Plasticity of Recognition of the 3′-End of Mischarged tRNA by Class I Aminoacyl-tRNA Synthetases

Nordin, Brian E.; Schimmel, Paul

doi:10.1074/jbc.m202023200

Cited by 57 publications

(71 citation statements)

References 44 publications

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“…In contrast to tRNA Ile , minihelix Ile is unable to trigger the hydrolysis of misactivated valine and misaminoacylated with non-cognate amino acids, although the mischarged minihelix Ile may be deacylated by E. coli IleRS (43,44). Previous studies additionally demonstrate tertiary structure interactions between D-and T C-loops or crucial identities within these structures that play important roles in the editing of ValRS, LeuRS, or IleRS (21,34,45).…”

Section: Discussionmentioning

confidence: 98%

Leucyl-tRNA Synthetase from the Hyperthermophilic Bacterium Aquifex aeolicus Recognizes Minihelices

Zhao

Wang

2004

Journal of Biological Chemistry

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Aminoacylation of the minihelix mimicking the amino acid acceptor arm of tRNA has been demonstrated in more than 10 aminoacyl-tRNA synthetase systems. Although Escherichia coli or Homo sapiens cytoplasmic leucyl-tRNA synthetase (LeuRS) is unable to charge the cognate minihelix or microhelix, we show here that minihelix Leu is efficiently charged by Aquifex aeolicus synthetase, the only known heterodimeric LeuRS (␣␤-LeuRS). Aminoacylation of minihelices is strongly dependent on the presence of the A73 identity nucleotide and greatly stimulated by destabilization of the first base pair as reported for the E. coli isoleucyl-tRNA synthetase and methionyl-tRNA synthetase systems. In the E. coli LeuRS system, the anticodon of tRNA Leu is not important for recognition by the synthetase. However, the addition of RNA helices that mimic the anticodon domain stimulates minihelix Leu charging by ␣␤-LeuRS, indicating possible domain-domain communication within ␣␤-LeuRS. The leucine-specific domain of ␣␤-LeuRS is responsible for minihelix recognition. To ensure accurate translation of the genetic code, LeuRS functions to hydrolyze misactivated amino acids (pretransfer editing) and misaminoacylated tRNA (posttransfer editing). In contrast to tRNA Leu , minihelix Leu is unable to induce posttransfer editing even upon the addition of the anticodon domain of tRNA. Therefore, the context of tRNA is crucial for the editing of mischarged products. However, the minihelix Leu cannot be misaminoacylated, perhaps because of the tRNA-independent pretransfer editing activity of ␣␤-LeuRS.Aminoacyl-tRNA synthetases (aaRSs) 1 establish the genetic code by catalyzing the esterification of cognate amino acids to their specific transfer RNAs (tRNA) that bear the corresponding anticodons, which are defined by the genetic code (1). Aminoacylation of tRNA catalyzed by aaRSs is a two-step reaction: (a) activation of amino acids with ATP by formation of aminoacyl adenylate and (b) transfer of the aminoacyl moiety from the aminoacyl adenylate to the cognate tRNA substrate. On the basis of the architecture of the conserved active site domain, aaRSs are divided into two groups (2). Class I enzymes have an active site based on the Rossmann fold, whereas the conserved active core of class II enzymes contains an antiparallel ␤-sheet flanked by ␣-helices.One hypothesis about the assembly of aminoacyl-tRNA synthetases is that the enzymes are assembled in a modular fashion, incorporating new domains around the conserved active site representing ancestral aaRS such as the tRNA-binding domain and editing domain (3). Interestingly, two domains of tRNA (specifically the amino acid-accepting stem (minihelix) and anticodon stem biloop (SBL)), which interact with the aminoacylation active site and tRNA-binding domain of aaRS, respectively, may have arisen independently (4). Chargeable minihelices and smaller helices (e.g. microhelices of 7 bp) mimicking the acceptor stem have been identified in more than 10 aaRS systems (5). Thus, whereas it is recognized that aaRS...

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Section: Discussionmentioning

confidence: 98%

Leucyl-tRNA Synthetase from the Hyperthermophilic Bacterium Aquifex aeolicus Recognizes Minihelices

Zhao

Wang

2004

Journal of Biological Chemistry

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“…Class I leucyltRNA synthetase and isoleucyl-tRNA synthetase and class II threonyl-tRNA synthetase and phenylalanyl-tRNA synthetase activate water molecules via interaction with conserved residues in their editing active sites. In addition, editing often occurs via substrate-assisted catalysis involving the hydroxyl groups of the A76 ribose on tRNA (44,56,57). In all of these systems, a double-sieve mechanism is used, involving steric exclusion of the cognate aminoacyl-tRNA from the editing domain.…”

