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Chapter 12 : Modified Nucleosides and Codon Recognition

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Abstract:

This chapter focuses on the mechanisms by which the post-transcriptional modifications regulate the codon recognition of tRNAs, primarily from the viewpoint of conformational characteristics of modified nucleosides. Post-transcriptional modifications are heavily involved in the specificities of codon recognition and also of aminoacylation. Interestingly, the roles of the modifications in the anticodon are in many cases the altered conformational properties such as conformational "rigidity" and "flexibility," which directly result in the rigidity or flexibility in codon recognition, although the chemical structures of the modified nucleosides are so much different from each other. It is quite natural because the "wobble" of the base from the original location for the Watson-Crick base pair is essential for non-Watson-Crick base pairing. In the future, more direct structural studies should be done on the anticodon-codon recognition in the decoding center of the ribosome. In addition to such studies at the level of molecular structures, biological studies on the roles of posttranscriptional modifications are required. For example, Q is mostly conserved from bacteria to higher eukaryotes but is missing in tRNAs from and mitochondria. If the Q modification is not indispensable for protein synthesis, it is a wonder that why many organisms have to have such a complicated hypermodification. The real biological role of Q may be to play an essential role in other unknown functions of tRNA. For answering this question, more biological approaches such as gene targeting of modification enzymes in mammalian systems appear to be important and are therefore in progress in laboratories.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12

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Nuclear Magnetic Resonance Spectroscopy
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Figures

Image of Figure 1.
Figure 1.

G•C and G•U base pairs.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 2.
Figure 2.

Base pairs of inosine (I) at first position of anticodon with U, C, A, A+, and G at third position of codon.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 3
Figure 3

C2′-endo and C3′-endo forms of ribose ring, the G andG forms about the C3′—03′ bond, and the gg, gt, and tg forms about C1′—C3′ bond of ribonucleotide unit.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 4.
Figure 4.

G- form about C3′—03′ bond with C2′-endo and C3′-endo forms of ribose ring.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 5
Figure 5

Wobble U•G base pair.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 6
Figure 6

Wobble U•U base pair.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 7
Figure 7

Base pairs of U (or xoU) at first position of anticodon with adenosine (a) and uridine (b) at third position of codons.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 8
Figure 8

U•G and C•A base pairs.•

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 9
Figure 9

C•U and U•U base pairs.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 10
Figure 10

Base pairs of A and G in syn form at first position of anticodon with A or G at third position of codons.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 11
Figure 11

Mechanisms of stabilization of C3′-endo form by 2-thiolation and 2′--methylation of pyrimidine nucleosides.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 12
Figure 12

Hydrogen bonding of 5-methylaminomethyl group of mnmU at position 34 and unmodified U at position 33 in U turn structure of tRNA.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 13
Figure 13

Putative k C•A base pairs in comparison with C•G base pair.

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Image of Figure 14
Figure 14

Queuosine and guanosine (A), conformation of Q at first position of anticodon (B), and Q•U and Q•C base pairs (C).

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12
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Tables

Generic image for table
Table 1.

“Wobble” base pairing of first nucleotide of anticodon with third letter of codon

xoU denotes a 5-hydroxyuridine derivative such as 5-methoxyuridine (moU) and 5-carboxymethoxyuridine (cmoU). xmsU, xmUm, and xmU denote 5-methyl-2-thiouridine, 5-methyl-2′-O-methyluridine, and 5-methyluridine derivatives, respectively, where “xm” denotes, e.g., methylaminomethyl (mum), carboxymethylaminomethyl (cmnm), or methoxycarbonylmethyl (mem) (see appendix 1).

Citation: Yokoyama S, Nishimura S. 1995. Modified Nucleosides and Codon Recognition , p 207-223. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch12

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