• BMB Reports
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• v.31 no.6
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• pp.525-535
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• 1998

A critical step in the faithful translation of genetic information is specific tRNA recognition by aminoacyl-tRNA synthetases. These enzymes catalyze the covalent attachment of particular amino acids to the terminal adenosine of cognate tRNA substrates. In general, there is one synthetase for each of the twenty amino acids and each enzyme must discriminate against all of the cellular tRNAs that are specific for the nineteen noncognate amino acids. Primary sequence information combined with structural data have resulted in the division of the twenty synthetases into two classes. In recent years, several high-resolution co-crystal structures along with biochemical data have led to an increased understanding of tRNA recognition by synthetases of both classes. The anticodon sequence and the amino acid acceptor stem are the most common locations for critical recognition elements. This review will focus on acceptor stem discrimination by class II synthetases. In particular, the results of in vitro aminoacylation assays and site-directed and atomic group mutagenesis studies will be discussed. These studies have revealed that even subtle atomic determinants can provide signals for specific tRNA aminoacylation.

• Asian-Australasian Journal of Animal Sciences
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• v.2 no.3
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• pp.424-424
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• 1989

• BMB Reports
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• v.28 no.4
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• pp.363-367
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• 1995

E. coli methionyl-tRNA synthetase is one of the class I tRNA synthetases. The Tryptophane residue at the position 461 located in the C-terminal domain of the enzyme is a key amino acid for the interaction with the anticodon of $tRNA^{Met}$. W461 was replaced with other amino acids to determine the chemical requirement for the interaction with the anticodon of $tRNA^{Met}$. Saturation mutagenesis at the position 461 generated a total of 12 substitution mutants of methionyl-tRNA synthetase. All the mutants showed the same in vivo stability as the wild-type enzyme, suggesting that the amino acid substitutions did not cause severe conformational change of the protein The mutants containing tyrosine, phenylalanine, histidine and cysteine substitutions showed in vivo activity while all the other mutants did not. The comparison of the in vitro aminoacylation activities of these mutants showed that aromatic ring structure, Van der Waals volume and hydrogen bond potential of the amino acid residue at the position 461 are the major determinants for the interaction with the anticodon of $tRNA^{Met}$.

• Biomedical Science Letters
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• v.13 no.2
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• pp.105-110
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• 2007

Aspartyl-tRNA synthetase (AspRS) exists in two different forms with respect to tRNA recognition. The discriminating enzyme (D-AspRS) recognizes only tRNA$^{Asp}$, while the non-discriminating one (ND-AspRS) also recognizes tRNA$^{Asn}$ and therefore forms both Asp-tRNA$^{Asn}$ and Asp-tRNA$^{Asp}$. Plus primary sequence distinguishes two general groups of AspRS. There is a predominantly bacterial-type, larger AspRS (about 580 aa) in addition to a shorter archaeal/eukaryotic type (about 430 aa). In vivo data made clear that discriminating and non-discriminating enzymes exist in both groups. The determinants in the protein sequence responsible for tRNA discrimination are not hewn. The AspRS from Acidithiobacillus ferrooxidans might be suggested ND-AspRS fur missing of AsnRS in genomic sequencing data. Therefore, we analyzed the AspRS from A. ferrooxidans with in vitro aminoacylation assay with E. coli unfractionated tRNA, in vivo missense suppression assay with tipA34 mutant and Northern hybridization with probes which were specific with tRNA$^{Asp}$ or tRNA$^{Asn}$. The AspRS from A. ferrooxidans produced more Asp-tRNA than that from E. coli. Only aspS gene from A. ferrooxidans suppressed trpA34 strain in minimal media without tryptophan. Only AspRS from A. ferrooxidans showed mischarged Asp-tRNA$^{Asn}$ band. Therefore, AspRS from A. ferrooxidans is definitely ND-AspRS.

• BMB Reports
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• v.28 no.6
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• pp.494-498
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• 1995

Maize mitochondrial tRNAs for isoleucine have been isolated using a putative $tRNA^{Ile}$ gene probe which has been previously isolated and characterized. It contains the 5'-CAT anticodon which would normally recognize the AUG methionine codon. The nucleotide sequence of one of these tRNAs has been partially determined, and contains a modified nucleotide at the first position of the anticodon. This type of posttranscriptional modification event could change the specificity of amino acid acceptance of a tRNA, unlike that deduced from the corresponding gene. An aminoacylation experiment also demonstrated that these purified tRNAs have isoleucine acceptance activity but no methionine-accepting activity.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.420-427
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• 2018