Section: Discussionmentioning

confidence: 99%

“…6A) (43,44,(55)(56)(57). Class I leucyltRNA synthetase and isoleucyl-tRNA synthetase and class II threonyl-tRNA synthetase and phenylalanyl-tRNA synthetase activate water molecules via interaction with conserved residues in their editing active sites.…”

Section: Discussionmentioning

confidence: 99%

“…3). Previous studies have shown that the cis-hydroxyl groups of the terminal A76 of tRNA are critical for deacylation by aaRSs (44,(55)(56)(57). To examine the role of the 3Ј-terminal hydroxyl groups in YbaK deacylation, Cys-tRNA analogs lacking either the 2Ј-or 3Ј-hydroxyl group were prepared.…”

Section: Substrate Specificity and Role Of Substrate Functional Groupmentioning

confidence: 99%

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Substrate-mediated Fidelity Mechanism Ensures Accurate Decoding of Proline Codons

Kumar

et al. 2011

Journal of Biological Chemistry

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Aminoacyl-tRNA synthetases attach specific amino acids to cognate tRNAs. Prolyl-tRNA synthetases are known to mischarge tRNA Pro with the smaller amino acid alanine and with cysteine, which is the same size as proline. Quality control in proline codon translation is partly ensured by an editing domain (INS) present in most bacterial prolyl-tRNA synthetases that hydrolyzes smaller Ala-tRNA Pro Aminoacyl-tRNA synthetases (aaRSs) 3 play a pivotal role in the decoding of genetic information by catalyzing the esterification of cognate amino acids onto specific transfer RNAs (tRNAs) in a two-step reaction (1). The first step involves amino acid activation with ATP to form an aminoacyl-adenylate intermediate and concomitant pyrophosphate release. The second step involves aminoacyl transfer to the cognate tRNA via a transesterification reaction. Although aaRSs display high substrate specificity, they often misactivate structurally similar amino acids. If left unchecked, these mistakes lead to errors in protein synthesis, and accumulation of such errors can be deleterious to cells (2, 3).To ensure high fidelity in translation, aaRSs have evolved several proofreading mechanisms (4 -7). In the first type of proofreading, misactivated aminoacyl-adenylates are enzymatically hydrolyzed or selectively released from the active site followed by solvent hydrolysis, in a process termed "pretransfer" editing. Another mechanism of proofreading known as "posttransfer" editing is generally believed to function via the socalled "double-sieve" mechanism (8). The model predicted that, whereas one active site could not completely discriminate Ile and Val, two separate active sites with distinct strategies for recognition could significantly enhance fidelity. The aminoacylation active site of the aaRS would act as a "coarse" sieve for adenylate synthesis, activating the cognate amino acid but also allowing, to a lesser extent, activation of isosteric or smaller amino acids that could fit into the amino acid binding pocket. The second "fine" sieve would selectively bind misactivated amino acids for editing while excluding the original cognate amino acid. Thus, substrates synthesized in the first sieve would be further screened by the second sieve to enhance fidelity. Subsequently, biochemical and structural data validated this steric exclusion mechanism for valyl-tRNA synthetase and isoleucyl-tRNA synthetase (9, 10). Indeed, members of both classes of synthetases are now known to possess a second active site spatially separated from the ancient catalytic core to carry out post-transfer editing. Structures of class I isoleucyl-tRNA synthetase (10), leucyl-tRNA synthetase (11), and valyl-tRNA synthetase (12) reveal the highly conserved connective peptide 1 domain that functions in editing. Class II alanyl-tRNA synthetase (AlaRS) (13, 14), threonyl-tRNA synthetase (15), prolyltRNA synthetase (ProRS) (16,17), and phenylalanyl-tRNA synthetase (18, 19) also possess distinct domains for post-transfer editing. A recent study of AlaRS revealed an ...

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“…Expression was induced in E. coli Rosetta TM BL21 (Novagen) at A 600 ϭ 0.6 with 1 mM isopropyl ␤-D-thiogalactoside for 6 h at 37°C. Enzymes were prepared as described previously (29,40).…”

Section: Methodsmentioning

confidence: 99%

Ancestral AlaX Editing Enzymes for Control of Genetic Code Fidelity Are Not tRNA-specific

Novoa

Vargas-Rodriguez

Lange

et al. 2015

Journal of Biological Chemistry

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Plasticity of Recognition of the 3′-End of Mischarged tRNA by Class I Aminoacyl-tRNA Synthetases

Cited by 57 publications

References 44 publications

Leucyl-tRNA Synthetase from the Hyperthermophilic Bacterium Aquifex aeolicus Recognizes Minihelices

Leucyl-tRNA Synthetase from the Hyperthermophilic Bacterium Aquifex aeolicus Recognizes Minihelices

Substrate-mediated Fidelity Mechanism Ensures Accurate Decoding of Proline Codons

Ancestral AlaX Editing Enzymes for Control of Genetic Code Fidelity Are Not tRNA-specific

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