Sequence of tRNA Ile IAU from brewer's yeast

The mechanism of discriminative aminoacylation by isoleucyl-tRNA synthetase based on wobble nucleotide recognition

The faithful charging of amino acids to cognate tRNAs by aminoacyl-tRNA synthetases (AARSs) determines the fidelity of protein translation. Isoleucyl-tRNA synthetase (IleRS) distinguishes tRNAIle from tRNAMet solely based on the nucleotide at wobble position (N34), and a single substitution at N34 could exchange the aminoacylation specificity between two tRNAs. Here, we report the structural and biochemical mechanism of N34 recognition-based tRNA discrimination by Saccharomyces cerevisiae IleRS (ScIleRS). ScIleRS utilizes a eukaryotic/archaeal-specific arginine as the H-bond donor to recognize the common carbonyl group (H-bond acceptor) of various N34s of tRNAIle, which induces mutual structural adaptations between ScIleRS and tRNAIle to achieve a preferable editing state. C34 of unmodified tRNAIle(CAU) (behaves like tRNAMet) lacks a relevant H-bond acceptor, which disrupts key H-bonding interactions and structural adaptations and suspends the ScIleRS·tRNAIle(CAU) complex in an initial non-reactive state. This wobble nucleotide recognition-based structural adaptation provides mechanistic insights into selective tRNA aminoacylation by AARSs.

A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine

Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNA^Arg isoacceptors. The anticodon stem and loop (ASL) domains of tRNA^Arg1 and tRNA^Arg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I₃₄) and 37 (m²A₃₇). tRNA^Arg1 is also modified from cytidine to 2-thiocytidine at position 32 (s²C₃₂). The s²C₃₂ modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s²C₃₂ for C₃₂ in the Saccharomyces cerevisiae tRNA^Ile_IAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s²C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASL^Arg1_ICG and ASL^Arg2_ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C_32-A₃₈ cross-loop interaction but failed to fully explain the means by which s²C₃₂ restricts I₃₄ wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C_32-A₃₈ cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.

TFIIIR is an isoleucine tRNA

Promoter-specific transcription by silkworm RNA polymerase III is dependent on several transcription factors (TFs) in addition to the polymerase itself. The activities present in silk gland nuclear extracts that are necessary to reconstitute transcription from class III genes in vitro have been resolved into several partially purified components. These include TFIIIR, which is unusual because it is composed of RNA. Here, we identify the RNA that provides TFIIIR activity as silkworm tRNA(IleIAU). This conclusion is based on copurification of tRNA(IleIAU) with TFIIIR activity, TFIIIR activity in synthetic tRNA(Ile), and hybrid selection of TFIIIR activity by antisense tRNA(IleIAU). We have tested the ability of a variety of other tRNAs to stimulate transcription and find that TFIIIR activity is highly specific to silkworm tRNA(IleIAU).

TFIIIR is an isoleucine tRNA

Promoter-specific transcription by silkworm RNA polymerase III is dependent on several transcription factors (TFs) in addition to the polymerase itself. The activities present in silk gland nuclear extracts that are necessary to reconstitute transcription from class III genes in vitro have been resolved into several partially purified components. These include TFIIIR, which is unusual because it is composed of RNA. Here, we identify the RNA that provides TFIIIR activity as silkworm tRNA(IleIAU). This conclusion is based on copurification of tRNA(IleIAU) with TFIIIR activity, TFIIIR activity in synthetic tRNA(Ile), and hybrid selection of TFIIIR activity by antisense tRNA(IleIAU). We have tested the ability of a variety of other tRNAs to stimulate transcription and find that TFIIIR activity is highly specific to silkworm tRNA(IleIAU).

Increase in fidelity of rat liver Ile-tRNA formation by both spermine and the aminoacyl-tRNA synthetase complex

To examine the polyamine effects on the fidelity at the aminoacylation level and the physiological significance of the existence of the aminoacyl-tRNA synthetase complex (ARSC) in animal cells, a single-chain Ile-tRNA synthetase (IRSS) was isolated from the complex by treatment with trypsin. Ile-tRNA formation by IRSS was strongly stimulated by spermine, similar to the results with ARSC. Two misacylations (Val-tRNAIle and Ile-tRNAiMet formation) by IRSS were measured. The error frequency was higher in Ile-tRNAiMet formation (tRNA misacylation) than in Val-tRNAIle formation (amino acid misacylation). Spermine did not influence significantly Ile-tRNAiMet formation, but it stimulated Val-tRNAIle formation by IRSS. Accordingly, spermine decreased the error frequency of tRNA misacylation, but not amino acid misacylation. These results suggest that the conformational changes of individual tRNA by spermine differ from each other, meaning that spermine influences the interaction between individual tRNA and aminoacyl-tRNA synthetase variously. When the aminoacylations of tRNAIle from rat liver, yeast, and Escherichia coli were compared with ARSC and IRSS, the relative speed of Ile-tRNA formation with tRNAIle from other species was faster with IRSS than with ARSC. This indicates that ARSC can recognize tRNAIle from the same species more specifically than IRSS. These results show that both spermine and ARSC are involved in the increase of fidelity of rat liver Ile-tRNA formation.

Correlation between spermine stimulation of rat liver Ile-tRNA formation and structural change of the acceptor stem by spermine

We have recently reported that the interaction of spermine with the acceptor and anticodon stems may be important for spermine stimulation of rat liver Ile-tRNA formation [Peng, Z. et al. (1990) Arch. Biochem. Biophys. 279, 138-145]. To pinpoint which interaction of spermine is more important for spermine stimulation of Ile-tRNA formation, Ile-tRNA formation and ribonuclease V1 sensitivity of tRNA(Ile) were studied using purified tRNAs(Ile) from rat liver, wheat germ, brewer's yeast, torula yeast and Escherichia coli. The results indicate that spermine stimulation of rat liver Ile-tRNA formation correlated with the structural change of the acceptor stem by spermine. The nucleotide sequence of wheat germ tRNA(Ile) was also determined.

