Chloroplast DNA Sequence Homologies among Vascular Plants

Lamppa, Gayle K.; Bendich, Arnold J.

doi:10.1104/pp.63.4.660

Cited by 29 publications

(17 citation statements)

References 29 publications

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“…In an earlier report we noted that ct DNA could increase by a factor of 2.5 'G. K during shoot development (13). Here we show that the increase can actually be as great as 5.6.…”

supporting

confidence: 52%

“…The reassociation procedure has been described (13). Reactions were carried out in 1 M NaClO4, 0.03 M Tris, 1 mm EDTA (pH 8), 0.1% Sarkosyl at 60 C. Double strands were separated from single strands on hydroxylapatite.…”

Section: Methodsmentioning

confidence: 99%

“…DNAs isolated from days 4 and 8 using method I were included with the series presented in Figure 3 to control for probe length decreases that occur as a probe "ages" (13) which result in reduced rates of reassociation (7). If the Pot1/2, 1.9 x 1O-5, for day 8 DNA, method I, represents 7.3% ct DNA, then in this group the ct DNA level increased from about 2% in a day 1 embryo to 5% at days 5 and 9.…”

Section: Changes In Percentage Of Chloroplast Dna In Shoots Duringmentioning

confidence: 99%

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Changes in Chloroplast DNA Levels during Development of Pea (Pisum sativum)

Lamppa¹,

Bendich²

1979

Plant Physiol.

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Determinations were made of the percentage of chloroplast DNA (ct DNA) in total cell DNA isolated from shoots of pea at different stages of development. Labeled pea ct DNA was reassociated with a high concentration of total DNA; the percentage of ct DNA was estimated by comparing the rate of reassociation of this reaction with that of a model reaction containing a known concentration of unlabeled ct DNA. The maximum change in ct DNA content was from 1.3% of total DNA in young shoots to 7.3% in fully greened shoots. Analyses were also performed on DNA from embryos, etiolated tissue, roots, and leaves. The first leaf set to develop in pea was excised over a growth period of 8 days during which leaf length increased from 4 to 12 millimeters. Young leaves contained about 8% ct DNA; in fuly greened leaves the level of ct DNA approached 12%, equivalent to as many as 9,575 copies of ct DNA per cell. Root tissue contained only 0.4% ct DNA.Chloroplast development is essentially a light-induced phenomenon. The process includes reorganization of the prolamellar bodies to form the thylakoids and grana, reduction of Pchl to Chl, and plastid enlargement (11). In higher plants the number of chloroplasts per cell can increase by as much as a factor of 20 during greening and leaf expansion (19).There is some evidence that chloroplast development is accompanied by ct DNA2 synthesis (6, 19, 20). However, the contribution of ct DNA to the total cellular DNA complement at any stage of higher plant development has not been accurately determined. A major difficulty is the similar base composition of chloroplast and nuclear DNAs (10), which has prevented resolution of these components by CsCl density gradient analysis of total cell DNA.In the algae the buoyant densities of the two DNAs may differ considerably. It has been found that ct DNA comprises about 5% of total DNA in the primitive alga Olisthodiscus throughout the growth cycle (2), and as much as 11 to 15% in Chlamydomonas (22,26). Although 9% ct DNA has been estimated for tobacco leaves by the density method (23), reassociation kinetics analysis has indicated that tobacco leaves contain 4% ct DNA and roots less than 1% (21).The purpose of this study was to determine the amount of ct DNA in total DNA extracted from shoots throughout development of peas using reassociation kinetics analysis. In an earlier report we noted that ct DNA could increase by a factor of 2.5

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“…In an earlier report we noted that ct DNA could increase by a factor of 2.5 'G. K during shoot development (13). Here we show that the increase can actually be as great as 5.6.…”

supporting

confidence: 52%

Section: Methodsmentioning

confidence: 99%

Section: Changes In Percentage Of Chloroplast Dna In Shoots Duringmentioning

confidence: 99%

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Changes in Chloroplast DNA Levels during Development of Pea (Pisum sativum)

Lamppa¹,

Bendich²

1979

Plant Physiol.

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“…The data are discussed with respect to the evolution of the chloroplast genome and the phylogenetic relationships of the plants in which they are found. Our results are also compared with those from recent similar experiments by Walbot (23) and Lamppa and Bendich (15 (10) with an electric knife fitted with razor blades and the resulting brei was sedimented through discontinuous gradients of 60, 45, and 20% sucrose (19). Chloroplasts were collected from the 20-45% discontinuity.…”

mentioning

confidence: 73%

Sequence Homology between Chloroplast DNAs from Several Higher Plants

Bisaro

Siegel²

1980

Plant Physiol.

