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Chapter 19 : Recognition in the Glutamine tRNA System: from Structure to Function

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Abstract:

The ability of aminoacyl-tRNA synthetases (aaRS) to faithfully recognize both their amino acid and tRNA substrates is essential for accurate protein synthesis. This chapter focuses on the recognition of tRNA by glutaminyl-tRNA synthetase (GlnRS). This system is arguably the best characterized aaRS-tRNA interaction both functionally and structurally, as the first high-resolution crystal structure of a protein-RNA complex was solved for GlnRS:tRNA. The chapter summarizes the characteristics of the GlnRS:tRNA system that make GlnRS unique among aaRS, as well as those that make the glutamine system an ideal model for the study of protein-RNA interaction, specifically aaRS-tRNA interaction. Together the crystal structure, genetic, and biochemical studies have identified the most important specificity determinants from among the hundreds of contacts between GlnRS and tRNA. The chapter also describes several of the more interesting aspects of the GlnRS:tRNA system: (1) the close evolutionary relationship between GlnRS and glutamyl-tRNA synthetase (GluRS); (2) GlnRS's relaxed discrimination against noncognate tRNAs coupled with its "overdetermined," tight recognition of its cognate tRNA; and (3) the enzyme mechanism of GlnRS, specifically the structural and functional communication that permits this small monomeric aaRS to recognize tRNA identity elements that are more than 75Å apart in uncomplexed tRNA. The information obtained from biophysical techniques (crystallography, fluorescence, and x-ray/neutron scattering) and from genetic and biochemical approaches is combined to yield a coherent and detailed picture of the specific recognition of tRNA by GlnRS.

Citation: Sherman J, Rogers M, Söll D. 1995. Recognition in the Glutamine tRNA System: from Structure to Function, p 395-409. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch19

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Amino Acids
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Transfer RNA
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Genetic Selection
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Gene Duplication
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Figures

Image of Figure 1.
Figure 1.

The relaxed tRNA specificity of GlnRS applies to amber (anticodon CUA), not opal (anticodon UCA) suppressor tRNAs. Shown are the acceptor stems of the various tRNAs. While many amber suppressors (top two rows) or their mutants (bottom row) insert glutamine (%Q) in vivo, the opal suppressors derived from these same tRNAs, which have been tested, insert little (*) or no (**) glutamine in vivo. (Adapted from references .)

Citation: Sherman J, Rogers M, Söll D. 1995. Recognition in the Glutamine tRNA System: from Structure to Function, p 395-409. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch19
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Image of Figure 2.
Figure 2.

Comparison of in vivo identity of amber (UAG) and opal (UGA) suppressors derived from tRNA. The amber suppressor , also known as (SuUAG), is overdetermined for glutamine identity, because even multiple mutations in this context do not severely impair the glutamine specificity of these mutant tRNAs. On the other hand, the opal suppressor op already inserts 88% tryptophan into dihydrofolate reductase. Additional mutations abolish GlnRS recognition. These mutant tRNAs are also probably not recognized well by other aaRS, as several of them are inactive suppressors. (Adapted from references , and .)

Citation: Sherman J, Rogers M, Söll D. 1995. Recognition in the Glutamine tRNA System: from Structure to Function, p 395-409. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch19
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Image of Figure 3.
Figure 3.

The effect of competition and tRNA context on the in vivo identity of amber suppressor tRNAs. In vitro, in its cognate tRNA context, GlnRS clearly prefers purine over pyrimidine discriminators ( ). However, in vivo, (SuUAG)-U73 inserts more glutamine into dihydrofolate reductase than the A/G73 variants, partially due to a lack of competition for (SuUAG)-U73 ( ). Similarly, of all the aaRS in , GlnRS, despite its tendency to favor purines in the discriminator position in tRNA, competes most effectively for the U73 mutants of the noncognate amber suppressors and (SuUAG). Even more surprisingly, the A73 mutant of is glutamate-specific, while , with its wild-type discriminator is not ( ). Clearly, the identity of in vivo is determined by competition, with GlnRS competing less effectively for - than for -G73.

Citation: Sherman J, Rogers M, Söll D. 1995. Recognition in the Glutamine tRNA System: from Structure to Function, p 395-409. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch19
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Image of Figure 4.
Figure 4.

Pathway for evolutionary divergence of the glutamate and glutamine aminoacylation systems. This model ( ) is based on the preference of GluRS for U34-containing anticodons and on the fact that, in gram-positive eubacteria, archaebacteria, and organelles, GlnRS does not exist, and both glutamate and glutamine tRNAs have a U at position 34. GlxRS is an ancestral aaRS specific for both glutamate and glutamine. In gram-positive bacteria, duplication of the gene for GlxRS, coupled with divergence at position 36 of tRNA and tRNA, may have led to the evolution of the Glu-tRNAamidotransferase and GluRS, with their respective glutamine and glutamate tRNA and amino acid specificities. In gram-negative bacteria, the creation by gene duplication and mutation of tRNA and duplication of the GlxRS gene is proposed to have led to co- evolution of GlnRS, with its C34-G36 specificity, and of tRNA. Dashed lines connect cognate tRNAs and aaRS and the broken arrow represents the possible divergence of the amidotransferase from a primitive GlxRS.

Citation: Sherman J, Rogers M, Söll D. 1995. Recognition in the Glutamine tRNA System: from Structure to Function, p 395-409. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch19
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