiolated uridines. In the case of tRNAGlu (12), the effect through the deprotonation may have been larger than the conformational effect. As xnm5U-* could grade no base pair with U(Three) or C(3), the observed misreading of the AAU/C codons by tRNALys during Asn starvation (eleven) should not have been due to the ionized form.
2-Selenouridine derivatives. Bacteria modifies mnm5s2U(34) into five-methylaminomethyl-2-selenouridine (mnm5SetwoU), when selenium is available (52). The pK a value for this nucleoside is ∼7.1, and a glutamate tRNA with mnm5Se2U(34) binds efficiently to the GAG codon (53). Thus, it has been proposed that the ionized course is responsible for the base pairing with G(III) (53). It seems that the low pK a was considered to be mainly due to the 2-seleno substitution, but the mnm5 substitution might also contribute.
xo v U. xo5U(34) has been proposed to recognize G(III) with the C2′-endo conformation (3,7). If the pGrand a value for pxo5U is depression plenty, it would be also possible that xo5U(34) could also be partially ionized. In fact, the pYard a value for pmo5U has been measured to exist 8.96 (l). The pThou a values for the xo5U nucleosides could also be predicted based on Hammett equation: pK a for mo5U and ho5U could be predicted to be ∼eight.vii, using the σ values for the methoxy and hydroxyl substituents at the meta position (0.12) and the above-estimated ρ value for uracil. Therefore the predicted value is consequent because the effect of the 5′-phosphate. In cmo5U, the pK a could be higher than in mo5U because of the negative charge in the carboxyl group. Thus, merely a small fraction could be ionized in these nucleotides under the physiological condition. In addition, the C3′-endo conformation is destabilized in these nucleotides. Therefore, it may be reasonable to consider that the main mechanism for the Thousand(III) recognition should be the germination of the neutral xovU(34)–Thousand(Iii) pair with the C2′-endo form of xo5U.
Eukaryotic xm 5 U* nucleosides. In mcm5U* and ncmfiveU* found in eukaryotic tRNAs (13,54), the substituents are unlikely to withdraw electrons as well as the xnm5 grouping may do. Therefore, information technology could be predicted that the tRNAs with the nucleoside could non pair efficiently with G(III). The experimental facts are as described above, and the Grand-catastrophe codons in eukaryotes seem to be recognized past tRNAs with C(34) in general (19,54). This could be an explanation for the prokaryote/eukaryote departure of the wobble dominion, if any, though it is still possible that the ribosomes are besides dissimilar. It is possible that the tRNA modifications and ribosome functions have coevolved to optimize the translational role. If the present model is correct, it would mean that the eukaryotic ribosomes dispense with the C2′-endo conformation of U*(34) and a wobble pair with the anticodon base shifted toward the major groove, as eukaryotes do not have xo5U(34) (13). Thus, it is possible that the eukaryotic ribosomes take lost the ability to accept eubacterial tRNAs with xovU(34) for the reading of the U- and G-ending codons.
TESTING THE MODEL
An obvious experimental test of the model is to measure the pK a values of the modified uridines. This could disprove the model if the pK a values for mnm5U* or τm5U* are non lower than ∼8.v, which is unlikely because the values for cmnm5U and cmnm5Um.
Some other possible experiment may be to mensurate the pH dependence of the relative efficiency of the U*(34)-containing tRNA in the reading of the G-catastrophe codon every bit compared to the efficiency of the tRNA with C(34) (35). However, the experiment could exist difficult because the overall fidelity in cell-gratis translation from E.coli depends on pH (28). Conventional ribosome-binding experiments and other advanced A-site binding methods may also exist possible (37,55).
It is known that mnmfives2U(34) in tRNA molecules could be reversibly oxidized by iodine (56). Therefore, it may exist possible to test the pH sensitivity of this reaction using prokaryotic and eukaryotic tRNA molecules, as the fraction of the ionized species should direct correlate with the reactivity. It may besides be possible to guess the pK a values of xnmfiveU* in tRNA molecules by measuring the pH-dependence of the aminoacylation reactions catalyzed by the respective aminoacyl-tRNA synthetases. Fortunately, bacterial Lys-, Glu- and Gln-tRNA synthetases are in direct contact with position 34 when complexed with the cognate tRNA molecules (57–59).
