The Anticodon Contains a Major Element of the Identity of Arginine Transfer RNAs

Schulman, LaDonne H.; Pelka, Heike

doi:10.1126/science.2688091

Cited by 97 publications

(75 citation statements)

References 22 publications

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“…Normanly and Abelson (23) estimate that about half of the E. coli tRNAs utilize nucleotides outside of the anticodon to determine amino acid specificity. On the other hand, Schulman and Pelka (28,29) have shown that the anticodon is the major determinant for the identities of E. coli methionine, valine, and arginine tRNAs, and Muramatsu et al (22) provided evidence that the anticodon is also critical for determining the efficiency and specificity of charging E. coli isoleucine tRNA. The three anticodon nucleotides are also among the five bases that act as determinants for yeast phenylalanine tRNA identity (26).…”

Section: Discussionmentioning

confidence: 99%

A single base pair dominates over the novel identity of an Escherichia coli tyrosine tRNA in Saccharomyces cerevisiae.

Trezeguet¹,

Edwards²,

Schimmel³

1991

Mol. Cell. Biol.

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The Escherichia coli su+3 tyrosine tRNA was shown recently to be a leucine-specific tRNA in Saccharomyces cerevisiae. This finding raises the possibility that some determinants for tRNA identity in E. coli may be different in S. cerevisiae. To investigate whether the fungal system is sensitive to the major determinant for alanine acceptance in E. coli, a single G3. U70 base pair was introduced into the acceptor helix of the su+3 tyrosine tRNA. This substitution converts the identity of the E. coli suppressor in S. cerevisiae from leucine to alanine. Thus, as in E. coli, G3-U70 is a strong determinant for alanine acceptance that can dominate over other features in a tRNA that might be recognized by alternative charging enzymes.In principle, the determinants for the identity of a tRNA can differ from organism to organism without compromising the conservation of the genetic code. The only requirement is that the anticodon triplet of each tRNA must specify the same amino acid from one organism to another. In the case of Escherichia coli alanine tRNA, a single G3 U70 base pair is a major determinant for identity (9, 13). Substitution of this base pair with G C, A. U, or U G abolishes aminoacylation with alanine, and transfer of G3 U70 into E. coli tRNACYS, tRNAPhe, and tRNATYr can confer total or partial alanine acceptance on each (13,14,21,25). Cytoplasmic Bombyx mori and human alanine tRNAs each encode a G3 U70 base pair, and the aminoacylation of these tRNAs by their homologous enzymes is abolished when that base pair is changed to G C or A. U. Moreover, expression of these eukaryotic tRNAs in E. coli results in charging with alanine and no other detectable amino acid (15). Thus, in the evolution of these alanine tRNAs, the G3 -U70 base pair has been conserved. Furthermore, nucleotide sequence differences in other parts of the B. mori and human cytoplasmic alanine tRNAs do not encode major determinants for any other E. coli aminoacyl-tRNA synthetase.In contrast to the results obtained with alanine tRNAs, the identity of the E. coli su+3 tyrosine tRNA is changed in the yeast Saccharomyces cerevisiae. This amber suppressor inserts only tyrosine in E. coli, but in S. cerevisiae only leucine is inserted at the position of an amber codon (7). This change in specificity may correlate with a switch in the type class of cytoplasmic tyrosine tRNAs in comparisons of E. coli with S. cerevisiae. In E. coli, tyrosine, leucine, and serine tRNAs are type II tRNAs, which have three base pairs in the dihydrouridine stem and 13 to 22 nucleotides in the variable loop (also known as the extra arm). The remaining E. coli tRNAs are type I tRNAs which typically have four base pairs in the dihydrouridine stem and five nucleotides in the variable loop. While the cytoplasmic leucine and serine tRNAs are also type II structures in S. cerevisiae, the tyrosine tRNA is a type I molecule. Thus, the switch in identity of the su+3 tyrosine tRNA in S. cerevisiae may mean that, in the evolution of some tRNAs, molecules in the The mode of recognitio...

