Codon recognition mechanisms in plant chloroplasts

Pfitzinger, H.; Weil, Jacques-Henry; Pillay, D.T.N.; Guillemaut, Pierre

doi:10.1007/bf00016513

Cited by 55 publications

(57 citation statements)

References 35 publications

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“…This mechanism has also been suggested to occur in chloroplasts (Shinozaki et al, 1986;Pfitzinger et al, 1990) and was demonstrated in tobacco (Nicotiana tabacum) when one of the two chloroplast (cp)-tRNA Gly genes was deleted (Rogalski et al, 2008). In this study, two out of three was ruled out for decoding of Gly codons, but superwobble was also shown to be inefficient.…”

Section: Introductionmentioning

confidence: 66%

“…This mechanism is supported by several examples (Lagerkvist, 1986). It has also been suggested to occur in chloroplasts (Shinozaki et al, 1986) and supported by in vitro experiments using wheat (Triticum aestivum) germ extracts and bean (Phaseolus vulgaris) chloroplast tRNAs (Pfitzinger et al, 1990). Further analysis showed that two out of three critically depends on the stability of the second base pair formed between the codon and anticodon and that this stability is influenced by the structure of the tRNA anticodon loop (Lehmann and Libchaber, 2008).…”

Section: Introductionmentioning

confidence: 75%

“…The genomes of higher-plant chloroplasts encode two Arg tRNAs: cp-tRNA Arg (ACG), thought to be required for decoding the codons CGA/U/G/C (CGN), and cp-tRNA Arg (UCU), thought to be required to read the codons AGA/G. It has been shown that cp-tRNA Arg (ACG) is deaminated to cp-tRNA Arg (ICG) in bean (Pfitzinger et al, 1990), which would be expected to allow efficient translation of CGC and CGA codons. This tRNA modification was inherited from the cyanobacterial ancestor of chloroplasts and is well conserved in prokaryotes where it is essential for cell survival (Wolf et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Introductionmentioning

confidence: 66%

Section: Introductionmentioning

confidence: 75%

Section: Introductionmentioning

confidence: 99%

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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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“…Thus, it is unlikely that tRNA CCU Arg would be able to decode both AGA and AGG codons. The remaining arginine codon (CGG) may be recognized by tRNA ICG Arg , as proposed for angiosperm chloroplasts (47). Nuclear DNA-encoded tRNA Populations in Monocotyledon, Dicotyledon, and Liverwort Mitochondria-The study reported here represents the most comprehensive sequence survey of nDNA-encoded mt-tRNA species in any plant system.…”

Section: Discussionmentioning

confidence: 89%

Identification and Structural Characterization of Nucleus-encoded Transfer RNAs Imported into Wheat Mitochondria

Glover

Spencer

Gray

2001

Journal of Biological Chemistry

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Despite its large size (200 -2400 kilobase pairs), the mitochondrial genome of angiosperms does not encode the minimal set of tRNAs required to support mitochondrial protein synthesis. Here we report the identification of cytosolic-like tRNAs in wheat mitochondria using a method involving quantitative hybridization to distinguish among three tRNA classes: (i) those encoded by mitochondrial DNA (mtDNA) and localized in mitochondria, (ii) those encoded by nuclear DNA and located in the cytosol, and (iii) those encoded by nuclear DNA and found in both the cytosol and mitochondria. The latter class comprises tRNA species that are considered to be imported into mitochondria to compensate for the deficiency of mtDNA-encoded tRNAs. In a comprehensive survey of the wheat mitochondrial tRNA population, we identified 14 such imported tRNAs, the structural characterization of which is presented here. These imported tRNAs complement 16 mtDNA-encoded tRNAs, for a total of at least 30 distinct tRNA species in wheat mitochondria. Considering differences in the set of mtDNA-encoded and imported tRNAs in the mitochondria of various land plants, the import system must be able to adapt relatively rapidly over evolutionary time with regard to the particular cytosolic-like tRNAs that are brought into mitochondria.