In vivo pre-tRNA processing in Saccharomyces cerevisiae

We have surveyed intron-containing RNAs of the yeast Saccharomyces cerevisiae by filter hybridization with pre-tRNA intron-specific oligonucleotide probes. We have classified various RNAs as pre-tRNAs, splicing intermediates, or excised intron products according to apparent size and structure. Linear, excised intron products were detected, and one example was isolated and sequenced directly. Additional probes designed to detect other precursor sequences were used to verify the identification of several intermediates. Pre-tRNA species with both 5' leader and 3' extension, with 3' extension only, and with mature ends were distinguished. From these results, we conclude that the processing reactions used to remove the 5' leader and 3' extension from the transcript are ordered 5' end trimming before 3' end trimming. Splicing intermediates containing the 5' exon plus the intron were detected. The splice site cleavage reactions are probably ordered 3' splice site cleavage before 5' splice site cleavage. Surprisingly, we also detected a splicing intermediate with the 5' leader and a spliced product with both 5' leader and 3' extension. Evidently, splicing and end trimming are not ordered relative to each other, splicing occurring either before or after end trimming.

In vivo pre-tRNA processing in Saccharomyces cerevisiae

We have surveyed intron-containing RNAs of the yeast Saccharomyces cerevisiae by filter hybridization with pre-tRNA intron-specific oligonucleotide probes. We have classified various RNAs as pre-tRNAs, splicing intermediates, or excised intron products according to apparent size and structure. Linear, excised intron products were detected, and one example was isolated and sequenced directly. Additional probes designed to detect other precursor sequences were used to verify the identification of several intermediates. Pre-tRNA species with both 5' leader and 3' extension, with 3' extension only, and with mature ends were distinguished. From these results, we conclude that the processing reactions used to remove the 5' leader and 3' extension from the transcript are ordered 5' end trimming before 3' end trimming. Splicing intermediates containing the 5' exon plus the intron were detected. The splice site cleavage reactions are probably ordered 3' splice site cleavage before 5' splice site cleavage. Surprisingly, we also detected a splicing intermediate with the 5' leader and a spliced product with both 5' leader and 3' extension. Evidently, splicing and end trimming are not ordered relative to each other, splicing occurring either before or after end trimming.

Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses

Ty3, a retrotransposon of Saccharomyces cerevisiae, is found within 20 base pairs (bp) of the 5' ends of different tRNA genes. Determination of the complete nucleotide sequence of one Ty3 retrotransposon (Ty3-2) shows that the element is composed of an internal domain 4,748 bp long flanked by long terminal repeats of the 340-bp sigma element. Three open reading frames (ORFs) longer than 100 codons are present in the sense strand. The first ORF, TYA3, encodes a protein with a motif found in the nucleic acid-binding protein of retroviruses. The second ORF, TYB3, has homology to retroviral pol genes. The deduced amino acid sequence of the reverse transcriptase domain shows the greatest similarity to Drosophila retrotransposon 17.6, with 43% identical residues. The inferred order of functional domains within TYB3--protease, reverse transcriptase, and endonuclease--resembles the order in Drosophila element 17.6 and in animal retroviruses but is different from that found in yeast elements Ty1 and Ty2. A second Ty3 element (Ty3-1) from a standard laboratory strain was overexpressed and shown to transpose.

Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses

Ty3, a retrotransposon of Saccharomyces cerevisiae, is found within 20 base pairs (bp) of the 5' ends of different tRNA genes. Determination of the complete nucleotide sequence of one Ty3 retrotransposon (Ty3-2) shows that the element is composed of an internal domain 4,748 bp long flanked by long terminal repeats of the 340-bp sigma element. Three open reading frames (ORFs) longer than 100 codons are present in the sense strand. The first ORF, TYA3, encodes a protein with a motif found in the nucleic acid-binding protein of retroviruses. The second ORF, TYB3, has homology to retroviral pol genes. The deduced amino acid sequence of the reverse transcriptase domain shows the greatest similarity to Drosophila retrotransposon 17.6, with 43% identical residues. The inferred order of functional domains within TYB3--protease, reverse transcriptase, and endonuclease--resembles the order in Drosophila element 17.6 and in animal retroviruses but is different from that found in yeast elements Ty1 and Ty2. A second Ty3 element (Ty3-1) from a standard laboratory strain was overexpressed and shown to transpose.

Sigma elements are position-specific for many different yeast tRNA genes

We determined the DNA sequence of seventeen sigma elements and flanking regions in order to investigate the extent of the association between the yeast repetitive element, sigma, and tRNA genes. Fifteen of seventeen sigma elements analyzed begin at position -19 to -16 with respect to the 5' end of a tRNA-coding sequence. This region is close to the initiation point of tRNA gene transcription and contains a sequence which is modestly conserved for a number of tRNA genes. Two pairs of identical sigma elements occur as the long terminal repeats of a sequence which, together with flanking sigma elements, has the structural properties of a retrotransposon; this element has been named Ty3 (manuscript submitted). Hybridization analysis of yeast chromosomal DNA separated by orthogonal field alternation gel electrophoresis (OFAGE) showed that Ty3 and isolated sigma elements are distributed over many chromosomes in the yeast genome.