Relation between aminoacyl-tRNA stability and the fixed amino acid

Hentzen, Danièle; Mandel, P.; Garel, Jean‐Pierre

doi:10.1016/0005-2787(72)90174-8

Cited by 83 publications

(58 citation statements)

References 15 publications

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“…Similar effects were observed with other model aminoacyl esters (55)(56)(57). Steric factors affect the rates of catalyzed (Table 1) and uncatalyzed (43) reactions to a similar extent, with a rate difference of ϳ3.5-fold between Ala and Val. This suggests that the sensitivity to steric effects is likely to be intrinsic to aminolysis and not altered by the ribosome to any appreciable extent.…”

Section: 22 and 43) Experiments With Trnasupporting

confidence: 71%

“…The side chains of Ala, Phe, Val, and Ser are uncharged, but sterically different (52)(53)(54). Depending on the C-terminal amino acid, the hydrolysis rate decreases in the order Ala Ͼ (Ser, Phe) Ͼ Val on the ribosome and in solution (43), which correlates with the bulkiness of the side chain (52). Similar effects were observed with other model aminoacyl esters (55)(56)(57).…”

Section: 22 and 43) Experiments With Trnasupporting

confidence: 58%

“…Furthermore, charged amino acid side chains may take part in electrostatic interactions that may change the electrostatic network in the peptidyltransferase center (6). The rate effect of charged amino acid side chains reported here is larger than that reported for the hydrolysis of aminoacyl-tRNA in solution (43), possibly because electrostatic effects may be enhanced and act over a longer range in the environment of the peptidyltransferase center than in aqueous solution.…”

mentioning

confidence: 55%

“…Our data suggest that the Pro side chain alone, without a larger regulating nascent chain reaching into the exit tunnel, greatly reduces the Pmn reactivity of peptidyl-tRNA on the ribosome. In contrast, in solution, ProtRNA Pro is no less reactive than other aminoacyl-tRNAs and is hydrolyzed rapidly (43). This implies that the strong inhibitory effect of Pro is facilitated by the environment of the peptidyltransferase center.…”

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confidence: 97%

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Modulation of the Rate of Peptidyl Transfer on the Ribosome by the Nature of Substrates

Wohlgemuth

Brenner

Beringer

et al. 2008

Journal of Biological Chemistry

159

194

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The ribosome catalyzes peptide bond formation between peptidyl-tRNA in the P site and aminoacyl-tRNA in the A site. Here, we show that the nature of the C-terminal amino acid residue in the P-site peptidyl-tRNA strongly affects the rate of peptidyl transfer. Depending on the C-terminal amino acid of the peptidyl-tRNA, the rate of reaction with the small A-site substrate puromycin varied between 100 and 0.14 s ؊1 , regardless of the tRNA identity. The reactivity decreased in the order Lys ‫؍‬ Arg > Ala > Ser > Phe ‫؍‬ Val > Asp Ͼ Ͼ Pro, with Pro being by far the slowest. However, when Phe-tRNA Phe was used as A-site substrate, the rate of peptide bond formation with any peptidyl-tRNA was ϳ7 s ؊1 , which corresponds to the rate of binding of Phe-tRNA Phe to the A site (accommodation). Because accommodation is rate-limiting for peptide bond formation, the reaction rate is uniform for all peptidyltRNAs, regardless of the variations of the intrinsic chemical reactivities. On the other hand, the 50-fold increase in the reaction rate for peptidyl-tRNA ending with Pro suggests that full-length aminoacyl-tRNA in the A site greatly accelerates peptide bond formation.The enzymatic activity of the ribosome is to catalyze peptide bond formation. During the peptidyl transfer reaction, the ␣-amino group of aminoacyl-tRNA bound to the A site of the ribosome attacks the ester bond of peptidyl-tRNA in the P site, which results in peptidyl-tRNA extended by one amino acid in the A site and deacylated tRNA in the P site. The tRNA substrates are aligned in the active center of the ribosome by interactions of their CCA ends with 23 S rRNA bases (1-3). The ribosome lowers the activation entropy of the reaction (4, 5) by orienting the reacting groups precisely relative to each other (2, 3), providing an electrostatic environment that reduces the free energy of forming the transition state, shielding the reaction against bulk water (6, 7), or a combination of these effects (8).The peptidyl transfer reaction is modulated by conformational changes at the active site (3, 8 -10) as well as by the nature of the substrates. Rapid peptide bond formation requires fulllength tRNA in both A and P sites, and the reaction rate is influenced by the length of the tRNA fragments when model substrates are used (8, 10 -14). The reaction rate is also influenced by the nature of the amino acid side chain of the A-site substrate (13,(15)(16)(17), but is independent of the nucleophilicity of the attacking amino group in model substrates (18). Moreover, the length of the peptidyl chain and the nature of the C-terminal amino acid of the peptidyl-tRNA in the P site seem to have an effect (10,12,13,19). Early studies with 50 S ribosomal subunits indicated that efficient peptidyl transfer was observed with 3Ј-terminal RNase T1 fragments of N-acetylArg-tRNA Arg and fMet-tRNA fMet as model P-site substrates and an analog of aminoacyl-tRNA, puromycin (Pmn 4 ; O-methyltyrosine linked to N 6 -dimethyladenosine via an amide bond), as A-site substrate (20). In contrast,...

