Switching tRNA(Gln) identity from glutamine to tryptophan.

Rogers, Michael J.; Adachi, Taiki; Inokuchi, Hachiro; Söll, Dieter

doi:10.1073/pnas.89.8.3463

Cited by 46 publications

(34 citation statements)

References 48 publications

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“…Steady-state MichaelisMenten kinetics of GlnRS mutants showed that its specific aminoacylation of tRNA Gln was primarily reflected in lower mutant k cat values (25,26). Pre-steady state observations were made more recently for selectivity of GlnRS for glutamine versus glutamic acid (27)(28)(29).…”

Section: Discussionmentioning

confidence: 99%

Enhanced Amino Acid Selection in Fully Evolved Tryptophanyl-tRNA Synthetase, Relative to Its Urzyme, Requires Domain Motion Sensed by the D1 Switch, a Remote Dynamic Packing Motif

Weinreb

Chandrasekaran

et al. 2014

Journal of Biological Chemistry

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Background: Amino acid selection by tryptophanyl-tRNA synthetase (TrpRS) requires intermodular coupling. Results: Dynamic repacking of four side chains increases amino acid specificity 500-fold in contemporary TrpRS by reducing pocket size near the transition state. Conclusion: An ancient tertiary packing motif not only activates the catalytic Mg 2ϩ ion during catalysis, but also determines cognate amino acid specificity. Significance: Allosteric enforcement of specificity increases robustness to mutation.

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Section: Discussionmentioning

confidence: 99%

Enhanced Amino Acid Selection in Fully Evolved Tryptophanyl-tRNA Synthetase, Relative to Its Urzyme, Requires Domain Motion Sensed by the D1 Switch, a Remote Dynamic Packing Motif

Weinreb

Chandrasekaran

et al. 2014

Journal of Biological Chemistry

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“…The fact that only Trp-inserting tRNA Trp suppressor tRNAs allowed induction raised the possibility that reading of codon 12 by tRNA Trp or insertion of Trp during translation of codon 12, or both, was necessary for induction. To distinguish between these possibilities, we examined the ability of an altered tRNA Gln opal suppressor tRNA that inserts tryptophan, described by Rogers et al (29), to allow tryptophan induction. The data in Table 5 indicate that replacing Trp codon 12 by TGA (strain PDG 1170) eliminates induction and appreciably reduces base-level expression of the operon, as expected.…”

Section: Resultsmentioning

confidence: 99%

Evidence suggesting cis action by the TnaC leader peptide in regulating transcription attenuation in the tryptophanase operon of Escherichia coli

Gish

Yanofsky

1995

J Bacteriol

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Expression of the tryptophanase (tna) operon in Escherichia coli is regulated by catabolite repression and transcription attenuation. Elevated levels of tryptophan induce transcription antitermination at one or more Rho factor-dependent termination sites in the leader region of the operon. Induction requires translation of a 24-residue coding region, tnaC, located in the 319-nucleotide transcribed leader region preceding tnaA, the structural gene for tryptophanase. In the present paper, we show that two bacterial species that lack tryptophanase activity, Enterobacter aerogenes and Salmonella typhimurium, allow tryptophanase induction and tna operon regulation when they carry a plasmid containing the E. coli tna operon. The role of tnaC in induction was examined by introducing mutations in a 24-nucleotide segment of tnaC of E. coli surrounding and including the crucial Trp codon 12. Some mutations resulted in a noninducible phenotype; these mostly introduced nonconservative amino acid substitutions in TnaC. Other mutations had little or no effect; these generally were in third positions of codons or introduced conservative amino acid replacements. A tryptophan-inserting, UGA-reading glutamine suppressor tRNA was observed to restore partial regulation when Trp codon 12 of tnaC was changed to UGA. Stop codons introduced downstream of Trp codon 12 in all three reading frames established that induction requires translation in the natural tnaC reading frame. Our findings suggest that the TnaC leader peptide acts in cis to prevent Rho-dependent termination.Tryptophanase is a catabolic enzyme produced by many bacterial species. This enzyme degrades tryptophan to indole, pyruvate, and ammonia and allows the organism to utilize tryptophan as a source of nitrogen or of carbon and energy (13,24). Tryptophanase also catalyzes the reverse reaction (43). In Escherichia coli, the tna operon consists of two major structural genes, tnaA, encoding tryptophanase (9), and tnaB, encoding a tryptophan permease (5,32,45). The leader region of the tna operon contains a region, designated tnaC, encoding a 24-amino-acid residue peptide. Transcription of the structural gene region of the tna operon is responsive to the presence of tryptophan but not other amino acids; addition of tryptophan to a growth medium results in a 10-to 100-fold elevation of the tryptophanase level (39). Although the precise mechanism of induction is unknown, previous studies established that addition of tryptophan induces transcription antitermination at one or more Rho factor-dependent termination sites located in the transcribed leader region of the operon (39, 40). Mutations in rho can elevate operon expression (39); also, deletion of a putative Rho utilization (rut) site, located immediately after the tnaC stop codon, resulted in constitutive operon expression (12). The major sites of termination were determined in vitro and in vivo and correspond to positions ϩ234 and ϩ291 relative to the start of transcription (38).Translation of tnaC appears to be required ...

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“…The top of the acceptor stem and the anticodon loop have been shown to interact with Gln-RS and are considered as important identity sites (14,16 (12). The first letter R or D depicts the RNA or DNA origin of the sequence; the second letter indicates the amino acid in the one-letter code; the three first numbers (166) come from the name of the organism (E.coli) and the last number is the number of a particular sequence among isoacceptors.)…”

Section: Resultsmentioning

confidence: 99%

“…Even unique nucleotides (e.g. 20A in tRNAArg, (7)) or nucleotide pairs (3G-70U in tRNAAla, (6,16,23)) are recognized by the corresponding synthetases not as they are, but together with their surroundings. In other words, an identity site can be considered to consist of a set of identity tiles.…”

Section: Discussionmentioning

confidence: 99%

Mosaic tile model for tRNA-enzyme recognition

Steinberg

Kisselev

1993

Nucl Acids Res

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An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucleotide and its neighbours as they are defined by the tertiary structure of the molecule. Informational content of each tile is calculated as its probability to occur exclusively in a set of cognate tRNAs. Based on this algorithm the identity sites of E.coli tRNAAIa and tRNAGIn were determined. The results are in a good agreement with the biochemical data and provide new information about identity sites of these tRNAs.

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Switching tRNA(Gln) identity from glutamine to tryptophan.

Cited by 46 publications

References 48 publications

Enhanced Amino Acid Selection in Fully Evolved Tryptophanyl-tRNA Synthetase, Relative to Its Urzyme, Requires Domain Motion Sensed by the D1 Switch, a Remote Dynamic Packing Motif

Enhanced Amino Acid Selection in Fully Evolved Tryptophanyl-tRNA Synthetase, Relative to Its Urzyme, Requires Domain Motion Sensed by the D1 Switch, a Remote Dynamic Packing Motif

Evidence suggesting cis action by the TnaC leader peptide in regulating transcription attenuation in the tryptophanase operon of Escherichia coli

Mosaic tile model for tRNA-enzyme recognition

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