A prokaryotic‐type cytidine deaminase from <i>Arabidopsis thaliana</i>

Faivre-Nitschke, Sandrine Emmanuelle; Grienenberger, Jean‐Michel; Gualberto, José M.

doi:10.1046/j.1432-1327.1999.00591.x

Cited by 47 publications

(30 citation statements)

References 35 publications

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“…Analogous observations with the in vitro systems for tobacco and pea chloroplasts further support the similarity between the editing processes in both organelles (8,9). The most likely enzyme able to catalyze this reaction could be one of (or a homologue of) the cytidine deaminases identified in plants (18) as well as in other organisms. One of these deaminases is in mammals the crucial enzyme of the apolipoprotein mRNA C to U editing (19).…”

supporting

confidence: 72%

“…Problematic for this group of deaminases, however, appears to be the reverse reaction, because none of the homologous enzymes from various organisms has been found to be able to catalyze the amination step leading to a U to C conversion. The recent identification of this class of enzymes in Arabidopsis thaliana will allow us to determine their potential involvement in RNA editing (18).…”

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confidence: 99%

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In Vitro RNA Editing in Pea Mitochondria Requires NTP or dNTP, Suggesting Involvement of an RNA Helicase

Takenaka

Brennicke

2003

Journal of Biological Chemistry

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To analyze the biochemical parameters of RNA editing in plant mitochondria and to eventually characterize the enzymes involved we developed a novel in vitro system. The high sensitivity of the mismatch-specific thymine glycosylase is exploited to facilitate reliable quantitative evaluation of the in vitro RNA editing products. A pea mitochondrial lysate correctly processes a C to U editing site in the cognate atp9 template. Reaction conditions were determined for a number of parameters, which allow first conclusions on the proteins involved. The apparent tolerance against specific Zn 2؉ chelators argues against the involvement of a cytidine deaminase enzyme, the theoretically most straightforward catalysator of the deamination reaction. Participation of a transaminase was investigated by testing potential amino group receptors, but none of these increased the RNA editing reaction. Most notable is the requirement of the RNA editing activity for NTPs. Any NTP or dNTP can substitute for ATP to the optimal concentration of 15 mM. This observation suggests the participation of an RNA helicase in the predicted RNA editing protein complex of plant mitochondria.RNA editing has been observed in various forms in diverse organisms including trypanosomes, mammals, slime molds, and land plants (1). In land plants, RNA editing has so far been reported in mitochondria and plastids. In flowering plants the majority of this organellar editing involves C to U conversions, with U to C changes occurring much more infrequently and only in mitochondria (2, 3, 4). In non-flowering plants this latter direction of RNA editing is much more common in mitochondria as well as in chloroplasts, the U to C reactions almost reaching the frequency of the C to U editing in the hornworts (5). Since its discovery more than a decade ago, progress into understanding how this process works has been hampered by the lack of manageable and reliable in vitro systems. The first in vitro system for plant mitochondrial RNA editing was successfully developed from wheat embryos (6), but has not been exploited further.Conclusions about the determinants of specificity during RNA editing in mitochondria and in plastids have initially been drawn from comparisons of transcribed sequence duplications (e.g. 7). Such comparisons suggested that upstream (5Ј) sequences are crucial in targeting the editing machinery and that downstream similarities are not sufficient to specify a site.These observations were corroborated by the recent breakthrough development of an in vitro editing system for plastids (8, 9) and an electroporation protocol for mitochondria (10,11). Mutational analysis of templates in these as well as in in vivo experiments in transgenic chloroplasts (12)(13)(14) showed that for several editing sites 20 -30 nucleotides upstream and 2-5 nucleotides downstream are sufficient to guide the editing activity, precisely what had initially been deduced for mitochondria (7).The biochemistry of this RNA editing activity is still largely unclear, and more detailed u...

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confidence: 72%

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confidence: 99%

In Vitro RNA Editing in Pea Mitochondria Requires NTP or dNTP, Suggesting Involvement of an RNA Helicase

Takenaka

Brennicke

2003

Journal of Biological Chemistry

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“…Fifteen genes were selected (see Supplemental Figure 1 online). Among them eight correspond to the CDA family of cytidine deaminases and were discounted because they lack the requirements for an organellar RNA editing enzyme, namely, organellar targeting sequences, affinity for RNA, deaminase activity on RNA substrates, and conservation in other plant species (Faivre-Nitschke et al, 1999;S.E. Faivre-Nitschke and J.M.…”

Section: Tada Is a Nuclear Gene Encoding A Protein Containing A Consementioning

confidence: 99%

Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNAArg(ACG) and Is Essential for Efficient Chloroplast Translation

et al. 2009

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RNA editing changes the coding/decoding information relayed by transcripts via nucleotide insertion, deletion, or conversion. Editing of tRNA anticodons by deamination of adenine to inosine is used both by eukaryotes and prokaryotes to expand the decoding capacity of individual tRNAs. This limits the number of tRNA species required for codon-anticodon recognition. We have identified the Arabidopsis thaliana gene that codes for tRNA adenosine deaminase arginine (TADA), a chloroplast tRNA editing protein specifically required for deamination of chloroplast (cp)-tRNA Arg (ACG) to cp-tRNA Arg (ICG). Land plant TADAs have a C-terminal domain similar in sequence and predicted structure to prokaryotic tRNA deaminases and also have very long N-terminal extensions of unknown origin and function. Biochemical and mutant complementation studies showed that the C-terminal domain is sufficient for cognate tRNA deamination both in vitro and in planta. Disruption of TADA has profound effects on chloroplast translation efficiency, leading to reduced yields of chloroplast-encoded proteins and impaired photosynthetic function. By contrast, chloroplast transcripts accumulate to levels significantly above those of wild-type plants. Nevertheless, absence of cp-tRNA Arg (ICG) is compatible with plant survival, implying that two out of three CGN codon recognition occurs in chloroplasts, though this mechanism is less efficient than wobble pairing.

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“…For example, cytidine deaminase genes have been pulled out of the database and some of them have been subsequently investigated biochemically and molecularly for their potential involvement in mitochondrial or chloroplast RNA editing, but no clear candidate has yet emerged (Faivre-Nitschke et al 1999). Another gene identified by its similarity to a yeast protein codes for a mitochondrial RNA helicase .…”

Section: Candidate Genes For Processing Enzymes In the Nuclear Genomementioning

confidence: 99%

Gene expression in plant mitochondria: transcriptional and post–transcriptional control

Binder

Brennicke

2003

Phil. Trans. R. Soc. Lond. B

114

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The informational content of the mitochondrial genome in plants is, although small, essential for each cell. Gene expression in these organelles involves a number of distinct transcriptional and post-transcriptional steps. The complex post-transcriptional processes of plant mitochondria such as 59 and 39 RNA processing, intron splicing, RNA editing and controlled RNA stability extensively modify individual steady-state RNA levels and influence the mRNA quantities available for translation. In this overview of the processes in mitochondrial gene expression, we focus on confirmed and potential sites of regulatory interference and discuss the evolutionary origins of the transcriptional and post-transcriptional processes.

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A prokaryotic‐type cytidine deaminase from Arabidopsis thaliana

Cited by 47 publications

References 35 publications

In Vitro RNA Editing in Pea Mitochondria Requires NTP or dNTP, Suggesting Involvement of an RNA Helicase

In Vitro RNA Editing in Pea Mitochondria Requires NTP or dNTP, Suggesting Involvement of an RNA Helicase

Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNAArg(ACG) and Is Essential for Efficient Chloroplast Translation

Gene expression in plant mitochondria: transcriptional and post–transcriptional control

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