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Chapter 16 : The tRNA Identity Problem: Past, Present, and Future

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Abstract:

This chapter describes the current understanding of the structural features in tRNA that determine the specificity of the interaction with the aminoacyl-tRNA synthetase (aaRS), and outlines future research in this area. Early methods of sequence comparison to predict tRNA identity determinants relied only on the structural similarities among isoacceptor tRNAs discerned by visual inspection of the sequences. Positions where the same nucleotide occurs in all isoacceptor species were considered more predictive of tRNA identity than were positions where the nucleotide differed among the isoacceptors. The newer approach relies on computer analysis of tRNA sequences and identifies not only conserved nucleotide positions within a tRNA acceptor group, but also positions with more than one nucleotide that differ from the corresponding nucleotide positions in other tRNA acceptor groups. In addition, because the between-group variation is considered, the newer method provides information for single tRNA sequences and can perform impressively when only two tRNA isoacceptor sequences are known. The chapter summarizes experiments that define specificity determinants in tRNAs for several amino acids, and includes illustrations of computer predictions. The implications of the study results are discussed, and the chapter closes with an outline of future prospects.

Citation: McClain W. 1995. The tRNA Identity Problem: Past, Present, and Future, p 335-347. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch16

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Figures

Image of Figure 1
Figure 1

General tRNA structures. (A) Cloverleaf structure with bases replaced by numbers indicating the standard 76 nucleotide positions. The constant nucleotides are noted. The • symbol indicates Watson-Crick base pairings, and the thin line, other base pairings. B: L-shaped structure with shading of bases 16, 17, 20, 59, and 60 of the variable pocket (VP). Adapted from references and , with permission.

Citation: McClain W. 1995. The tRNA Identity Problem: Past, Present, and Future, p 335-347. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch16
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Image of Figure 2
Figure 2

Histogram showing predicted determinants of tRNA identity obtained by analysis of 67 tRNA sequences. Histograms are shown for tRNA, which has five isoacceptors (A); tRNA, which has two isoacceptors (B); and tRNA, which has one acceptor (C). Frequency of correlation on the vertical axis is a function of tRNA position on the horizontal axis. Cloverleaf parts are indicated on the horizontal axis. A = acceptor stem; D = D stem; C = anticodon stem; X = anticodon; and T = T stem. The middle anticodon nucleotide, residue 35, is indicated. The base and position number of an established specificity determinant is indicated above each data bar. Adapted from references , and , with permission.

Citation: McClain W. 1995. The tRNA Identity Problem: Past, Present, and Future, p 335-347. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch16
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Image of Figure 3
Figure 3

Cloverleaf arrangement of nucleotide sequences of tRNAs corresponding to amber suppressors, indicating standard position numbers for Gly (A), Phe (B), and Lys (C). Nucleotide modifications are not indicated. The ′ symbol represents an alignment gap. Adapted from reference , with permission.

Citation: McClain W. 1995. The tRNA Identity Problem: Past, Present, and Future, p 335-347. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch16
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Figure 4

Comparison of composite nucleotide sequences of amber suppressors representing tRNA-like U73 mutants of tRNA and tRNA and isoacceptors of tRNA (A); non-tRNA-like U73 mutants of tRNA and tRNA (C); and nucleotides common to A and C (B). The positions where the two composites do not contain a common nucleotide are underlined and marked with the * symbol in (B). Incompletely specified nucleotides are designated as M = AC; R = AG; W = AU; S = CG; Y = CU; K = GU; V = ACG; H = ACU; D = AGU; B = CGU; and N = ACGU. An alignment gap is indicated by the ′ symbol. Lowercase letters indicate the position contains either an alignment gap or the indicated nucleotide. Adapted from reference , with permission.

Citation: McClain W. 1995. The tRNA Identity Problem: Past, Present, and Future, p 335-347. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch16
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Figure 5

Histogram showing percentage of Ala inserted in suppressed protein by mutants of amber-suppressor tRNA. Panel A shows wild-type G3•U70 and the 15 possible base 3-base 70 mutant combinations. Panel B shows wild-type G3•U70, several mutants with a G•U wobble pair at position 2•71 or position 4•69, and a mutant with G3•U70 flanked by mutant base pairs. Reproduced from reference , with permission.

Citation: McClain W. 1995. The tRNA Identity Problem: Past, Present, and Future, p 335-347. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch16
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Image of Figure 6
Figure 6

Model of variable pocket of yeast tRNA. The acceptor stem and T stem and part of the D loop are shown as viewed by looking down from a point behind and to the right of the acceptor stem, as shown in Fig. 1B . Bases are represented as hatched circles, phosphates and sugars are shown as open circles, and hydrogen bonds are shown as dashed lines. Open arrows indicate points where the polynucleotide chain continues to other parts of the molecule. Note that the variable pocket is segregated from the constant nucleotides 18, 19, 54, 55, 56, and 58. Reproduced from reference , with permission.

Citation: McClain W. 1995. The tRNA Identity Problem: Past, Present, and Future, p 335-347. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch16
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Image of Figure 7
Figure 7

Structure of small RNAs, including amber- suppressor tRNA (A), deleted derivative lacking the D region (B), and minihelix RNA (C). Modified nucleotides are not indicated. The ′ symbol indicates a deleted nucleotide. Adapted from reference , with permission.

Citation: McClain W. 1995. The tRNA Identity Problem: Past, Present, and Future, p 335-347. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch16
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