RNA editing sites in tobacco chloroplast transcripts: editing as a possible regulator of chloroplast RNA polymerase activity

Hirose, Tetsuro; Kusumegi, Takahiro; Tsudzuki, Takahiko; Sugiura, Masahiro

doi:10.1007/s004380051106

Cited by 111 publications

(106 citation statements)

References 43 publications

(40 reference statements)

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“…The distribution patterns of mitochondrial introns among basal land plants are consistent with this hypothesis and also indicate that all five trans-spliced introns conserved among angiosperm mtDNAs arose from cis-spliced intron homologs (21)(22)(23)(24)(25). RNA-editing events involving mainly the conversions of cytidine into uridine have been observed in the mitochondria of basal land plants and angiosperms (26)(27)(28)(29) as well as in their chloro-plasts (26,(30)(31)(32) but appear to be absent in both organelles of Marchantia and the few algae examined thus far. These events are more frequent in mitochondria, where they affect essentially every protein-encoding mRNA in angiosperms.…”

supporting

confidence: 76%

The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum : Insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants

Turmel

Otis

Lemieux

2002

Proc. Natl. Acad. Sci. U.S.A.

167

114

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The land plants and their immediate green algal ancestors, the charophytes, form the Streptophyta. There is evidence that both the chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) underwent substantial changes in their architecture (intron insertions, gene losses, scrambling in gene order, and genome expansion in the case of mtDNA) during the evolution of streptophytes; however, because no charophyte organelle DNAs have been sequenced completely thus far, the suite of events that shaped streptophyte organelle genomes remains largely unknown. Here, we have determined the complete cpDNA (131,183 bp) and mtDNA (56,574 bp) sequences of the charophyte Chaetosphaeridium globosum (Coleochaetales). At the levels of gene content (124 genes), intron composition (18 introns), and gene order, Chaetosphaeridium cpDNA is remarkably similar to land-plant cpDNAs, implying that most of the features characteristic of land-plant lineages were gained during the evolution of charophytes. Although the gene content of Chaetosphaeridium mtDNA (67 genes) closely resembles that of the bryophyte Marchantia polymorpha (69 genes), this charophyte mtDNA differs substantially from its landplant relatives at the levels of size, intron composition (11 introns), and gene order. Our finding that it shares only one intron with its land-plant counterparts supports the idea that the vast majority of mitochondrial introns in land plants appeared after the emergence of these organisms. Our results also suggest that the events accounting for the spacious intergenic spacers found in land-plant mtDNAs took place late during the evolution of charophytes or coincided with the transition from charophytes to land plants.

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supporting

confidence: 76%

The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum : Insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants

Turmel

Otis

Lemieux

2002

Proc. Natl. Acad. Sci. U.S.A.

167

114

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“…Editing sites possessing G at the 5Ј neighboring position (Ϫ1) are not found in tobacco chloroplast transcripts (12,17), and only a limited number are found in Arabidopsis mitochondrial mRNAs (16). Consistent with these observations, conversion to G abolished both psbE and petB mRNA editing in vitro.…”

Section: Discussionmentioning

confidence: 64%

“…Cis-analysis has been pursued for several sites by transplastomic approaches, and all defined cis-acting elements are located within Ϸ30 nucleotides of editing sites (13)(14)(15). Sequences surrounding editing sites exhibit no common characteristics, except most of the 5Ј neighboring residues of editing sites are pyrimidines and the 3Ј neighbors are A residues, both in chloroplast and mitochondrial transcripts (16,17). The importance of 5Ј neighbors for editing efficiency has been reported in psbL and ndhB mRNA (site V) editing (13,14).…”

mentioning

confidence: 99%

A site-specific factor interacts directly with its cognate RNA editing site in chloroplast transcripts

Miyamoto

Obokata

Sugiura

2003

Proc. Natl. Acad. Sci. U.S.A.

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RNA editing involves a variety of genetic systems and occurs by different mechanisms. In higher plant chloroplasts, specific sites of some transcripts are subject to C-to-U conversion. We have previously shown that site-specific trans-acting factors for psbE and petB mRNA editing bind corresponding cis-elements, which are located 5 nucleotides upstream from the editing site. Here we report that, by using mRNAs labeled either at the center of the upstream cis-element or at the editing site, the site-specific factors can be cross-linked with nucleotides at both positions. Mutations of nucleotides in the proximal region of the editing site revealed a correlation between editing activity and cross-linking efficiency of factors with the editing site, even though cross-linking with the upstream cis-element was unaffected. These observations suggest that the site-specific factor binds stably to the upstream ciselement, whereas it interacts weakly with the editing site. This finding raises the intriguing possibility that the site-specific factor is involved in both site-determination and C-to-U conversion in chloroplast RNA editing. R NA editing is one of the posttranscriptional processes involved in transcript maturation in a variety of organisms, including viruses, fungi, plants, and mammals (1). This process can be subdivided into insertion͞deletion of nucleotides and base modification. RNA editing in plant organelles belongs to the latter case; specific sites of some transcripts are subject to C-to-U (and rarely U-to-C) conversions (2-7). Most editing events occur in protein-coding regions and restore codons to conserved amino acids. In chloroplasts, editing of psbF, petB, and accD mRNAs has been reported to be necessary for the function of their products (8-10), indicating that at least some RNA editing events are essential posttranscriptional steps. However, one RNA editing event was observed in the third position of a codon and did not lead to amino acid substitution (11). Hence, at least one case of editing seems to have no biological significance.At present, 34 C-to-U editing sites have been found in tobacco chloroplast transcripts (12). Cis-analysis has been pursued for several sites by transplastomic approaches, and all defined cis-acting elements are located within Ϸ30 nucleotides of editing sites (13-15). Sequences surrounding editing sites exhibit no common characteristics, except most of the 5Ј neighboring residues of editing sites are pyrimidines and the 3Ј neighbors are A residues, both in chloroplast and mitochondrial transcripts (16,17). The importance of 5Ј neighbors for editing efficiency has been reported in psbL and ndhB mRNA (site V) editing (13,14).We have recently studied the mechanism of psbE and petB mRNA editing in tobacco and pea chloroplasts (18). Both chloroplast genes possess single editing sites that depend on plant species. The 72nd codon of psbE is encoded as Ser (UCU) at the DNA level in spinach, pea, and maize, whereas tobacco, Arabidopsis, and black pine restore this codon from Pro...

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“…Another breakthrough was the establishment of an in vitro translation system from tobacco chloroplasts (10). This system promotes accurate initiation of translation from several chloroplast RNAs and revealed important cis-acting elements within the chloroplast 5Ј-untranslated regions (UTRs).…”

Section: Establishing In Vitro Systems For Specific Steps Of Chloroplmentioning

confidence: 99%

Posttranscriptional Control of Chloroplast Gene Expression. From RNA to Photosynthetic Complex

Rochaix

2001

Plant Physiology

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RNA editing sites in tobacco chloroplast transcripts: editing as a possible regulator of chloroplast RNA polymerase activity

Cited by 111 publications

References 43 publications

The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum : Insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants

The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum : Insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants

A site-specific factor interacts directly with its cognate RNA editing site in chloroplast transcripts

Posttranscriptional Control of Chloroplast Gene Expression. From RNA to Photosynthetic Complex

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