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Chapter 3 : Structure and Expression of Prokaryotic tRNA Genes

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Abstract:

This chapter presents a summary of information on the structures and organization of prokaryotic tRNA genes based on recent work surveying the total tRNA populations and tRNA genes in by Ozeki’s group at Kyoto and in by Osawa’s group at Nagoya. Most importantly, and are the only cases to date in which the total tRNA systems have been well elucidated, including the sequences of a complete set of tRNAs, the organization and expression of their genes, composition of the full anticodon set, and the relative levels of each tRNA species in the cells. In general, tRNA genes are found in clusters. For example, among 79 tRNA genes of , only 20 exist as a single gene. The remaining 59 are organized in polycistronic operons containing identical or unrelated tRNA, rRNA genes, and protein-encoding genes. In , 22 of 30 tRNA genes are organized in five clusters comprising nine, five, four, and two genes, respectively. The other eight genes exist as single transcription units. In summary, the decoding system of is significantly different from that of in the number of anticodons, codon recognition patterns, and, in two cases, codon assignment.

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3

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Figures

Image of Figure 1
Figure 1

Screen for tRNA genes: example of autoradiogram from screen for clones encoding tRNAs. Four gels (20 samples each) analyzing clones 101 to 180 from Kohara's miniset of λ clones ( ) are shown. P-labeled RNA samples were prepared as follows: cultures of strain CA274, heavily irradiated with UV light (3 min at a dose of 10 ergs/mm per second), were infected with each phage clone (multiplicity of infection, about 10) and labeled with [P]orthophosphate in a scaled-down version (25 ml per sample) of the method previously described ( ). After a 3-h incubation at 37°C in the presence of chloramphenicol (150g/ml), P-labeled RNAs were isolated from the infected cultures by phenol extraction and were separated by electrophoresis in 10% (wt/vol) polyacrylamide gel slabs (45 cm long, 30 cm wide, and 0.35 mm thick) containing 50 mM Tris-borate buffer (pH 8.3) and 8 M urea. The serial numbers of clones that encode tRNAs are shown. Arrows indicate 5S rRNA and tRNA. The asterisk indicates a partial transcript of the λ N gene. This band indicated a successful infection by each clone and acted as an internal size marker, dividing the bands of tRNAs from 5S rRNA and other small RNAs on the autoradiogram. The top scale indicates physical map locations.

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Figure 2

Comprehensive map of the tRNA genes in K-12. The tRNA gene designations specify the various isoacceptor species encoded and their order of transcription. Designations for tRNA genes in the rRNA operons are followed by the name of the operon in parentheses, in which each operon is indicated. Small arrows inside the outer circle indicate the orientation of each transcriptional unit. The numbers in the outer circle indicate the scale of the physical map in kilobases. The numbers in the inner circle are the corresponding scale of the genetic map in minutes (min). The replication origin (oriC) and termination (terC) sites are indicated. Although the information in this map was based on studies using Kohara's clone library, a large inversion was found in Kohara's physical map for strain W3110; the correct orientation of the chromosome is depicted here.

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Figure 3

Numbers of isoacceptors in . tRNAs specific for individual amino acids were labeled by Andachi et al. ( ) according to the method of Traboni et al. ( ). Deacylated total tRNAs (100 g) of were aminoacylated at 30°C for 1 hour, with each amino acid present at 120 mM in a reaction mixture (300 l) containing 100 mM sodium cacodylate (pH 7.0), 10 mM magnesium acetate, 10 mM KC1, 2 mM ATP, 2 mM -mercaptoethanoI, and 30 l of S-100 fraction. The tRNAs were recovered from the mixture by extraction with phenol and incubated in 50 l of 100 mM sodium metaperiodate (pH 4.5) for 30 min at room temperature in the dark to oxidize ribose at the 3′ end of nonaminoacylated tRNAs, leaving aminoacylated tRNA unoxidized. The reaction was stopped by the addition of 5 l of 1 M rhamnose, and incubation was continued for 30 min at room temperature in the dark. After precipitation with ethanol, the tRNAs were incubated in 100 l of 0.5 M lysine (pH 8.8) at 37°C for 30 min for -elimination of oxidized, or for deacylation of unoxidized, tRNAs. For selective 3′ end labeling of unoxidized tRNA species, total tRNAs (2 g) treated as described above were incubated at 4°C for 2 hours with 10 Ci of 5′-[P]pCp (3,000 Ci/mmol) and 1 unit of phage T4 RNA ligase in a volume of 10 l, as described by England et al. ( ). The labeled tRNA for each of the 20 amino acids was separated by electrophoresis with 12% polyacrylamide-7 M urea gel and exposed on an x-ray film.