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Section: 22 and 43) Experiments With Trnasupporting

confidence: 71%

Section: 22 and 43) Experiments With Trnasupporting

confidence: 58%

mentioning

confidence: 55%

mentioning

confidence: 97%

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Modulation of the Rate of Peptidyl Transfer on the Ribosome by the Nature of Substrates

Wohlgemuth

Brenner

Beringer

et al. 2008

Journal of Biological Chemistry

159

194

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“…The reason for this is unkown, since arginyl-tRNA esters are relative stable at the pH used [19] and since the column was shown not to be overloaded.…”

Section: Separation Qf Isoaccepting Trnasmentioning

confidence: 99%

Alteration of the Intracellular Concentration of Aminoacyl‐tRNA Synthetases and Isoaccepting tRNAs during Amino‐Acid‐Limited Growth in Escherichia coli

Thomale

Nass

1978

European Journal of Biochemistry

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Growth of Escherichia coli AB 2271 under threonine or isoleucine deficiency leads to a derepression of the threonyl‐tRNA synthetase and isoleucyl‐tRNA synthetase respectively. During this amino‐acid‐limited growth the concentrations of isoaccepting fractions of the cognate tRNA species were changed, as demonstrated by their altered reversed‐phase‐5 chromatograms. But, in addition, the profiles of the isoacceptors of all other tRNA species investigated, i.e. of tRNAsLeu, tRNAsSer and tRNAsArg were also altered. This means that, if there is a correlation between regulation of the level of an aminoacyl‐tRNA synthetase and its cognate isoaccepting tRNAs, it is superimposed by the effect of amino acid limitation upon the concentration of all isoaccepting tRNAs. So far drastic changes in profiles of isoaccepting tRNAs have only been observed under unbalanced growth in relaxed cells or during treatment with antibotis. Here we demonstrate that similar heavy alterations in patterns of isoaccepting tRNAs occur in a proven stringent E. coli strain growing exponentially under amino acid limitation signal a meaningful biological function of those newly or increasingly occuring isoaccepting tRNAs. During the growth under amino acid limitation the total acceptor activity of eight investigated tRNA species, however, stayed unchanged, except that under threonine‐limited growth the total amount of tRNAIle was reduced to about half and that of tRNAGlu increased; both tRNA species of these isoacceptors are known [30,31] as spacers between ribosomal RNAs.

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Synthesis of Stable Aminoacyl‐tRNA Analogs

Chemama

Fonvielle

Lecerf

et al. 2011

CP Nucleic Acid Chemistry

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Aminoacyl-tRNAs have important roles in a variety of biological processes. Here, we describe the synthesis of stable aminoacyl-tRNA analogs containing 1,4-substituted 1,2,3-triazole rings. The procedure involves (i) copper-catalyzed cycloadditions of 3'-or 2'-azido-adenosine and alkynes, (ii) coupling between the resulting triazole-deoxyadenosine derivatives and a deoxycytidine phosphoramidite, and (iii) the enzymatic ligation of the 2'- or 3'-triazole-dinucleotides with a 22-nt RNA microhelix that mimics the acceptor arm of tRNA. Each nucleoside and nucleotide intermediate was characterized by MS spectrometry and (1)H, (31)P, and (13)C NMR spectroscopy, and the tRNA-analogs were assayed for inhibition of FemXWv, an alanyl-transferase essential for the formation of the peptidoglycan network of Gram-positive bacterial pathogens. The low IC(50) values obtained (2 to 4 µM) indicate that the five-membered triazole rings acted as an isosteres of esters and can be used for the design of stable aminoacyl-tRNA analogs.

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Relation between aminoacyl-tRNA stability and the fixed amino acid

Cited by 83 publications

References 15 publications

Modulation of the Rate of Peptidyl Transfer on the Ribosome by the Nature of Substrates

Modulation of the Rate of Peptidyl Transfer on the Ribosome by the Nature of Substrates

Alteration of the Intracellular Concentration of Aminoacyl‐tRNA Synthetases and Isoaccepting tRNAs during Amino‐Acid‐Limited Growth in Escherichia coli

Synthesis of Stable Aminoacyl‐tRNA Analogs

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