Electron microscopic localization of replication origins in Oenothera chloroplast DNA

Chiu, Wan-Ling; Sears, Barbara B.

doi:10.1007/bf00299134

Cited by 50 publications

(32 citation statements)

References 28 publications

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“…Interestingly, two of the ends (Fig. 1C, maps c and e) lie near a sequence homologous to replication origins previously identified in Oenothera (Chiu and Sears, 1992); the other ends could be near previously unclassified origins. These results suggest that the ends may represent initiation sites for recombinationdependent DNA replication of linear molecules, as we inferred for maize (Oldenburg and Bendich, 2004b).…”

Section: Fragment Mapping Of the Chloroplast Genomementioning

confidence: 59%

“…For all three species, ends are located at positions near regions homologous to tobacco oriA (homologous to Oenothera oriB) and Oenothera oriA (Fig. 1C, maps c and e; Chiu and Sears, 1992;Kunnimalaiyaan and Nielsen, 1997b;Oldenburg and Bendich, 2004b), but for each species there are additional ends. For example, an end for tobacco, but not maize or M. truncatula, is located near tobacco oriB Koop, 2006, 2007).…”

Section: Structure Of Cpdna Moleculesmentioning

confidence: 99%

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The Structure of Chloroplast DNA Molecules and the Effects of Light on the Amount of Chloroplast DNA during Development in Medicago truncatula

2008

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We used pulsed-field gel electrophoresis and restriction fragment mapping to analyze the structure of Medicago truncatula chloroplast DNA (cpDNA). We find most cpDNA in genome-sized linear molecules, head-to-tail genomic concatemers, and complex branched forms with ends at defined sites rather than at random sites as expected from broken circles. Our data suggest that cpDNA replication is initiated predominantly on linear DNA molecules with one of five possible ends serving as putative origins of replication. We also used 4#,6-diamidino-2-phenylindole staining of isolated plastids to determine the DNA content per plastid for seedlings grown in the dark for 3 d and then transferred to light before being returned to the dark. The cpDNA content in cotyledons increased after 3 h of light, decreased with 9 h of light, and decreased sharply with 24 h of light. In addition, we used real-time quantitative polymerase chain reaction to determine cpDNA levels of cotyledons in dark-and lightgrown (low white, high white, blue, and red light) seedlings, as well as in cotyledons and leaves from plants grown in a greenhouse. In white, blue, and red light, cpDNA increased initially and then declined, but cpDNA declined further in white and blue light while remaining constant in red light. The initial decline in cpDNA occurred more rapidly with increased white light intensity, but the final DNA level was similar to that in less intense light. The patterns of increase and then decrease in cpDNA level during development were similar for cotyledons and leaves. We conclude that the absence in M. truncatula of the prominent inverted repeat cpDNA sequence found in most plant species does not lead to unusual properties with respect to the structure of plastid DNA molecules, cpDNA replication, or the loss of cpDNA during light-stimulated chloroplast development.

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Section: Fragment Mapping Of the Chloroplast Genomementioning

confidence: 59%

Section: Structure Of Cpdna Moleculesmentioning

confidence: 99%

The Structure of Chloroplast DNA Molecules and the Effects of Light on the Amount of Chloroplast DNA during Development in Medicago truncatula

2008

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“…It is unknown which, if any, of these mechanisms is involved in the autonomous replication of the extrachromosomal elements. Interestingly, one of the D-loops implicated in ptDNA replication was mapped to the region containing NICE1 sequences in other plant species (19,20), although not in tobacco (21 genome and the extrachromosomal copies may be generated by excision of the shuttle plasmid from the main genome at any location of the 1.4-kb duplicated ptDNA sequence (Fig. 5).…”

Section: Discussionmentioning

confidence: 99%

Extrachromosomal elements in tobacco plastids.

Staub

Maliga

1994

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

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The plastid genome of higher plants is a circular double-stranded DNA molecule which is present in multiple Identical copies. We report here an 868-bp plastid DNA minicircle, NICE1, that formed in tobacco (Nicoiana tabacum) plastids during transformation, as an unexpected product of homologous recombination. Such extrachromosomal elements are normally absent in plastids of higher plants. We have constructed shuttle plAids conaining NICEl sequences which are maitd extrachromosomally when reintroduced into plastids by particle bombardment. Furthermore, recombination between homologous sequences in the shuttle plasmids and the main plastid genome occurs. Recombination products were characterized after recovery of the shuttle plasmids in Escherchia colU and of recombinant plasd genomes in the progeny of transormed plants. Our findings indicate that shuttle plasmIds can be used to engineer plastid genes without concomitant inteaton of foreign DNA and to recover plastid mutations in E. coil.

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“…For details on the definition of the gene classes, see text. For macro repeat identification, see Greiner et al (2008a), and for location of the origins of replication, see Chiu and Sears (1992). exclusively representing duplications; Figure 3), 11 with photosystem II, and six within the cytochrome b 6 f complex. Furthermore, four mutations were found in ycf3 and one in ycf4 (as ycf3 involved in photosystem I assembly; Ruf et al, 1997;Krech et al, 2012), three within rbcL (encoding the large subunit of Rubisco), and four within ccsA (a gene involved in cytochrome c biogenesis; Xie and Merchant, 1996).…”

Section: Molecular Cause Of Mutations and Phenotypic Relevance Of Thementioning

confidence: 99%

Spontaneous Chloroplast Mutants Mostly Occur by Replication Slippage and Show a Biased Pattern in the Plastome of Oenothera

et al. 2016

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Spontaneous plastome mutants have been used as a research tool since the beginning of genetics. However, technical restrictions have severely limited their contributions to research in physiology and molecular biology. Here, we used full plastome sequencing to systematically characterize a collection of 51 spontaneous chloroplast mutants in Oenothera (evening primrose). Most mutants carry only a single mutation. Unexpectedly, the vast majority of mutations do not represent single nucleotide polymorphisms but are insertions/deletions originating from DNA replication slippage events. Only very few mutations appear to be caused by imprecise double-strand break repair, nucleotide misincorporation during replication, or incorrect nucleotide excision repair following oxidative damage. U-turn inversions were not detected. Replication slippage is induced at repetitive sequences that can be very small and tend to have high A/T content. Interestingly, the mutations are not distributed randomly in the genome. The underrepresentation of mutations caused by faulty double-strand break repair might explain the high structural conservation of seed plant plastomes throughout evolution. In addition to providing a fully characterized mutant collection for future research on plastid genetics, gene expression, and photosynthesis, our work identified the spectrum of spontaneous mutations in plastids and reveals that this spectrum is very different from that in the nucleus.

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Electron microscopic localization of replication origins in Oenothera chloroplast DNA

Cited by 50 publications

References 28 publications

The Structure of Chloroplast DNA Molecules and the Effects of Light on the Amount of Chloroplast DNA during Development in Medicago truncatula

The Structure of Chloroplast DNA Molecules and the Effects of Light on the Amount of Chloroplast DNA during Development in Medicago truncatula

Extrachromosomal elements in tobacco plastids.

Spontaneous Chloroplast Mutants Mostly Occur by Replication Slippage and Show a Biased Pattern in the Plastome of Oenothera

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