tRNA-dependent Aminoacyl-adenylate Hydrolysis by a Nonediting Class I Aminoacyl-tRNA Synthetase

Abstract

Glutaminyl-tRNA synthetase generates Gln-tRNA Gln 10 7 -fold more efficiently than Glu-tRNA Gln and requires tRNA to synthesize the activated aminoacyl adenylate in the first step of the reaction. To examine the role of tRNA in amino acid activation more closely, several assays employing a tRNA analog in which the 2-OH group at the 3-terminal A76 nucleotide is replaced with hydrogen (tRNA 2H Gln ) were developed. These experiments revealed a 10 4 -fold reduction in k cat /K m in the presence of the analog, suggesting a direct catalytic role for tRNA in the activation reaction. The catalytic importance of the A76 2-OH group in aminoacylation mirrors a similar role for this moiety that has recently been demonstrated during peptidyl transfer on the ribosome. Unexpectedly, tracking of Gln-AMP formation utilizing an ␣-32 P-labeled ATP substrate in the presence of tRNA 2H Gln showed that AMP accumulates 5-fold more rapidly than Gln-AMP. A cold-trapping experiment revealed that the nonenzymatic rate of Gln-AMP hydrolysis is too slow to account for the rapid AMP formation; hence, the hydrolysis of Gln-AMP to form glutamine and AMP must be directly catalyzed by the GlnRS⅐tRNA 2H Gln complex. This hydrolysis of glutaminyl adenylate represents a novel reaction that is directly analogous to the pre-transfer editing hydrolysis of noncognate aminoacyl adenylates by editing synthetases such as isoleucyl-tRNA synthetase. Because glutaminyltRNA synthetase does not possess a spatially separate editing domain, these data demonstrate that a pre-transfer editing-like reaction can occur within the synthetic site of a class I tRNA synthetase.The specificity of protein synthesis depends upon the fidelity of aminoacyl-tRNA synthetases (aaRS).1 These enzymes attach amino acids to the 3Ј terminus of transfer RNAs in a two-step reaction (1). First, the amino acid is activated by reaction with ATP, to yield an aminoacyl adenylate intermediate and pyrophosphate. In the second step, one of the two hydroxyl oxygens of the 3Ј-terminal A76 nucleotide of tRNA attacks the carbonyl carbon of the adenylate, producing aminoacyl-tRNA with release of AMP. Each synthetase must discriminate among both structurally similar amino acids and tRNAs, selecting only the cognate species from cellular pools with an overall accuracy of approximately one error per 10 4 -10 5 codons (2). While the subsequent interaction of aminoacyl-tRNA with elongation factors may also provide some selection (3), it is clear that the specificity of protein synthesis primarily arises from the tRNA synthetase-mediated step.It is well established that some tRNA synthetases are unable to accurately discriminate among chemically similar amino acids based solely on interactions made in the synthetic active site (reviewed in Ref. 4). These enzymes possess an additional hydrolytic activity for deacylation of misaminoacylated tRNAs. This reaction occurs in a second active site that effectively excludes correctly aminoacylated products. For example, in IleRS the synthetic active site canno...

Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases

“…By constructing parallel reactions where one series employs labeled [ 14 C]-amino acid, and a second set that employs [α-32 P] ATP, one can experimentally measure the ratio of ATP consumption to production of AAtRNA AA formed ( Figure 5B). Such experiments have provided insight into the role that tRNA plays in the kinetics of adenylation reaction [66], and into mechanisms for pre-transfer editing [55].…”

“…The pyrophosphate exchange assay described above technically measures the rate of isotopic exchange of 32 P into ATP, and can provide information about the kinetic mechanism (i.e., whether substrate binding is random or ordered) [54]. As described in Section 2.9, the forward reaction alone may be measured directly by use of [α-32 P]-labeled ATP, monitoring conversion of ATP to AMP using thin-layer chromatography [55]. The advantage of this approach is that it enables separate detection of AMP and aminoacyl~AMP on the TLC plates.…”

Mutational unmasking of a tRNA-dependent pathway for preventing genetic code ambiguity

“…A fluorescent-based translocation assay in IleRS has shown that ATP evacuates the aminoacylation active site during editing (14,17,34,35), but the molecular details of translocation remain unclear. Alternatively, a recent investigation with glutaminyl (Gln)-tRNA synthetase proposed that some tRNA synthetases may hydrolyze aminoacyl-adenylate intermediates directly within the synthetic active site (8).…”

“…It was recently hypothesized that a pretransfer editing activity might be conferred in the synthetic active site (8). Under pyrophosphate exchange conditions (see Fig.…”

“…Pretransfer editing, where misactivated noncognate aminoacyl-adenylate intermediates are hydrolyzed by tRNA synthetases (7), has persisted as a controversial fidelity pathway in protein synthesis (8). Although posttransfer editing (6, 9) of mischarged tRNAs can be directly measured, the adenylate substrates for pretransfer editing are highly labile and transient.…”