Evidence for variation in the quantity of DNA among plastids of Acetabularia

Implications of mutation of organelle genomes for organelle function and evolution

Organelle genomes undergo more variation, including that resulting from damage, than eukaryotic nuclear genomes, or bacterial genomes, under the same conditions. Recent advances in characterizing the changes to genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help our understanding of how damage to organelle genomes relates to how organelle function is maintained through the life of individuals and in succeeding generations. Understanding of the degree of variation in the changes to organelle DNA and its repair among photosynthetic organisms might help to explain the variations in the rate of nucleotide substitution among organelle genomes. Further studies of organelle DNA variation, including that due to damage and its repair might also help us to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, from the available data, even the longest-lived organelle-encoded proteins, and the RNAs needed for their synthesis, are unlikely to maintain organelle function for much more than a week after the complete loss of organelle DNA.

Size of the Chloroplast Genome in Codium fragile

Chloroplasts isolated from the siphonous green alga Codium fragile yield circular DNA molecules averaging 27.3 micrometers in length and 56 x 10(6) daltons in molecular size. This chloroplast genome is 25 to 30 percent smaller than any reported. The small size of the Codium chloroplast genome may represent a primitive evolutionary condition in green plants.

The loss of DNA from chloroplasts as leaves mature: fact or artefact?

In this review, the controversy regarding the preservation or degradation of chloroplast DNA (cpDNA) as chloroplasts develop their photosynthetic capacity and leaves reach maturity is addressed. A constant amount of cpDNA during maturity might be expected in order to support photosynthesis over the lifespan of the leaf. Nevertheless, a decline in cpDNA during leaf development was found for all seven plant species investigated. Initial measurements showed that Arabidopsis was similar to the other seven. The controversy arose with two recent studies concluding that the amount of cpDNA remains constant as Arabidopsis leaves mature. These authors proposed that the observation of Arabidopsis chloroplasts with undetectable levels of DNA was an artefact, although the most recent data support the original findings. If the amount of cpDNA remains constant, then Arabidopsis is atypical and would not serve as a good model for chloroplast development. It is shown that the apparently contradictory data may be attributed to methodology and the choice of leaves to be compared. Thus, it is concluded that the controversy can be resolved, Arabidopsis can serve as a representative model, and cpDNA degradation is a common event in chloroplast development.

The effect of nalidixic acid on growth and reproductive events in nucleocytosolic and chloroplast compartments in the algaScenedesmus quadricauda

The courses of rRNA accumulation, DNA replication, and nuclear division were followed both in the chloroplast and the nucleocytosolic compartments during the cell cycle in synchronized populations of the chlorococcal alga Scenedesmus quadricauda. Control and nalidixic acid-treated cultures were compared. Nalidixic acid (150 mg/L) was added either at the beginning of the cell cycle or consecutively during the cell cycle to subcultures transferred into the dark. If the inhibitor was applied at the beginning of the cell cycle, chloroplast DNA did not replicate and nucleoids did not divide. Chloroplast division, however, was coordinated in a timely fashion with cytokinesis even under conditions of blocked chloroplast DNA replication. While the growth rate was slowed down, the courses of reproductive processes in the nucleocytosolic compartment were not affected and their timing and the number of rounds were coordinated with growth rate as in the control culture. The rate of cytosolic rRNA synthesis was lower but no apparent effect was seen on the amount of rRNA that accumulated during the cell cycle. In contrast, lower levels of chloroplast rRNA were found at the end of the cell cycle compared with the control culture. Experiments in which cells were transferred to the dark during the cell cycle showed that the inhibitor affected none of the reproductive events in the nucleocytosolic compartment. In the chloroplast compartment, DNA replication was inhibited in inhibitor-treated cultures, but was unaffected in controls. The chloroplast nucleoids themselves divided even in the presence of the inhibitor, reducing their DNA content to a level which corresponded to that in freshly formed control daughter cells.