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Section: Discussionmentioning

confidence: 99%

A single base pair dominates over the novel identity of an Escherichia coli tyrosine tRNA in Saccharomyces cerevisiae.

Trezeguet¹,

Edwards²,

Schimmel³

1991

Mol. Cell. Biol.

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“…It is possible in vitro to alter a tRNA's amino acid charging identity by anticodon mutations (Schulman and Pelka 1989;Pallanck and Schulman 1991). It has also been shown that mutations outside the anticodon, for example, involving acceptor stem nucleotides that are strong identity determinants, can also effectively switch the identity of a tRNA (Hipps et al 1995).…”

Section: Introductionmentioning

confidence: 99%

tRNA anticodon shifts in eukaryotic genomes

Rogers

Griffiths-Jones

2014

RNA

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Embedded in the sequence of each transfer RNA are elements that promote specific interactions with its cognate aminoacyl tRNAsynthetase. Although many such "identity elements" are known, their detection is difficult since they rely on unique structural signatures and the combinatorial action of multiple elements spread throughout the tRNA molecule. Since the anticodon is often a major identity determinant itself, it is possible to switch between certain tRNA functional types by means of anticodon substitutions. This has been shown to have occurred during the evolution of some genomes; however, the scale and relevance of "anticodon shifts" to the evolution of the tRNA multigene family is unclear. Using a synteny-conservation-based method, we detected tRNA anticodon shifts in groups of closely related species: five primates, 12 Drosophila, six nematodes, 11 Saccharomycetes, and 61 Enterobacteriaceae. We found a total of 75 anticodon shifts: 31 involving switches of identity (alloacceptor shifts) and 44 between isoacceptors that code for the same amino acid (isoacceptor shifts). The relative numbers of shifts in each taxa suggest that tRNA gene redundancy is likely the driving factor, with greater constraint on changes of identity. Sites that frequently covary with alloacceptor shifts are located at the extreme ends of the molecule, in common with most known identity determinants. Isoacceptor shifts are associated with changes in the midsections of the tRNA sequence. However, the mutation patterns of anticodon shifts involving the same identities are often dissimilar, suggesting that alternate sets of mutation may achieve the same functional compensation.

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“…This tendency corresponds well to the fact that the A20 mutations of E. coli tRNA Arg mostly affected V max , rather than K m , in the arginylation (16). These results suggest that the A20 recognition mainly contributes to the ''enzyme activation,'' which may include changes in the spatial arrangement of important residues in the catalytic cleft and͞or the CCA terminus of the tRNA.…”

Section: Mutational Analyses Of the Argrsmentioning

confidence: 61%

“…In contrast, tRNA Arg utilizes an adenosine at position 20 for the nonanticodon major identity element, which is completely conserved among the tRNA Arg species in most organisms, and is missing in other tRNA species (14,15). Actually, genetic and biochemical studies of Escherichia coli tRNA Arg demonstrated that A20 is one of the major identity elements of tRNA Arg , with a very high discrimination rate of three orders of magnitude on average (14,(16)(17)(18)(19). A20 is located in a small, single-stranded region in the D loop at the outside corner of the L-shaped tRNA structure, which is far from both the anticodon and the acceptor stem.…”

mentioning

confidence: 99%

Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase

Shimada

Nureki

Goto

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNA Arg : A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few exceptional organisms, such as the yeast Saccharomyces cerevisiae, lack A20 in tRNA Arg . In the present study, we solved the crystal structure of a typical A20-recognizing ArgRS from Thermus thermophilus at 2.3 Å resolution. The structure of the T. thermophilus ArgRS was found to be similar to that of the previously reported

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The Anticodon Contains a Major Element of the Identity of Arginine Transfer RNAs

Cited by 97 publications

References 22 publications

A single base pair dominates over the novel identity of an Escherichia coli tyrosine tRNA in Saccharomyces cerevisiae.

A single base pair dominates over the novel identity of an Escherichia coli tyrosine tRNA in Saccharomyces cerevisiae.

tRNA anticodon shifts in eukaryotic genomes

Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase

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