It may also be possible to mensurate the efficiency of the reading of a codon with an inosine at the third position. If the displacement of the uracil ring of the modified uridine to the major groove side is possible, it is expected that the I(III)-containing codon also could be recognized (see Fig. 2c). On the other hand, if the ionization is responsible for the pairing with G(Three), the codon with I(III) could not be recognized. Some other methods may also be possible that could determine whether the 2-amino group of G(III) participates in the base pair hydrogen bonding.
The 3D structure of the decoding site is emerging in detail in these years (43,51,threescore,61). However, the position of the base of 1000(34) in the crystal was somewhat deviated from the normal wobble configuration. Therefore, it may still have some time to localize the uracil ring of some of the modified uridines on the A site precisely enough to tell the base pair configuration.
ACKNOWLEDGEMENTS
We thank Dr Mitsuo Sekine (Tokyo Institute of Technology) and Dr Kensaku Sakamoto (Tokyo University) for discussion. This work was supported in part by the Sumitomo Foundation, Tokyo, Japan (no. 020764).
REFERENCES
1. Crick F.H.C. (1966) Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol., nineteen, 548–555. [PubMed] [Google Scholar]
ii. Mizuno H. and Sundaralingam,M. (1978) Stacking of Crick wobble pair and Watson–Crick pair: stability rules of G-U pairs at ends of helical stems in tRNAs and the relation to codon–anticodon wobble interaction. Nucleic Acids Res., 5, 4451–4461. [PMC free commodity] [PubMed] [Google Scholar]
3. Yokoyama S., Watanabe,T., Murao,Thousand., Ishikura,H., Yamaizumi,Z., Nishimura,S. and Miyazawa,T. (1985) Molecular mechanism of codon recognition by tRNA species with modified uridine in the showtime position of the anticodon. Proc. Natl Acad. Sci. Us, 82, 4905–4909. [PMC free article] [PubMed] [Google Scholar]
4. Agris P.F. (1991) Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified wobble hypothesis. Biochimie, 73, 1345–1349. [PubMed] [Google Scholar]
5. Sakamoto Thousand., Kawai,G., Watanabe,Southward., Niimi,T., Hayashi,Due north., Muto,Y. Watanabe,G., Satoh,T., Sekine,Thou. and Yokoyama,S. (1996) NMR studies of the effects of the 5′-phosphate group on conformational backdrop of 5-methylaminomethyluridine found in the beginning position of the anticodon of Escherichia coli tRNAiv Arg. Biochemistry, 35, 6533–6538. [PubMed] [Google Scholar]
vi. Horie N., Yamaizumi,Z., Kuchino,Y., Takai,K., Goldman,Due east., Miyazawa,T., Nishimura,S. and Yokoyama,South. (1999) Modified nucleoside in the first positions of the anticodons of tRNAfour Leu and tRNAv Leu from Escherichia coli. Biochemistry, 38, 207–217. [PubMed] [Google Scholar]
7. Takai K., Okumura,S., Hosono,K., Yokoyama,S. and Takaku,H. (1999) A single uridine modification at the wobble position of an artificial tRNA enhances wobbling in an Escherichia coli cell-free translation system. FEBS Lett., 447, one–4. [PubMed] [Google Scholar]
eight. Lagerkvist U. (1978) 'Two out of three': an culling method for codon reading. Proc. Natl Acad. Sci. Us, 75, 1759–1762. [PMC free commodity] [PubMed] [Google Scholar]
ix. Lagerkvist U. (1981) Unorthodox codon reading and the development of the genetic lawmaking. Cell, 23, 305–306. [PubMed] [Google Scholar]
ten. Sundaram Yard., Durant,P.C. and Davis,D.R. (2000) Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-plow structure. Biochemistry, 39, 12575–12584. [PubMed] [Google Scholar]
xi. Hagervall T.G., Pomerantz,S.C. and McCloskey,J.A. (1998) Reduced misreading of asparagine codons past Escherichia coli tRNALys with hypermodified derivatives of 5-methylaminomethyl-2-thiouridine in the wobble position. J. Mol. Biol., 284, 33–42. [PubMed] [Google Scholar]