Changes in the structure of DNA molecules and the amount of DNA per plastid during chloroplast development in maize

We examined the DNA from chloroplasts obtained from different tissues of juvenile maize seedlings (from eight to 16 days old) and adult plants (50-58 days old). During plastid development, we found a striking progression from complex multigenomic DNA molecules to simple subgenomic molecules. The decrease in molecular size and complexity of the DNA paralleled a progressive decrease in DNA content per plastid. Most surprising, we were unable to detect DNA of any size in most chloroplasts from mature leaves, long before the onset of leaf senescence. Thus, the DNA content per plastid is not constant but varies during development from hundreds of genome copies in the proplastid to undetectable levels in the mature chloroplast. This loss of DNA from isolated, mature chloroplasts was monitored by three independent methods: staining intact chloroplasts with 4',6-diamidino-2-phenylindole (DAPI); staining at the single-molecule level with ethidium bromide after exhaustive deproteinization of lysed chloroplasts; and blot-hybridization after standard DNA isolation procedures. We propose a mechanism for the production of multigenomic chloroplast chromosomes that begins at paired DNA replication origins on linear molecules to generate a head-to-tail linear concatemer, followed by recombination-dependent replication.

The demise of chloroplast DNA in Arabidopsis

Although it might be expected that chloroplast DNA (cpDNA) would be stably maintained in mature leaves, we report the surprising observation that cpDNA levels decline during plastid development in Arabidopsis thaliana (Col.) until most of the leaves contain little or no DNA long before the onset of senescence. We measured the cpDNA content in developing cotyledons, rosette leaves, and cauline leaves. The amount of cpDNA per chloroplast decreases as the chloroplasts develop, reaching undetectable levels in mature leaves. In young cauline leaves, most individual molecules of cpDNA are found in complex, branched forms. In expanded cauline leaves, cpDNA is present in smaller branched forms only at the base of the leaf and is virtually absent in the distal part of the leaf. We conclude that photosynthetic activity may persist long after the demise of the cpDNA.

Plastid division: its origins and evolution

Photosynthetic eukaryotes have evolved plastid division mechanisms since acquisition of plastids through endosymbiosis. The emerging evolutionary origin of the plastid division mechanism is remarkably complex. The constituents of the division apparatus of plastids may have complex origins. The one constituent is the plastid FtsZ ring taken over from the cyanobacteria-like ancestral endosymbionts. The second is the doublet of concentric plastid dividing rings (or triplet in red algae), possibly acquired by ancestral host eukaryotes following the primary endosymbiotic event. Placement of the division apparatus at the correct division site may involve a system analogous to the bacterial Min system. Plastid nucleoid partitioning may be mediated by binding to envelope or thylakoid membranes. Multiple copies of plastid DNA and symmetrical distribution of the nucleoids in the plastids may permit faithful transmission to daughter plastids via equal binary plastid divisions. Cyanelles retain peptidoglycan wall and cyanelle division occurs through septum formation such as bacterial cell division. Cyanelle division involves the cyanelle ring analogous to the inner stromal plastid-dividing (PD) ring. According to the prevailing hypothesis that primary endosymbiosis occurred only once, cyanelle division may represent an intermediate stage between cyanobacterial division and the well-known plastid division among extant plants. With the secondary plastids, which are surrounded by three or four membranes, the PD ring also participates in division of the inner two "true" plastid envelope membranes, and the third and the outermost membranes divide by unknown mechanisms.

Engineering chloroplasts: an alternative site for foreign genes, proteins, reactions and products

Plant genetic engineering via the nucleus is a mature technology that has been used very productively for research and commercial biotechnology. By contrast, the ability to introduce foreign genes at specific locations on a chloroplast's chromosome has been acquired relatively recently. Certain limitations of nuclear genome transformation methods might be overcome by the site-specific introduction of genes into plastid chromosomes. In addition, plastids, mitochondria and other subcellular organelles might provide more favorable environments than the nuclear-cytoplasmic compartment for certain biochemical reactions and for accumulating large amounts of some gene and enzyme products.

Differences in amino acid sequence of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from two species of Dasycladaceae

In contrast to other plants the plastid genome of Acetabularia is larger in size and shows a high degree of variability. This study on the chloroplast-encoded large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase demonstrates that strongly conserved areas also exist in the plastid genome of the Dasycladaceae. Searching for differences in the amino acid sequence of the large subunit from Acetabularia mediterranea and Acicularia schenckii, proteolytic peptides which differ in their elution behaviour in reverse-phase high-performance liquid chromatography were sequenced. Only six amino acids were found to be exchanged in the large subunit from these two species. Since these two species diverged approx. 150 million years ago, these results imply that 0.84 amino-acid exchanges per 100 amino acids have occurred in 10(8) years, underlining the strong conservatism of the large subunit.

