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Chapter 13 : tRNA Sequences and Variations in the Genetic Code

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Abstract:

This chapter reviews the recent status of variations in the genetic code in various mitochondrial and nuclear systems. It explains relationship between the reading patterns of the changed codons and the anticodons of the tRNAs involved. It also considers mRNA editing in plant and protozoan organelles and a revision of codon assignments on the basis of protein gene sequences in the universal code, which is based on mRNA sequences for the proteins.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13

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Saccharomyces cerevisiae
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Figures

Image of Figure 1a
Figure 1a

Nucleotide sequences of tRNA or its gene from mitochondria of various organisms shown in cloverleaf form ( ). Almost all sequences are derived from the tRNA gene sequences; those of bovine animals ( ), rats ( ), ( ), ( ), and ( ) are derived from the tRNA sequences. The secondary structures are constructed according to the common rule for the cloverleaf form of usual tRNAs. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 1b
Figure 1b

Nucleotide sequences of tRNA or its gene from mitochondria of various organisms shown in cloverleaf form ( ). Almost all sequences are derived from the tRNA gene sequences; those of bovine animals ( ), rats ( ), ( ), ( ), and ( ) are derived from the tRNA sequences. The secondary structures are constructed according to the common rule for the cloverleaf form of usual tRNAs. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 1c
Figure 1c

Nucleotide sequences of tRNA or its gene from mitochondria of various organisms shown in cloverleaf form ( ). Almost all sequences are derived from the tRNA gene sequences; those of bovine animals ( ), rats ( ), ( ), ( ), and ( ) are derived from the tRNA sequences. The secondary structures are constructed according to the common rule for the cloverleaf form of usual tRNAs. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 2
Figure 2

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). Only the sequence of was determined at RNA level. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 3
Figure 3

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). Only the sequence of yeast ( ) was determined at the RNA level. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 4
Figure 4

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 5
Figure 5

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 6
Figure 6

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). The sequence of yeast tRNA ( ) was determined at RNA level. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 7
Figure 7

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). The sequences of hamster ( ) and yeast ( ) tRNAs were determined at RNA level. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 8
Figure 8

Incorporation of [3H]amino acids into hot trichloroacetic acid-insoluble material in cell-free translation systems from (a) and (b and c). The mRNAs used are shown above the figures. In (c), two UGAs are replaced by UGGs. (From reference with permission.)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 9
Figure 9

Secondary structure of tRNA and tRNA . (From reference .)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 10
Figure 10

Tryptophan tRNA genes from three spp. of (a) (from reference ); (b) (from reference and with permission); and (c) M. (from reference ).

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 11
Figure 11

Secondary structure of three species of glutamine tRNAs. (From reference with permission of Oxford University Press.)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 12
Figure 12

Incorporation of [H]amino acids into hot trichloroacetic acid-insoluble material in cell-free translation systems from and The mRNA used is shown above the figure. (Reprinted with permission from [ ]. Copyright 1989 Macmillan Magazines Limited.)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 13
Figure 13

Secondary structure of tRNA (a) and its gene (b) in In b, the anticodon CAG is highlighted. Splicing sites for the tRNA gene are shown by solid arrows and possible splicing sites for the putative ancestral tRNA gene are shown by dotted arrows. (Adapted from reference .)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Image of Figure 14
Figure 14

Model for translation blockage by unassigned codon CGG (A to B). Compare B with C and D, in which release factor recognizes a stop codon UAA, followed by release of peptidyl-tRNA (D). (Adapted from reference .)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
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Tables

Generic image for table
Table 1

Current Status of codon-anticodon pairing rules

Adapted from reference .

For modified bases, see chapter 12.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 2

Variations in mitochondrial genetic code

ND = not determined; — = same as universal code.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 3

Summary of the correlation between altered codons and the corresponding tRNA anticodons in mitochondrial systems of various organisms

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 4

Variations in eubacterial and in nuclear genetic code from “universal” genetic code

— = same as universal code, or not determined; N = not known; *U - cmnm5Um.

Determined for Mycoplasma capricolum ( ). Gene for tRNA with anticodon UCA was found in , , and ( ).

Determined for , , , , , and ( ).

Determined for ( ).

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 5

Effeet of genomic G+C content on eubacterial tRNA anticodon compositions and codon-anticodon pairing patterns

Table shows the general tendency of anticodon compositions in eubacteria with various genomic G+C contents and does not necessarily indicate that all boxes and sets actually have these compositions. Modification of U is not indicated (see Table 1 ). Reprinted from reference .

The bacteria are arranged in descending order of G+C content. c D = deletion.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 6

Unassigned or nonsense codons

Yeast mitochondria

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 7

Examples of RNA editing occurring in plant mitochondria

+, RNA ediring in mitochondria.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13

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