Genetic analysis of chloroplast DNA in Chlamydomonas

Rapid adaptation of microalgae to bodies of water with extreme pollution from uranium mining: an explanation of how mesophilic organisms can rapidly colonise extremely toxic environments

Extreme environments may support communities of microalgae living at the limits of their tolerance. It is usually assumed that these extreme environments are inhabited by extremophile species. However, global anthropogenic environmental changes are generating new extreme environments, such as mining-effluent pools of residual waters from uranium mining with high U levels, acidity and radioactivity in Salamanca (Spain). Certain microalgal species have rapidly adapted to these extreme waters (uranium mining in this area began in 1960). Experiments have demonstrated that physiological acclimatisation would be unable to achieve adaptation. In contrast, rapid genetic adaptation was observed in waters ostensibly lethal to microalgae by means of rare spontaneous mutations that occurred prior to the exposure to effluent waters from uranium mining. However, adaptation to the most extreme conditions was only possible after recombination through sexual mating because adaptation requires more than one mutation. Microalgae living in extreme environments could be the descendants of pre-selective mutants that confer significant adaptive value to extreme contamination. These "lucky mutants" could allow for the evolutionary rescue of populations faced with rapid environmental change.

Uniparental inheritance of chloroplast DNA sequences in interspecific hybrids of Chlamydomonas

The meiotic transmission of chloroplast DNA (cpDNA) was studied in crosses between two species of Chlamydomonas (C. moewusii and C. eugametos) which have substantial differences in cpDNA restriction patterns. The results provide a direct demonstration that cpDNA can be inherited in a uniparental pattern, paralleling the transmission of a uniparentally inherited antibiotic resistance marker. Thus, cpDNA could carry the uniparental genes of these species, but other extrachromosomal DNAs are not excluded as possible carriers. For example, C. moewusii was found to contain a set of low molecular weight (LMW) DNA species which cannot be detected in C. eugametos. These LMW DNA species are also transmitted uniparentally in the tetrads studied. Uniparentai transmission may not be an exclusive property of cpDNA in Chlamydomonas species.

Chloroplast gene inheritance studied by somatic fusion in Chlamydomonas reinhardtii

Somatic fusion between strains of Chlamydomonas containing complementing cell-wall and auxotrophic mutations, having the same mating-type (mt) and bearing chloroplast markers, have been performed to study the mode of chloroplast gene inheritance in the fusion products. About one third of the fusion products (mt (+)/mt (+) or mt (-)/mt (-)) transmitted chloroplast markers from both parents (= biparental fusion products). The rest of the population was equally distributed between fusion products transmitting the chloroplast marker of one parent or the other (uniparental fusion products) exclusively. Incubation of the fusion products in the dark for 48 hours, immediately after the fusion, decreases the frequency of biparental fusion products. The results indicate that the general process of elimination of chloroplast alleles is independent of the presence of both mt (+) and mt (-) alleles in the cell. In contrast, directional elimination (i.e. preferential elimination of paternal chloroplast alleles) does appear to depend upon heterozygosity at the mt locus. These results are discussed in relation to the models which have been proposed to explain the maternal inheritance of chloroplast genes in Chlamydomonas.

Chloroplast gene suppression of defective ribulosebisphosphate carboxylase/oxygenase in Chlamydomonas reinhardii: evidence for stable heteroplasmic genes

The rcl-u-1-18-5B chloroplast mutation results in the absence of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) holoenzyme in the green alga Chlamydomonas reinhardii. The 18-5B mutant strain lacks photosynthesis and displays alight-sensitive, acetate-requiring phenotype. In the present investigations, revertants of 18-5B were recovered that regained photosynthetic competence. These revertants have decreased levels of Rubisco holoenzyme relative to wild type and display heteroplasmicity, segregating wild-type (revertant) and acetate-requiring phenotypes during vegetative growth or through meiosis. One of these revertants, R10-I, was studied further. The heteroplasmicity associated with photoautotrophically-grown R10-I was found to be stable through subcloning and heritable through several crosses. During growth in acetate medium in the dark, where photosynthesis provides no selective advantage, the wild-type phenotype was lost. Acetate-requiring segregants became homoplasmic but wild-type segregants did not. Organellar intergenic-suppression is discussed in light of the observed stable heteroplasmicity.