Tandemly repeated nonribosomal DNA sequences in the chloroplast genome of an Acetabularia mediterranea strain

A purified chloroplast fraction was prepared from caps of the giant unicellular green alga Acetabularia mediterranea (strain 17). High molecular weight DNA obtained from these chloroplasts contains at least five copies of a 10-kilobase-pair (kbp) sequence tandemly arranged. This unique sequence is present in DNA from chloroplasts of all stages of the life cycle examined. A chloroplast rDNA clone from mustard hybridized with some restriction fragments from Acetabularia chloroplast DNA but not with the repeated sequence. An 8-kbp EcoRI-Pst I fragment of the repeated sequence was cloned into pBR322 and used as a hybridization probe. No homology was found between the cloned 8-kbp sequence and chloroplast DNA from related species Acetabularia crenulata or chloroplast DNA from spinach.

The partitioning of cytoplasmic organelles at cell division

When an organism has only one or two mitochondria or chloroplasts per cell, it is probable that their partitioning is always stringently controlled so that each daughter cell always receives half the organelles in the parent cell. When there are more copies of an organelle, the available data suggest that partitioning is stochastic but far from random, with a strong tendency toward equality. The molecular mechanisms that promote equal partitioning are not known in any case, but the great variety of organelle behavior suggests that many different mechanisms are involved in different organisms. As Wilson (1925) pointed out, the precision of partitioning of cytoplasmic organelles rarely if ever equals that of mitosis, but it is still an expression of selection for mechanisms that will ensure the hereditary continuity of the organelles. How cells compensate for unequal partitioning by controlling organelle replication is known for only one case. But when one considers that Tetrahymena and Paramecium use different methods to compensate for unequal partitioning of macronuclear DNA, it would not be surprising if organisms use a variety of different compensating replication modes for organelles as well. What is surprising is that so little attention has been paid to these problems. Nothing could be simpler than counting organelles in dividing cells, but this has been done on a large scale in only two systems. Quantitative techniques in cell biology have been developed to the point where such studies could be done even on cells that have too many organelles for direct counting. Molecular mechanisms of partitioning have scarcely been touched on. Much more has been done on the role of the cytoskeleton in determining cell shape, and some observations have been made on its role in positioning organelles in interphase cells, but these kinds of studies have not been extended to dividing cells. Some experiments and observations have been made on the role of microtubules and microfilaments in moving cytoplasmic organelles around the cell during interphase, but again nothing has been done on their possible role in partitioning organelles at cytokinesis. The major lesson of this article is how little has been done, and how much can be done. The partitioning of cytoplasmic organelles at cell division is a wide-open field for future research, and one of great importance for both genetics and cell biology.

Chloroplast DNA of Acetabularia mediterranea: Cell cycle related changes in distribution

Chloroplast DNA (cpDNA) distribution in the giant unicellular, uninucleate alga Acetabularia mediterranea was analyzed with the DNA-specific fluorochrome 4'6-diamidino-2-phenylindole (DAPI) at various stages of the cell cycle. The number of chloroplasts exhibiting DNA/DAPI fluorescence changes during the cell's developmental cycle: (1) all chloroplasts in germlings contain DNA; (2) the number of plastids with DNA declines during polar growth of the vegetative cell; (3) it increases again prior to the transition from the vegetative to the generative phase; (4) several nucleoids of low fluorescence intensity are present in the chloroplasts of the gametes. The temporal distribution of the number of chloroplasts with DNA appears to be linked to the different mode of chloroplast division and growth during the various stages of development. The chloroplast cycle in relation to the cell cycle is discussed.

Localization of DNA in Mature and Young Wheat Chloroplasts Using the Fluorescent Probe 4'-6-Diamidino-2-phenylindole

The spatial organization of chloroplast DNA in developing and dividing wheat chloroplasts was studied in the light microscope using the fluorescent probe 4'-6-diamidino-2-phenylindole, which binds specifically to DNA.The DNA of wheat chloroplasts was localized at the periphery of the plastid, frequently in a discrete band. No relocalization of the DNA was observed during plastid replication. This peripheral location of the DNA was shown to differ from the central random location of DNA in tobacco and spinach chloroplasts.

