Variation in copy number of a 24-base pair tandem repeat in the chloroplast DNA of Oenothera hookeri strain Johansen

Blasko, Kimberly; Kaplan, Sara A.; Higgins, Kelly G.; Wolfson, Ruth; Sears, Barbara B.

doi:10.1007/bf00376749

Cited by 39 publications

(24 citation statements)

References 29 publications

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“…Small indels (Ͻ10 bp) probably originate via slippage and mispairing during DNA replication or repair, mediated by very short direct repeats (Palmer 1991). Larger mutations more likely arise by intramolecular recombination between short repeats (Ogihara, Terachi, andSasakuma 1988, 1992) or unequal crossing over between misaligned tandem repeats (Blasko et al 1988;Nimzyk, Schöndorf, and Hachtel 1993). Inversions are associated with repeated sequences (Howe 1985;Palmer, Nugent, and Herbon 1987), as well as with tRNA genes Shimada and Sugiura 1989).…”

Section: Introductionmentioning

confidence: 99%

Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses

Vijverberg¹,

Bachmann²

1999

Molecular Biology and Evolution

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We sequenced the first ca. 900 bp of the 5Ј-trnL(UAA)-trnV(UAC)/ndhJ region of the chloroplast DNA of different Microseris accessions in order to resolve homoplasious length variation detected in the trnL(UAA)-trnF(GAA) region. We found two to four tandemly repeated trnF genes in the species of Microseris (Asteraceae, Lactuceae) and two in their sister genus Uropappus. Sequences indicated nonhomologous transitions between two, three, and four trnF genes in different Microseris taxa. Independent origins of similar trnF copy numbers were inferred from a chloroplast phylogeny of Microseris. The taxa involved grow on separate continents, supporting parallel origins of similar length variants. The changes in trnF copy numbers were best explained by interchromosomal recombination with unequal crossing over. The 5Ј copies of the repeats showed the highest sequence conservation, suggesting that these copies are likely to be functional trnF genes, whereas the other ones probably represent pseudogenes. Our results show that length polymorphisms accumulate once a duplicated sequence has become incorporated. Due to parallel gains of similar trnF copy numbers, homoplasious length variation was introduced into the data matrix. The data demonstrate that length polymorphisms cannot be used as indicators for phylogenetic distance unless they can be analyzed at the sequence level.

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Section: Introductionmentioning

confidence: 99%

Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses

Vijverberg¹,

Bachmann²

1999

Molecular Biology and Evolution

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“…The amino acid sequence conservation between the ORF in tobacco and spinach is 80-90~o while the spinach and Marchantia ORFs contain blocks of deduced amino acids with high and low degrees of similarity (71-73 ~o and 35-50)'0, respectively) [36]. Homology has also been noted in partial sequence data from this ORF in cpDNA from Oenothera [3,25] and broad bean [ 12]. This conservation suggests that the ORF is a functional gene in the plastid, although the ORF is absent from rice cpDNA [ 13].…”

Section: Introductionmentioning

confidence: 79%

“…Variability in the copy numbers of several different tandem repeats were found to be the cause of the polymorphisms [3,25]. Although the large ORF from Oenothera has not been completely sequenced, the finding that none of the insertions alter or interrupt the reading frame of the ORF suggests that the ORF in Oenothera probably encodes a protein that is similar to the ORFs in the other species except for the addition of segments of seven or eight amino acids encoded by the repeat sequences.…”

Section: Introductionmentioning

confidence: 89%

“…5 shows that the plastome types are distinguished by a polymorphism in the length of a Bcl I-Eco RI fragment that hybridizes to the probe. In this region, the Duesseldorf wild-type line of plastome I (shown here) contains eight copies of a 24 bp tandem repeat, in comparison to the tobacco and spinach sequences [3]; each 24 bp repeat adds eight codons to the reading frame. Sequencing of cloned DNA from plastomes II and IV showed that they contain three additional copies of the repeat (data not shown).…”

Section: Polymorphism Of Orf Sequence In Oenothera Plastomesmentioning

confidence: 99%

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Large unidentified open reading frame in plastid DNA (ORF2280) is expressed in chloroplasts