Adaptation of microalgae to lindane: a new approach for bioremediation

Lindane is especially worrisome because its persistence in aquatic ecosystems, tendency to bioaccumulation and toxicity. We studied the adaptation of freshwater cyanobacteria and microalgae to resist lindane using an experimental model to distinguish if lindane-resistant cells had their origin in random spontaneous pre-selective mutations (which occur prior to the lindane exposure), or if lindane-resistant cells arose by a mechanism of physiological acclimation during the exposure to the selective agent. Although further research is needed to determine the different mechanisms contributing to the bio-elimination of lindane, this study, however, provides an approach to the bioremediation abilities of the lindane-resistant cells. Wild type strains of the experimental organisms were exposed to increasing lindane levels to estimate lethal concentrations. Growth of wild-type cells was completely inhibited at 5mg/L concentration of lindane. However, after further incubation in lindane for several weeks, occasionally the growth of rare lindane-resistant cells was found. A fluctuation analysis demonstrated that lindane-resistant cells arise only by rare spontaneous mutations that occur randomly prior to exposure to lindane (lindane-resistance did not occur as a result of physiological mechanisms). The rate of mutation from lindane sensitivity to resistance was between 1.48 × 10(-5) and 2.35 × 10(-7) mutations per cell per generation. Lindane-resistant mutants exhibited a diminished fitness in the absence of lindane, but only these variants were able to grow at lindane concentrations higher than 5mg/L (until concentrations as high as 40 mg/L). Lindane-resistant mutants may be maintained in uncontaminated waters as the result of a balance between new resistant mutants arising from spontaneous mutation and resistant cells eliminated by natural selection waters via clone selection. The lindane-resistant cells were also used to test the potential of microalgae to remove lindane. Three concentrations (4, 15 and 40 mg/L) were chosen as a model. In these exposures the lindane-resistant cells showed a great capacity to remove lindane (until 99% lindane was eliminated). Apparently, bioremediation based on lindane-resistant cells could be a great opportunity for cleaning up of lindane- and other chlorinated organics-polluted habitats.

Adaptation of microalgae to a gradient of continuous petroleum contamination

In order to study adaptation of microalgae to petroleum contamination, we have examined an environmental stress gradient by crude oil contamination in the Arroyo Minero River (AMR), Argentina. Underground crude oil has constantly leaked out since 1915 as a consequence of test drilling for possible petroleum exploitation. Numerous microalgae species proliferated in AMR upstream of the crude oil spill. In contrast, only four microalgal species were detected in the crude oil spill area. Species richness increases again downstream. Microalgae biomass in the crude oil spill area is dominated by a mesophile species, Scenedesmus sp. Effects of oil samples from AMR spill on photosynthetic performance and growth were studied using laboratory cultures of two Scenedesmus sp. strains. One strain (Se-co) was isolated from the crude oil spill area. The other strain (Se-pr) was isolated from a pristine area without petroleum contamination. Crude oil has undetectable effects on Se-co strain. In contrast crude oil rapidly destroys Se-pr strain. However, Se-pr strain can adapt to low doses of petroleum (≤ 3% v/v total hydrocarbons/water) by means of physiological acclimatization. In contrast, only rare crude oil-resistant mutants are able to grow under high levels of crude oil (≥ 10% v/v total hydrocarbons/water). These crude oil-resistant mutants have arisen through rare spontaneous mutations that occur prior to crude oil exposure. Species richness in different areas of AMR is closely connected to the kind of mechanism (genetic adaptation vs. physiological acclimatization) that allows adaptation. Resistant-mutants are enough to assure the survival of microalgal species under catastrophic crude oil spill.

Herbicide resistance in Chlamydomonas reinhardtii results from a mutation in the chloroplast gene for the 32-kilodalton protein of photosystem II

We report the isolation and characterization of a uniparental mutant of Chlamydomonas reinhardtii that is resistant to 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (atrazine). Such herbicides inhibit photosynthesis by preventing transfer of electrons in photosystem II from the primary stable electron acceptor Q to the secondary stable electron acceptor complex B, which is thought to contain a protein of 32 kDa and a bound quinone. It has been proposed that herbicide binding to the 32-kDa protein alters the B complex so that electron transfer from Q is prohibited. Both whole and broken-cell preparations of the mutant alga show a resistance to the effects of herbicide on electron transfer from Q to B, as measured by fluorescence-induction kinetics. In the absence of herbicide, mutant cells exhibit a slower rate of Q to B electron transfer than do wild-type cells. The 32-kDa protein from wild-type cells, but not mutant cells, binds azido[(14)C]atrazine at 0.1 muM. We have isolated psbA, the chloroplast gene for the 32-kDa protein, from both wild-type and herbicide-resistant algae and sequenced the coding regions of the gene that are contained in five exons. The only difference between the exon nucleotide sequences of the wild-type and mutant psbA is a single T-A to G-C transversion. This mutation results in a predicted amino acid change of serine in the wild-type protein to alanine in the mutant. We suggest that this alteration in the 32-kDa protein is the molecular basis for herbicide resistance in the C. reinhardtii mutant.