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Figure 4

Organization of tRNA gene clusters. Tandemly arrayed tRNA genes in (a) and (b). Individual tRNA genes are represented by hatched boxes. The symbols P, AT, and T indicate promoter, attenuator, and terminator of transcription, respectively. The anticodons of each tRNA species are shown in parentheses as DNA sequences. The numbers represent base pairs between the tRNA genes. The position of each cluster on the linkage map of ( ) is shown in the hollow box preceding each array.

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Figure 5

Structures of rRNA operons of K-12. The overall organization of the seven operons is represented schematically in the upper part of the figure. The brackets mark tRNA or 5S RNA genes that are not common to all operons. The direction of transcription is from left to right. The identities of the known tRNA genes are given for each operon in the lower portion of the figure. Sequenced tRNA genes are identified with bold letters.

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Figure 6

DNA sequence similarity of 16S and 23S rRNA genes in H and D operons. Stars indicate the bases identical in both sequences. Stippled regions represent coding regions for the 16S and 23S rRNA genes (partial) and the spacer tRNAs (tRNA and tRNA ).

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Figure 7

Mixed-function operons containing tRNA and protein-encoding genes in . The open boxes represent the open reading frame (ORF) or gene indicated. For explanation of symbols, see Fig. 4 legend.

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Figure 8

Comparison of tRNA gene promoters and prokaryotic promoter consensus sequence. The overall organization and sequences of the promoter elements are shown in schematic form in the upper part of the figure. Distances between the elements and tRNA gene (stippled box) are not drawn to scale. The numbers in the lower portion of the figure indicate the numbers of tRNA gene promoters carrying the consensus residue at each position; 34 promoters and 14 promoters were compared.

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Image of Figure 9
Figure 9

Repeat structures found in 3′ regions of tRNA genes and in distal flanking sequences. Arrows indicate repeated sequences. Dashed arrows indicate weak homology. The stippled part of the tRNA gene represents the 18 to 19 bp of the 3′ terminal region of tRNA. The minutes (min) correspond to those of the genetic map of ( Fig. 2 ).

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Figure 10

Temperate phage attachment sites in the 3′ regions of tRNA genes. Integration occurs by recombination in the hatched region. The bold line represents the phage genome. The putative products of several integration events are represented in the lower portion of the figure.

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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Figure 11

Correlation between tRNA levels and amino acid usage. Relative tRNA content for each amino acid in (closed circle) and (open circle) is plotted against the usage of each amino acid in proteins. (Values taken from Table 2 .)

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
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References

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Tables

Generic image for table
Table 1

Anticodon tables

In each codon box, the sequence of the anticodon species is shown, followed by the corresponding gene copy number and the relative abundance of each tRNA in the cell. Values in the last column = relative usage (0.1%) of each codon, as calculated from codon usage table integrated from GenBank data on genes (see reference ) or from sequences of ribosomal protein genes of (about 6,800 codons) (see reference ). Minor = abundance too low for accurate measurement; ND = no data available.

Modifications of anticodon first nucleosides are as follows: 5-Carboxymethylaminomethyl-2′-O-methyluridine(cmnmUm).

Uridine-5-oxyacetic acid (oU).

Queuosine (Q).

Probably modified.

Probably 2-thiouridine (sU).

Inosine (I).

4-Amino-2-(N-lysino)-l-(-ᴅ-ribofuranosyl) pyrimidinium (lysidine).

N-Acetylcytidine (acC).

5-Methylaminomethyl-2-thiouridine (mnmsU).

5-Methoxycarbonylmethyluridine (mcmU).

Unidentified modification.

Partially 2′--methylcytidine (Cm).

5-Carboxymethylaminomethyluridine (cmnmU).

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3
Generic image for table
Table 2

Amino acid usage and relative content of cognate tRNAs in cells

tRNA content is shown as total amount of tRNAs for that amino acid, normalized to that of tRNALeu3/UAG for and to that of tRNALeuUAA for . ND = no data available.

Amino acid usage (%) of was calculated from codon usage tabulated from the GenBank genetic sequence data by Aota et al. ( ), and that of was calculated from the codon usage in its ribosomal protein genes ( ).

Amino acid composition in total cellular proteins (%) ( ).

Citation: Inokuchi H, Yamao F. 1995. Structure and Expression of Prokaryotic tRNA Genes, p 17-30. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch3

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