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“…d tRNA Trp (UCA) is able to recognize TGA as well as TGG, consistent with the presence of numerous TGA codons in P. purpurea mitochondrial protein-coding genes. e The A is assumed to be converted to I (inosine) post-transcriptionally, with the resulting tRNA Arg (ICG) able to decode all four CGN arginine codons (Pfitzinger et al, 1990). f Separate elongator (e) and initiator (f, formyl) tRNA Met are present.…”

Section: Mitochondrial 5s Rrna Genes In Red Algaementioning

confidence: 99%

Complete Sequence of the Mitochondrial DNA of the Red Alga Porphyra purpurea: Cyanobacterial Introns and Shared Ancestry of Red and Green Algae

et al. 1999

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The mitochondrial DNA (mtDNA) of Porphyra purpurea , a circular-mapping genome of 36,753 bp, has been completely sequenced. A total of 57 densely packed genes has been identified, including the basic set typically found in animals and fungi, as well as seven genes characteristic of protist and plant mtDNAs and specifying ribosomal proteins and subunits of succinate:ubiquinone oxidoreductase. The mitochondrial large subunit rRNA gene contains two group II introns that are extraordinarily similar to those found in the cyanobacterium Calothrix sp, suggesting a recent lateral intron transfer between a bacterial and a mitochondrial genome. Notable features of P. purpurea mtDNA include the presence of two 291-bp inverted repeats that likely mediate homologous recombination, resulting in genome rearrangement, and of numerous sequence polymorphisms in the coding and intergenic regions. Comparative analysis of red algal mitochondrial genomes from five different, evolutionarily distant orders reveals that rhodophyte mtDNAs are unusually uniform in size and gene order. Finally, phylogenetic analyses provide strong evidence that red algae share a common ancestry with green algae and plants. INTRODUCTIONHistorically considered to be "red plants," red algae (rhodophytes) were grouped together with protists only in the middle of this century; however, debate continues as to when this taxonomic group first appeared in the evolutionary history of mitochondria-containing eukaryotes. Because the red algal cell lacks flagellar basal bodies and centrioles, some workers have claimed that rhodophytes are the most early diverging and primitive group among photosynthetic eukaryotes (e.g., Lee, 1989). This view also has been suggested by certain molecular phylogenies (e.g., Lipscomb, 1989;Stiller and Hall, 1997). Some authors even advocate that red algae, in particular Cyanidioschyzon spp and Cyanidium spp, represent the evolutionary bridge between cyanobacteria and eukaryotes (Seckbach, 1994). An opposite interpretation contends that the red algae represent a derived group that has secondarily lost many of the distinctive features of the protistan cytoskeleton (Pueschel, 1990;Scott and Broadwater, 1990). Finally, it has been proposed that red algae may have given rise to the fungi (Demoulin, 1985) or that red algae are affiliated with the plant kingdom via common ancestry with green algae (see, e.g., Bhattacharya et al., 1993; Cavalier-Smith, 1993;McFadden et al., 1994;Schlegel, 1994;Paquin et al., 1997;Lang et al., 1998). This broad spectrum of coexisting, mutually exclusive hypotheses highlights our limited knowledge about the phylogenetic relationship between rhodophytes and other eukaryotic phyla.Rhodophytes form a morphologically heterogeneous phylum that has more species ( ‫ف‬ 2500 to 6000 in at least 12 orders; Woelkerling, 1990) than all other seaweeds combined. Multicellular as well as unicellular rhodophyte genera exist, and there is also considerable variety in morphology and physiology throughout the phylum. On the basis...

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Codon recognition mechanisms in plant chloroplasts

Cited by 55 publications

References 35 publications

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

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

Identification and Structural Characterization of Nucleus-encoded Transfer RNAs Imported into Wheat Mitochondria

Complete Sequence of the Mitochondrial DNA of the Red Alga Porphyra purpurea: Cyanobacterial Introns and Shared Ancestry of Red and Green Algae

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