Use of the fluorochrome 4'6-diamidino-2-phenylindole in genetic and developmental studies of chloroplast DNA

Use of the DNA-specific fluorochrome 4'6-diamidino-2-phenylindole (DAPI) makes it possible to examine in situ the structure of chloroplast DNA (chDNA) with the fluorescence microscope. This simplifies the study of genetic and developmental changes in chloroplast DNA. Three examples are presented. (a) Wild-type Euglena gracilis B contains several chloroplast DNA nucleoids per chloroplast. A yellow mutant lacking functional chloroplasts is similar, but such nucleoids are absent in an aplastidic mutant strain known from biochemical studies to have lost its chDNA. (b) In vegetative cells of the giant-celled marine algae Acetabularia and Batophora, only about a quarter of the chloroplasts have even one discernible chloroplast DNA particle, and such particles vary in size, showing a 30-fold variation in the amount of DNA-bound DAPI fluorescence detected per chloroplast. By contrast, 98% of chloroplasts in developing Acetabularia cysts contain chDNA, with as many as nine nucleoids per chloroplast. (c) DAPI-stained chloroplasts of chromophyte algae display the peripheral ring of DNA expected from electron microscope studies. However, these rings are not uniform in thickness, but are necklace-like, with the appearance of beads on a string. Since the multiple nucleoids in plastids of chlorophyte algae also appear to be interconnected throughout the chloroplast, a common structural plan may underlie chDNA morphology in both groups of algae.

The kinetic complexity of Acetabularia chloroplast DNA

The kinetic complexity of Acetabularia cliftonii chloroplast DNA is 1.52 +/- 0.26 . 10(9) daltons, compared to 0.2 .10(9) daltons for Chlamydomonas chloroplast DNA. There is an average of three genomes per chloroplast. The unusually large size of the Acetabularia genome may reflect the ancient evolutionary history of this organism.

Variation in Plastid Number: Effect on Chloroplast and Nuclear Deoxyribonucleic Acid Complement in the Unicellular Alga Olisthodiscus luteus

Changes in the physiological state of the multiplastidic alga Olisthodiscus luteus result in a shift in chloroplast complement from 33 to 21 plastids. The effect of this induced change in organelle complement on nuclear and chloroplast DNA levels has been analyzed. Data suggest that the absolute amount of chloroplast and nuclear DNA found within a cell remains constant but that the amount of chloroplast DNA per plastid is inversely proportional to the number of chloroplasts to which that DNA must be distributed.

Covalently closed minicircular DNA associated with Acetabularia chloroplasts

When Acetabularia cliftonii chloroplast DNA (p = 1.706 g/cm3) is centrifuged in an ethidium bromide-CsCl gradient, the lower band is enriched for DNA with a buoyant density of 1.712 g/cm3 containing small covalently closed circular molecules. The minicircles measure 4.15 +/- 0.30 mum in the closed conformation and 4.35 +/- 0.20 mum in the open conformation. They are not of nuclear or bacterial origin, and appear to exist as independent entities within the chloroplast, although a mitochondrial origin cannot be completely ruled out. No 40-45 mum circles, as found in other chloroplasts, were found in either ethidium bromide-CsCl fraction. None were found in total chloroplast DNA by any of a number of methods tried. Linear molecules up to 200 mum were measured in chloroplast lysates. The main chloroplast genome may consist of very large circular molecules which are broken by even small shear forces.

Biosynthesis in isolated Acetabularia chloroplasts. I. Protein amino acids

The ability of chloroplasts isolated from Acetabulana mediterranea to synthesize the protein amino acids has been investigated. When this chloroplast isolate was presented with (14)CO(2) for periods of 6-8 hr, tracer was found in essentially all amino acid species of their hydrolyzed protein Phenylalanine labeling was not detected, probably due to technical problems, and hydroxyproline labeling was not tested for The incorporation of (14)CO(2) into the amino acids is driven by light and, as indicated by the amount of radioactivity lost during ninhydrin decarboxylation on the chromatograms, the amino acids appear to be uniformly labeled. The amino acid labeling pattern of the isolate is similar to that found in plastids labeled with (14)CO(2) in vivo. The chloroplast isolate did not utilize detectable amounts of externally supplied amino acids in light or, with added adenosine triphosphate (ATP), in darkness. It is concluded that these chloroplasts are a tight cytoplasmic compartment that is independent in supplying the amino acids used for its own protein synthesis. These results are discussed in terms of the role of contaminants in the observed synthesis, the "normalcy" of Acetabularia chloroplasts, the synthetic pathways for amino acids in plastids, and the implications of these observations for cell compartmentation and chloroplast autonomy.

Circular chloroplast DNA from Euglena gracilis

Chloroplast DNA of the protozoan flagellate, Euglena gracilis, exists as circular molecules, 40 mum in contour length, as shown by electron microscopy and buoyant density analyses.