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Chapter 17 : RNA Editing by Base Conversion in Plant Organellar RNAs

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Abstract:

Awareness of the RNA editing process in plants grew gradually. The first discrepancies in nucleotide identities between mRNA and DNA were noted as the appearance of thymidylates in the sequence ladders of cDNAs at positions of cytidylates in the genomic sequence. The existence of RNA editing in plant mitochondria resolved initial problems with nonconserved amino acid codons found in the plant gene sequences. A schematic view of RNA editing in plant organelles is discussed in this chapter. In analogy to the analysis of RNA editing in other systems, the chapter also presents a separate discussion of the process in plant organelles, that is, the biochemistry of the modification of nucleotide identity and the specificity determinants, which decide where editing should occur. Evolutionary selection and streamlining should have eliminated RNA editing, unless there is some advantage to be gained for the genetic system. RNA editing significantly increases the efforts required to analyze gene expression in plant organelles. RNA editing in plastids and mitochondria also complicates in vitro manipulation of organellar genes and expression. The similarity of the RNA editing processes in plastids and mitochondria of a given plant cell suggests a common evolution of the respective editing processes and very similar mechanistic features.

Citation: Marchfelder A, Binder S, Brennicke A, Knoop V. 1998. RNA Editing by Base Conversion in Plant Organellar RNAs, p 307-323. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch17

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Figures

Image of Figure 1
Figure 1

RNA editing in plastids and mitochondria requires specificity and/or enzymatic factors from the cytoplasm. The enzymatic reaction from C to U has all the characteristics of a deamination, but the reverse reaction U to C requires the amino group at an accessible redox potential. This could possibly be achieved by a transamination rather than a deamination, parking the amino group at an unidentified cofactor X, which presumably can be moved between the different compartments.

Citation: Marchfelder A, Binder S, Brennicke A, Knoop V. 1998. RNA Editing by Base Conversion in Plant Organellar RNAs, p 307-323. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch17
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Image of Figure 2
Figure 2

Protein products of incompletely edited transcripts probably are indiscriminately synthesized and degraded only at the level of folding or complex assembly, both processes being partially organized by chaperones. A large number of slightly variant proteins probably are made from the population of partially edited mRNAs in plant organelles. However, in a mature enzymatic complex only the single functional and “fully edited” protein sequence appears to be stably present.

Citation: Marchfelder A, Binder S, Brennicke A, Knoop V. 1998. RNA Editing by Base Conversion in Plant Organellar RNAs, p 307-323. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch17
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Figure 3

The biochemical process of RNA editing in plant organelles is most likely a deamination or transamination reaction. (A) A deamination reaction catalyzed by an RNA cytosine deaminase would be characterized by the in vitro ion and metal dependencies for the C to U conversion predominant in vascular plants. The reverse reaction, which is much more frequent in hornworts, would require a different enzyme, an RNA cytosine synthase possibly of the CTP synthase type, which requires magnesium ions and GTP as cofactors. (B) Alternatively, a transamination reaction by a putative RNA cytosine transaminase would store the amino group at a fairly high energy level to facilitate the reverse reaction that may be catalyzed by the same enzyme. Such transaminases often require pyridoxal phosphate as a cofactor. Experimental approaches must determine potential dependencies on amino group carriers.

Citation: Marchfelder A, Binder S, Brennicke A, Knoop V. 1998. RNA Editing by Base Conversion in Plant Organellar RNAs, p 307-323. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch17
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Figure 4

There could be ample space for guide RNAs in the mitochondrial genomes of plants. Similarity searches for sequences encoding potential guide RNAs for some selected editing sites in identify candidates that, however, could also be attributed to a chance coincidence in the large chondriome. Shown are examples of potential gRNAs from searches of sequence trains upstream, straddling, and downstream of several identified editing sites. The edited nucleotide position is given for the corresponding database entry, and the edited C nucleotides are highlighted in bold and framed. Analogous guide RNAs (small nucleolar RNAs [snoRNAs]) have been found to specify ribose methylation sites in ribosomal RNA molecules by base pairing, which is not restricted to the rRNAs, but can also target this modification to other RNA molecules ( ).

Citation: Marchfelder A, Binder S, Brennicke A, Knoop V. 1998. RNA Editing by Base Conversion in Plant Organellar RNAs, p 307-323. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch17
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Figure 5

RNA editing is seen in all extant land plants except the Marchantiidae liverworts. The border between plants with editing and plants without (continuous line) is not congruent with the dividing line between land plants and algae (dotted line). Interpretation of independent loss or absence of gain of RNA editing in the Marchantiidae depends on the actual phylogeny, which is not clear at present.

Citation: Marchfelder A, Binder S, Brennicke A, Knoop V. 1998. RNA Editing by Base Conversion in Plant Organellar RNAs, p 307-323. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch17
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