12. Krüger M.Chiliad., Pedersen,S., Hagervall,T.Chiliad. and Sørensen,M.A. (1998) The modification of the wobble base of operations of tRNAGlu modulates the translation rate of glutamic acrid codons in vivo. J. Mol. Biol., 284, 621–631. [PubMed] [Google Scholar]
13. Rozenski J., Crain,P.F. and McCloskey,J.A. (1999) The RNA Modification Database: 1999 update. Nucleic Acids Res., 27, 196–197. [PMC free commodity] [PubMed] [Google Scholar]
fourteen. Sakamoto 1000., Kawai,G., Niimi,T., Satoh,T., Sekine,M., Yamaizumi,Z., Nishimura,Due south., Miyazawa,T. and Yokoyama,Due south. (1993) A modified uridine in the first position of the anticodon of a minor species of arginine tRNA, the argU gene production, from Escherichia coli. Eur. J. Biochem., 216, 369–375. [PubMed] [Google Scholar]
xv. Komine Y., Adachi,T., Inokuchi,H. and Ozeki,H. (1990) Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J. Mol. Biol., 212, 579–598. [PubMed] [Google Scholar]
sixteen. Yoshimura M., Inokuchi,H. and Ozeki,H. (1984) Identification of transfer RNA suppressors in E. coli. IV. Bister suppressor Su+six a double mutant of a new species. J. Mol. Biol., 177, 627–644. [PubMed] [Google Scholar]
17. Spanjaard R.A., Chen,K., Walker,J.R. and van Duin,J. (1990) Frameshift suppression at tandem AGA and AGG codons by cloned tRNA genes: assigning a codon to argU tRNA and T4 tRNAArg. Nucleic Acids Res., 18, 5031–5036. [PMC free article] [PubMed] [Google Scholar]
18. Suzuki T., Suzuki,T., Wada,T., Saigo,Grand. and Watanabe,Chiliad. (2002) Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and man mitochondrial diseases. EMBO J., 21, 6581–6589. [PMC free article] [PubMed] [Google Scholar]
nineteen. Marck C. and Grosjean,H. (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA, 8, 1189–1232. [PMC gratis commodity] [PubMed] [Google Scholar]
20. Percudani R. (2001) Restricted wobble rules for eukaryotic genomes. Trends Genet., 17, 133–135. [PubMed] [Google Scholar]
21. Barrell B.G., Anderson,S., Bankier,A.T., de Bruijn,M.H., Coulson,A.R., Drouin,J., Eperon,I.C., Nierlich,D.P., Roe,B.A., Sanger,F., Schreier,P.H., Smith,A.J., Staden,R. and Young,I.G. (1980) Different pattern of codon recognition past mammalian mitochondrial tRNAs. Proc. Natl Acad. Sci. USA, 77, 3164–3166. [PMC free article] [PubMed] [Google Scholar]
22. Bonitz S.G., Berlani,R., Coruzzi,Thou., Li,Chiliad., Macino,Grand., Nobrega,F.G., Nobrega,Thou.P., Thalenfeld,B.E. and Tzagoloff,A. (1980) Codon recognition rules in yeast mitochondria. Proc. Natl Acad. Sci. USA, 77, 3167–3170. [PMC gratuitous article] [PubMed] [Google Scholar]
23. Heckman J.E., Sarnoff,J., Alzner-DeWeerd,B., Yin,S., RajBhandary,U.50. (1980) Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc. Natl Acad. Sci. Us, 77, 3159–3163. [PMC free commodity] [PubMed] [Google Scholar]
24. Andachi Y., Yamao,F., Muto,A. and Osawa,S. (1989) Codon recognition pattern as deduced from sequences of the complete gear up of transfer RNA species in Mycoplasma capricolum. J. Mol. Biol., 209, 37–54. [PubMed] [Google Scholar]
25. Lustig F., Elias,P., Axberg,T., Samuelsson,T., Tittawella,I. and Lagerkvist,U. (1981) Codon reading and translational error. Reading of the glutamine and lysine codons during protein synthesis in vitro. J. Biol. Chem., 256, 2635–2643. [PubMed] [Google Scholar]
26. Mitra S.K., Lustig,F., Åkesson,B., Axberg,T., Elias,P. and Lagerkvist,U. (1979) Relative efficiency of anticodons in reading the valine codons during poly peptide synthesis in vitro. J. Biol. Chem., 254, 6397–6401. [PubMed] [Google Scholar]
27. Takai Thou., Horie,N., Yamaizumi,Z., Nishimura,S., Miyazawa,T. and Yokoyama,Southward. (1994) Recognition of UUN codons by two leucine tRNA species from Escherichia coli. FEBS Lett., 344, 31–34. [PubMed] [Google Scholar]
