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Chapter 16 : Editing of tRNA

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Abstract:

The term "RNA editing" was first coined more than a decade ago to describe the phenomenon of uridine insertion into trypanosomatid mitochondrial transcripts. Unlike mRNAs, transcripts of tRNA and rRNA genes are themselves converted into the functional entities they encode. RNA editing events represent additional steps in posttranscriptional processing and, like nucleoside modifications, they may occur at different stages in the pathway. To quantify RNA editing one usually compares the intensity of the bands on a sequencing (or primer extension) ladder that correspond to the edited and unedited versions of the RNA. The first example of tRNA editing in a mitochondrial (mt) system is that reported to occur in the ameboid protozoon . The observed nucleotide substitutions consisted of both purine-to-purine and pyrimidine- to-purine changes, suggesting a mechanism involving base or nucleotide replacement. More recently, it has been shown that nascent mRNAs present in stalled RNA polymerase complexes are substrates for editing by both cytidine and dinucleotide insertion. In a particular study the isolated RNAs were found to be edited to within 14 to 22 nucleotides of the stalled polymerase, suggesting that the insertional editing activity in is able to act quite close to the site of RNA synthesis. The most recently described mode of tRNA editing is that found in the mitochondria of metazoa.

Citation: Price D, Gray M. 1998. Editing of tRNA, p 289-305. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch16

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Figures

Image of Figure 1
Figure 1

Generalized tRNA processing pathway, showing the major steps in the maturation of a typical pre-tRNA. The various known tRNA editing systems (bold captions) act at different stages in the maturation of tRNA, thereby constituting additional steps in the processing pathway. The final diagram is of a generalized tRNA secondary structure, showing the various helical and loop regions and conserved nucleosides that are discussed in the text [Y, pyrimidine; T, 5-methyluridine (‘ribothymidine’); Ψ, pseudouridine (5-ribosyluracil)]. Positions encompassing the anticodon sequence (residues 34–36) are shaded. The extra 5′-nucleotide that is present only in tRNA is drawn lightly.

Citation: Price D, Gray M. 1998. Editing of tRNA, p 289-305. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch16
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Image of Figure 2
Figure 2

Diagrammatic representations of tRNA secondary structure indicating the positions (filled circles) at which editing is known to occur in different mitochondrial tRNA editing systems. (A) spp., nucleotide replacements at one or more of the first three positions at the 5′-end; (B) , nucleotide insertions at the indicated positions (solid lines denote that a single-nucleotide insertion occurs within the delineated region [shaded circles], but cannot be localized precisely); (C) nucleotide replacements within the 3′-half of the acceptor stem in metazoan animals; C-to-U substitution in the central position of the anticodon sequence of marsupial mitochondrial tRNA; (D) land plants (angiosperms and gymnosperms), C-to-U substitutions at the indicated positions.

Citation: Price D, Gray M. 1998. Editing of tRNA, p 289-305. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch16
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Image of Figure 3
Figure 3

Structures of the acceptor stems of the 13 mtDNA-encoded tRNAs that are edited, with arrows indicating the 26 edits that generate G:C or A:U base pairs at initially mispaired, or U•G/G•U-paired, positions. All of the predicted edits have been verified experimentally ( ).

Citation: Price D, Gray M. 1998. Editing of tRNA, p 289-305. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch16
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Image of Figure 4
Figure 4

Working models of mitochondrial tRNA editing. (A) (mt-tRNAAsp): (1) 5′ and 3′ processing by specific endo- and exonucleases to remove flanking sequences (boxed); (2) removal of the first three 5′-nucleotides (boxed) by a specific endonuclease or 5′-to-3′ exonuclease; (3) replacement of the first three 5′-nucleotides by a template-dependent 3′-to-5′ nucleotidyltransferase; (4) addition of the -CCA extension by a template-independent 5′-to-3′ tRNA nucleotidyltransferase. (B) Metazoan animals (the example provided is mt-tRNAGly of ): (1) 5′ processing of a downstream, overlapping tRNA sequence results in loss of several 3′-nucleotides (boxed nucleotides); (2) template-independent 5′-to-3′ addition of A residues (oligoadenylation); (3) 3′ processing immediately after the discriminator nucleotide (position 73 [ Fig. 1 ]); (4) addition of the -CCA extension by a template-independent 5′-to-3′ tRNA nucleotidyltransferase.

Citation: Price D, Gray M. 1998. Editing of tRNA, p 289-305. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch16
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Image of Figure 5
Figure 5

Aminoacylation of edited and unedited mt-tRNA in . Following transcription from a single gene, the 5′- and 3′-processed mt-tRNA transcript may undergo C-to-U editing at position 35. The unedited isoform, mt-tRNA(GCC), is aminoacylated with glycine, whereas the edited isoform, mt-tRNA(GUC), is aminoacylated with aspartate.

Citation: Price D, Gray M. 1998. Editing of tRNA, p 289-305. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch16
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Figure 6

Generalized evolutionary scheme for the emergence of an RNA editing activity.

Citation: Price D, Gray M. 1998. Editing of tRNA, p 289-305. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch16
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Tables

Generic image for table
Table 1

Editing and processing of plant mt-tRNAs

Citation: Price D, Gray M. 1998. Editing of tRNA, p 289-305. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch16

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