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An estimate has been made of the amount of sequence homology present in the chloroplast DNA (ctDNA) of several higher plants by the technique of DNA-DNA hybridization. Approximately 85% of tomato, 60% of spinach, 45% of kale, and 15% of barley ctDNA sequences were found to hybridize with tobacco ctDNA under conditions in which maximum hybridization in homologous reactions reached 85%. All heteroduplexes contained significant amounts of sequence mismatch as indicated by a 3 to 9 C decrease in melting temperature as compared to homoduplex.The data suggest that considerable sequence homology exists between the ctDNAs of these plants and that some sequences are held in common among all of the species tested.The DNA found in the chloroplasts of higher plants exists as a covalently closed circle with a mol wt, depending on the species, of 85-95 x 106 daltons (12). Several chloroplast-specific components are now known to be coded for by higher plant ctDNA'.These include the chloroplast ribosomal RNAs (2, 20, 21), a nearly complete set of transfer RNAs (9), the large subunit of the enzyme ribulose-bisP carboxylase (6, 7) and possibly several other as.yet unidentified soluble and membrane bound proteins (4).Investigations comparing chloroplast ribosomal RNAs (21) and the large subunit of ribulose-bisP carboxylase (13, 14) from different plant species suggest that the primary structure of these molecules is highly conserved. Although this result would indicate that a certain amount of sequence homology exists between different ctDNAs, the coding sequences required to specify these molecules probably represent only a small fraction of the chloroplast genome (11). In contrast, distinct fragmentation patterns result when ctDNA from different species are digested with restriction endonucleases (1,22 (10) with an electric knife fitted with razor blades and the resulting brei was sedimented through discontinuous gradients of 60, 45, and 20% sucrose (19). Chloroplasts were collected from the 20-45% discontinuity. ctDNA was prepared by a modification of the urea phosphate DNA extraction procedure (5). Chloroplasts from 50 g of leaf tissue were lysed in a solution containing 8 M urea, 0.24 M PB, I mim EDTA, and 1% SDS. The lysate was extracted three times with phenol saturated with 50 mm Tris. The aqueous fraction was loaded on a column containing 2 g of HAP and washed successively with 80-100 ml of 8 M urea-0.24 M PB, 40 ml of 10 nm PB, and 10 ml of 0.4 M PB to elute DNA. DNAcontaining fractions were pooled and centrifuged for 14 h at 45,000 rpm in a Beckman SW 50 rotor. The resulting pellets were resuspended in I ml of 5 mm PB and stored at 4 C over a drop of chloroform. Purity of ctDNA preparations was monitored by cesium chloride density gradient analysis in a Beckman model E analytical ultracentrifuge. Native, denatured and reassociated (Cot 0.32) samples were run simultaneously. Failure of reassociated samples to renature and thus recover to within 4 mg/ml of native buoyant density was taken as evidence of contaminat...

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“…This latter point is especially relevant because a number of other examples in the literature (28)(29)(30) suggest that rearrangement events, particularly small deletions/insertions, occur at a fairly high frequency during chloroplast genome evolution, even though the genomes ofdistantly related plants retain high levels of base sequence homology (31,32). Most notably, restriction maps of the five principal chloroplast genomes of the genus Oenothera indicate that most of the differences in restriction fragment sizes reflect small deletions/insertions (28).…”

mentioning

confidence: 99%

Rearrangements in the chloroplast genomes of mung bean and pea

Palmer

Thompson²

1981

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

206

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We have mapped all the cleavage sites for the restriction endonucleases BstEII, Kpn I, Pst I, Pvu H, Sac I, Sal I, Sma I, and Xho I on the circular chloroplast chromosomes from mung bean and pea. The mung bean chloroplast genome measures 150 kilobase pairs (kb) in length; it includes two identical sequences of 23 kb that contain the ribosomal genes and are arranged as an inverted repeat separated by single-copy regions of 21 and 83 kb. The pea chloroplast genome is only 120 kb in size, has only one set of ribosomal genes, and does not possess any detectable repeated sequences. The mung bean inverted repeat structure is common to all other nonleguminous higher plant chloroplast genomes studied, whereas the pea structure has been found only in the closely related legume Viciafaba. We conclude from these data that loss ofone copy of the inverted repeat sequence has occurred only rarely during the evolution of the Angiosperms, and in the case of the legumes after the divergence of the mung bean line from the pea-Vicia line. We present hybridization data indicating that rearrangements that change the linear order of homologous sequences within the chloroplast genome have been quite frequent during the course of legume evolution.The great majority of higher plant chloroplast genomes studied consist of a circular molecule 134 kilobase pairs (kb) to 150 kb in length, which contains a large inverted repeat sequence of 20-25 kb. This pattern has been demonstrated in corn, spinach, and lettuce by intramolecular homoduplex formation (1) and in corn, wheat, spinach, Oenothera, tobacco, petunia, and Spirodela by restriction endonuclease mapping (2-7). The only exceptions to this pattern so far reported are pea and broad bean (Viciafaba), both members ofthe legume family. Pea chloroplast DNA lacks the inverted repeat structure as judged by electron microscopy (1) but is reported to possess two copies of the ribosomal RNA genes (8, 9), which may be repeated in tandem (10). Electron microscopy and restriction mapping reveal the absence of an inverted repeat in broad bean, as well as the presence of only one copy of the ribosomal RNA genes (11).We have constructed detailed restriction maps of the chloroplast genomes of mung bean and pea. The mung bean genome, unlike that ofpea and broad bean, possesses the inverted repeat structure common to all other higher plant chloroplast genomes. We confirm that the pea genome lacks an inverted repeat and demonstrate that it contains only one set ofribosomal genes and no detectable repeated sequences. From these data we conclude that deletion of one segment of the highly conserved inverted repeat has occurred during the evolution ofthe legumes. In addition, we have mapped a number of rearrangements of sequences common to the mung bean and pea chloroplast genomes. MATERIALS AND METHODSChloroplast DNA was isolated as described by Kolodner and Tewari (12). Recombinant plasmids containing mung bean and pea chloroplast DNA restriction fragments (13) (16) and hybridized to the filters in...

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Chloroplast DNA Sequence Homologies among Vascular Plants

Cited by 29 publications

References 29 publications

Changes in Chloroplast DNA Levels during Development of Pea (Pisum sativum)

Changes in Chloroplast DNA Levels during Development of Pea (Pisum sativum)

Sequence Homology between Chloroplast DNAs from Several Higher Plants

Rearrangements in the chloroplast genomes of mung bean and pea

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