28. Bartetzko A. and Nierhaus,1000.H. (1988) Mg2+/NH4 +/polyamine organisation for polyuridine-dependent polyphenylalanine synthesis with nearly in vivo characteristics. Methods Enzymol., 164, 650–658. [PubMed] [Google Scholar]
29. Samuelsson T., Axberg,T., Borén,T. and Lagerkvist,U. (1983) Anarchistic reading of the glycine codons. J. Biol. Chem., 258, 13178–13184. [PubMed] [Google Scholar]
30. Lustig F., Borén,T., Guindy,Y.Due south., Elias,P., Samuelsson,T., Gehrke,C.W., Kuo,K.C. and Lagerkvist,U. (1989) Codon bigotry and anticodon structural context. Proc. Natl Acad. Sci. USA, 86, 6873–6877. [PMC free article] [PubMed] [Google Scholar]
31. Claesson C., Samuelsson,T., Lustig,F. and Borén,T. (1990) Codon reading properties of an unmodified transfer RNA. FEBS Lett., 273, 173–176. [PubMed] [Google Scholar]
32. Lustig F., Borén,T., Claesson,C., Simonsson,C., Barciszewska,K. and Lagerkvist,U. (1993) The nucleotide in position 32 of the tRNA anticodon loop determines ability of anticodon UCC to discriminate among glycine codons. Proc. Natl Acad. Sci. USA, 90, 3343–3347. [PMC free commodity] [PubMed] [Google Scholar]
33. Claesson C., Lustig,F., Borén,T., Simonsson,C., Barciszewska,M. and Lagerkvist,U. (1995) Glycine codon bigotry and the nucleotide in position 32 of the anticodon loop. J. Mol. Biol., 247, 191–196. [PubMed] [Google Scholar]
34. Inagaki Y., Kojima,A., Bessho,Y., Hori,H., Ohama,T. and Osawa,S. (1995) Translation of synonymous codons in family boxes by Mycoplasma capricolum tRNAs with unmodified uridine or adenosine at the first anticodon position. J. Mol. Biol., 251, 486–492. [PubMed] [Google Scholar]
35. Takai Yard., Takaku,H. and Yokoyama,South. (1996) Codon-reading specificity of an unmodified form of Escherichia coli tRNAone Ser in cell-free protein synthesis. Nucleic Acids Res., 24, 2894–2899. [PMC gratuitous article] [PubMed] [Google Scholar]
36. Takai K., Takaku,H. and Yokoyama,S. (1999) In vitro codon-reading specificities of unmodified tRNA molecules with different anticodons on the sequence background of Escherichia coli tRNAane Ser. Biochem. Biophys. Res. Commun., 257, 662–667. [PubMed] [Google Scholar]
37. Yarian C., Townsend,H., Czestkowski,West., Sochacka,East., Malkiewicz,A.J., Guenther,R., Miskiewicz,A. and Agris,P.F. (2002) Accurate translation of the genetic code depends on tRNA modified nucleosides. J. Biol. Chem., 277, 16391–16395. [PubMed] [Google Scholar]
38. Sekiya T., Takeishi,K. and Ukita,T. (1969) Specificity of yeast glutamic acid transfer RNA for codon recognition. Biochim. Biophys Acta, 182, 411–426. [PubMed] [Google Scholar]
39. Weissenbach J. and Dirheimer,G. (1978) Pairing properties of the methylester of 5-carboxymethyl uridine in the wobble position of yeast tRNA3 Arg. Biochim. Biophys Acta, 518, 530–534. [PubMed] [Google Scholar]
40. Brierley I., Meredith,M.R., Bloys,A.J., Hagervall,T.G. (1997) Expression of a coronavirus ribosomal frameshift signal in Escherichia coli: influence of tRNA anticodon modification on frameshifting. J. Mol. Biol., 270, 360–373. [PMC free article] [PubMed] [Google Scholar]
41. Yokoyama Southward. and Nishimura,Southward. (1995) Modified nucleosides and codon recognition. In: Söll,D. and RajBhandary,U. (eds), tRNA: Structure, Biosynthesis and Office. ASM Press, Washington, DC, pp. 207–223. [Google Scholar]
42. Lim V.I. and Venclovas,C. (1992) Codon-anticodon pairing. A model for interacting codon-anticodon duplexes located at the ribosomal A- and P-sites. FEBS Lett., 313, 133–137. [PubMed] [Google Scholar]
43. Ogle J.M., Carter,A.P. and Ramakrishnan,V. (2003) Insights into the decoding mechanism from contempo ribosome structures. Trends Biochem. Sci., 28, 259–266. [PubMed] [Google Scholar]