Glick

Sears

1993

Plant Mol Biol

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The chloroplast DNA encodes genes for components of photosynthesis and the transcription-translation machinery; a number of unidentified open reading frames (ORFs) are also present. To determine whether a large ORF in the inverted repeat of chloroplast DNA of tobacco (ORF2280) encodes a chloroplast protein, a conserved region of the ORF was expressed in Escherichia coli. An antibody against the ORF protein was prepared using the purified fusion protein as an antigen. When incubated with proteins from the soluble fraction of tobacco, spinach and Oenothera chloroplasts, the antiserum detects relatively labile polypeptides, which have apparent molecular weights of 170 to 180 kDa. The ORF in tobacco and spinach is large enough to encode a protein of 240-250 kDa, thus it is possible that post-transcriptional or post-translational processing reduces the size of the expression product. Analysis of Oenothera chloroplasts representing four different plastome types revealed endonuclease restriction fragment length polymorphisms in chloroplast DNA indicative of insertion/deletion events in a region of the chloroplast DNA that shared significant sequence similarity with ORF2280. The ORF2280 antiserum was used to demonstrate that there are qualitative differences in the ORF proteins from different Oenothera plastome types.

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“…Two green isolates from Oenothera hookeri plastome mutator line were used; both represent photosynthetically competent wild-type plastids of plastome type 1 (28), but they differ slightly in their cpDNA3 restriction fragment patterns. To distinguish these, we refer to one as the Cornell-I (C1) line, while the other is the Cornell-2 (C2) line (1,9). The pm7 mutant was derived from the wild-type C2 line.…”

Section: Plant Materialsmentioning

confidence: 99%

Membrane Composition and Physiological Activity of Plastids from an Oenothera Plastome Mutator-Induced Chloroplast Mutant

Johnson¹,

Sears²

1990

Plant Physiol.

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Plastids were isolated from a plastome mutator-induced mutant (pm7) of Oenothera hookeri and were analyzed for various physiological and biochemical attributes. No photosynthetic electron transport activity was detected in the mutant plastids. This is consistent with previous ultrastructural analysis showing the absence of thylakoid membranes in the pm7 plastids and with the observation of aberrant processing and accumulation of chloroplast proteins in the mutant. In comparison to wild type, the mutant tissue lacks chlorophyll, and has significant differences in levels of four fatty acids. The analyses did not reveal any differences in carotenoid levels nor in the synthesis of several chloroplast lipids. The consequences of the altered composition of the chloroplast membrane are discussed in terms of their relation to the aberrant protein processing of the pm7 plastids. The pigment, fatty acid, and lipid measurements were also performed on two distinct nuclear genotypes (A/A and A/C) which differ in their compatibility with the plastid genome (type 1) contained in these lines. In these cases, only chlorophyll concentrations differed significantly.A large number of plastome (or plastid genome) mutants have been generated through the use of the plastome mutator system in the Johansen strain of Oenothera hookeri (15). The mutants thus far accumulated in this collection display various degrees ofchlorosis as well as differing extents ofaberrant chloroplast development as seen at the ultrastructural level (13,14). Immunological analysis of plastid proteins from one of these plastome mutants, pm7, has provided evidence that indicates the existence of a defect in chloroplast protein processing (EM Johnson, BB Sears, L Schnabelrauch, unpublished data). Proteins affected include one encoded by a chloroplast gene (Cytf) as well as the 16-and 23-kD subunits of the oxygen evolving complex of PSII, which are nuclear gene products. The suggestion that the processing of these three proteins in pm7 may be inhibited by a lesion of some shared feature of the proteolytic machinery is

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Variation in copy number of a 24-base pair tandem repeat in the chloroplast DNA of Oenothera hookeri strain Johansen

Cited by 39 publications

References 29 publications

Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses

Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses

Large unidentified open reading frame in plastid DNA (ORF2280) is expressed in chloroplasts

Membrane Composition and Physiological Activity of Plastids from an Oenothera Plastome Mutator-Induced Chloroplast Mutant

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