The orthogonal pair of Saccharomyces cerevisiae tyrosyl-tRNA synthetase (Sc YRS) and a variant of E. coli initiator tRNA, fMam $tRNA_{CUA}$ which recognizes the amber stop codon is an effective tool for site-specific incorporation of unnatural amino acids into the protein in E. coli. To evolve the amber suppression activity of the orthogonal pair, we generated a mutant library of Sc YRS by randomizing two amino acids at 320 and 321 which involve recognition of the first base of anticodon in fMam $tRNA_{CUA}$. Two positive clones are selected from the library screening with chloramphenicol resistance mediated by amber suppression. They showed growth resistance against high concentration of chloramphenicol and their $IC_{50}$ values were approximately 1.7~2.3 fold higher than the wild type YRS. In vivo amber suppression assay reveals that mutant YRS-3 (mYRS-3) clone containing amino acid substitutions of P320A and D321A showed 6.5-fold higher activity of amber suppression compared with the wild type. In addition, in vitro aminoacylation kinetics of mYRS-3 also showed approximately 7-fold higher activity than the wild type, and the enhancement was mainly due to the increase of tRNA binding affinity. These results demonstrate that optimization of anticodon recognition by engineered aminoacyl tRNA synthetase improves the efficiency of unnatural amino acid incorporation in response to nonsense codon.

• BMB Reports
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• v.32 no.6
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• pp.547-553
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• 1999

Aminoacyl-tRNA synthetases are essential enzymes catalyzing the attachment of specific amino acids to cognate tRNAs. In the present work, the substrate analogue L-methionine hydroxamate was used to identify functional residues located in the active site of the E. coli methionyl-tRNA synthetase (MetRS). This compound inhibited bacteria, yeast, and human MetRS activities to a similar degree, suggesting a conserved active site structure and mechanism between MetRSs of different phylogenetic domains. Mutants of the E. coli MetRS resistant to methionine hydroxamate were also isolated. These mutants contained a substitution either at T10, Y15, or Y94. These residues are highly conserved among the different MetRSs and the mutants showed decreased aminoacylation activity, suggesting their functional and structural significances. The putative roles of these residues are discussed on a structural basis.

• Bulletin of the Korean Chemical Society
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• v.28 no.2
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• pp.207-210
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• 2007

To identify structural or functional common subunit(s) in the CP1 (editing) domains of class Ia tRNA synthetases, five available structures were compared and analyzed. Through the sequence alignments and structural overlapping of the CP1 domains, three conserved regions were identified near the amino acid binding site in the editing domain. Structural overlapping of the three subunits clearly showed the existence of three common structural subunits in all of the five editing RS structures. Based on the established experimental results and our modeling results, it is proposed that subunits 1 and 3 accommodate the incoming amino acid binding, while subunit 2 contributes to the interactions with the adenosine ring of the A76 to stabilize the overall tRNA binding. Since these subunits are critical for the editing reaction, we expect that these key structures should be conserved through the most class Ia editing RSs.

• Journal of Food Hygiene and Safety
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• v.13 no.2
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• pp.121-128
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• 1998

Ochratoxin A (OA) is a mycotoxin produced by Aspergillus ochraceus as well as other molds. It is a natural contaminant of mouldy food and feed. OA has a number of toxic effects, the most prominant being nephrotoxicity. Futhermore, OA is immunosuppressive, genotoxic, teratogenic and carcinogenic. OA inhibits protein synthesis by competition with phenylalanine in the phenylalanine-tRNA aminoacylation reaction. Recently, lipid peroxidation induced by OA has been reported, indicating that the lesion induced by this mycotoxin could be also related to oxidative pathway. Since it seems impossible to avoid contamination of foodstuffs by toxigenic fungi, detoxification and detoxication of OA are needed. In this study we investigated the protective effects of aspartame (Asp), phenylalanine (Phe), polyphenol 70S (PP) and aloe extract (AE) on the nephrotoxicity induced by subacute exposure to the OA. Asp and Phe are structural analogues of OA. PP, an ingredient of Green Tea and AE have been known as antioxidant and radical scavenger. Phe (40 mg/kg, i.p.) and Asp (25 mg/kg, p.o.) were administered to Sprague-Dawley rats simultaneously with OA (2.0 mg/kg, p.o.) for 2 weeks. PP (200 mg/kg, p.o.) and AE (50 mg/kg, i.v.) were pretreated before administration of OA, for 2 weeks and 3 days, respectively. Using enzymuria, BUN level, creatinemia and histophathologic examination as indices of renal damage, we observed that all of four compounds prevented the nephrotoxic effects induced by OA. It seems that structural analogues of OA such as Asp and Phe have better protective effect on the nephrotoxicity of OA than antioxidants. These results indicate that 1) formation of free radical and lipid peroxidation are likely to be involved in the nephrotoxicity of OA in vivo, 2) Asp, PP and AE might be used for prevention of renal lesions in cases of ochratoxicosis.