44. Curran J.F. (1998) Modified nucleosides in translation. In: Grosjean,H. and Benne,R. (eds), Modification and Editing of RNA. ASM Press, Washington, DC, pp. 493–516. [Google Scholar]
45. Tinoco I. Jr, Tapping,P.North., Dengler,B., Levine,Chiliad.D., Uhlenbeck,O., Crothers,D.One thousand. and Gralla,J. (1973) Improved estimation of secondary structure in ribonucleic acids. Nature New Biol., 246, xl–41. [PubMed] [Google Scholar]
46. Turner D.H., Sugimoto,N. and Freier,S.Chiliad. (1988) RNA structure prediction. Ann. Rev. Biophys. Biophys. Chem., 17, 167–192. [PubMed] [Google Scholar]
47. Lim V.I. and Curran,J.F. (2001) Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure. RNA, vii, 942–957. [PMC free article] [PubMed] [Google Scholar]
48. Hammett L.P. (1970) Physical Organic Chemistry, 2nd Ed. McGraw Hill, New York, NY. [Google Scholar]
49. Saenger W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York, NY. Japanese translation by Nishimura,Y., Springer-Verlag Tokyo, Nippon. [Google Scholar]
50. Shibaev V.N., Eliseeva,G.I. and Kochetkov,N.K. (1975) Interaction of uridine diphosphate glucose analogs with calf liver uridine diphosphate glucose dehydrogenase. Influence of substituents at C-5 of pyrimidine nucleus. Biochim. Biophys Acta, 403, nine–16. [PubMed] [Google Scholar]
51. Ogle J.One thousand., Brodersen,D.E., Clemons,W.M.,Jr, Tarry,M.J., Carter,A.P., Ramakrishnan,V. (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science, 292, 897–902. [PubMed] [Google Scholar]
52. Wittwer A.J., Tsai,L., Ching,Westward.M. and Stadtman,T.C. (1984) Identification and synthesis of a naturally occurring selenonucleoside in bacterial tRNAs: 5-[(methylamino)methyl]-two-selenouridine. Biochemistry, 23, 4650–4655. [PubMed] [Google Scholar]
53. Ching West.K. (1986) Characterization of selenium-containing tRNAGlu from Clostridium sticklandii. Arch. Biochem. Biophys., 244, 137–146. [PubMed] [Google Scholar]
54. Björk Chiliad. (1998) Appendix 6: Modified nucleosides at positions 34 and 37 of tRNAs and their predicted coding capacities. In: Grosjean,H. and Benne,R. (eds), Modification and Editing of RNA. ASM Press, Washington, DC, pp. 577–581. [Google Scholar]
55. Phelps Due south.R., Jerinic,O. and Joseph,S. (2002) Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Mol. Jail cell, 10, 799–807. [PubMed] [Google Scholar]
56. Carbon J.A., Hung,50. and Jones,D.Southward. (1965) A reversible oxidative inactivation of specific transfer RNA species. Proc. Natl Acad. Sci. USA, 53, 979–986. [PMC free article] [PubMed] [Google Scholar]
57. Cusack S., Yaremchuk,A. and Tukalo,1000. (1996) The crylstal structures of T.thermophilus lysyl-tRNA synthetase complexed with Eastward.coli tRNALys and a T.thermophilus tRNALys transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J., xv, 6321–6334. [PMC free commodity] [PubMed] [Google Scholar]
58. Rould One thousand.A., Perona,J.J., Söll,D. and Steitz,T.A. (1989) Construction of East. coli glutaminyl-tRNA synthetase complexed with tRNAGln and ATP at 2.8 Å resolution. Science, 246, 1135–1142. [PubMed] [Google Scholar]
59. Sekine S., Nureki,O., Shimada,A., Vassylyev,D.G. and Yokoyama,S. (2001) Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Nat. Struct. Biol., 8, 189–191. [PubMed] [Google Scholar]
60. Ramakrishnan 5. (2002) Ribosome construction and the machinery of translation. Cell, 108, 557–572. [PubMed] [Google Scholar]
61. Ogle J.M., Murphy,F.Five., Tarry,Yard.J. and Ramakrishnan,V. (2002) Pick of tRNA past the ribosome requires a transition from an open to closed form. Jail cell, 111, 721–732. [PubMed] [Google Scholar]
Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press
Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC275538/
0 Response to "According to Wobble Rules, What Codons Should Be Recognized by the Anticodon 5ã¢â‚¬â²-gcu-3ã¢â‚¬â²?"
Enviar um comentário