The foundation of extranuclear inheritance: plastid and mitochondrial genetics

In 1909 two papers by Correns and by Baur published in volume 1 of Zeitschrift für induktive Abstammungs- und Vererbungslehre (now Molecular Genetics and Genomics) reported on the non-Mendelian inheritance of chlorophyll deficiencies. These papers, reporting the very first cases of extranuclear inheritance, laid the foundation for a new field: non-Mendelian or extranuclear genetics. Correns observed a purely maternal inheritance (in Mirabilis), whereas Baur found a biparental inheritance (in Pelargonium). Correns suspected the non-Mendelian factors in the cytoplasm, while Baur believed that the plastids carry these extranuclear factors. In the following years, Baur's hypothesis was proved to be correct. Baur subsequently developed the theory of plastid inheritance. In many genera the plastids are transmitted only uniparentally by the mother, while in a few genera there is a biparental plastid inheritance. Commonly there is random sorting of plastids during ontogenetic development. Renner and Schwemmle as well as geneticists in other countries added additional details to this theory. Pioneering studies on mitochondrial inheritance in yeast started in 1949 in the group of Ephrussi and Slonimski; respiration-deficient cells (petites in yeast, poky in Neurospora) were demonstrated to be due to mitochondrial mutations. Electron microscopical and biochemical studies (1962-1964) showed that plastids and mitochondria contain organelle-specific DNA molecules. These findings laid the molecular basis for the two branches of extranuclear inheritance: plastid and mitochondrial genetics.

Parasite diversity and the evolution of diploidy, multicellularity and anisogamy

It may be reasonably assumed that a diversity of parasite genotypes in any one cell or organism is more harmful than a population of uniform genotypes. If this is accepted the following consequences follow: (i) Parasite mixing, due to cytoplasm mixing, at the time of zygote formation is a new and additional cost of sex. The rapid divisions typical of zygotic cleavage may be viewed as an adaptation to minimize the degree of mixing of parasites in each daughter cell. The faster the divisions the less chance parasite populations have to grow and mix. Mitosis is the fastest form of cell division. Prolongation of the diploid phase follows as a consequence of mitosis in a diploid zygote. This view is unusual in that it demands no advantage per se to the possession of two chromosome sets. (ii) The cells of the blastula formed from rapid zygotic divisions are different as regards their symbiotic inclusions. If the right to gametogenesis is restricted, then every replicator symbiont and nuclear genome alike and hence every cell of the developing embryo, will have an incentive to compete. Selection between the clonal blastula cells would result in the cells of low parasite diversity forming the gametes. Thus, germ line restriction is in the interests of the nuclear genome. Controlling the right to gametogenesis is only possible if the blastula remains intact. Hence, multicellularity might have evolved so as to enable the limitation of the right to gametogenesis and hence reduce the parasite diversity of gametes. Inter-cell competition during embryogenesis is central to Buss's seminal notion of the evolution of developmental complexity within the metazoa. The above theory provides the missing motive force behind such competition. (iii) For a given zygote size, the fittest zygotes are those produced by the gametes most disparate in size because these have a lower diversity of parasites. This may be the advantage of anisogamy. The novelty of this new view of anisogamy is that it puts a premium on sperm being very small, in order to exclude parasites from sperm cytoplasm. The hypothesis is briefly tested by examining if there are alternative means of parasite limitation in organisms with large gametes.

Limited chloroplast gene transfer via recombination overcomes plastomegenome incompatibility between Nicotiana tabacum and Solanum tuberosum

Green cybrids with a new nucleus-chloroplast combination cannot be selected after protoplast fusion in the intersubfamilial Nicotiana-Solanum combination. As an approach to overcome the supposed plastomegenome incompatibility, a partial plastome transfer by genetic recombination has been considered. After fusions of protoplasts of a light-sensitive Nicotiana tabacum (tobacco) plastome mutant and lethally irradiated protoplasts of wild-type Solanum tuberosum (potato), a single green colony was recovered among 2.5×10(4) colonies. The regenerated plants had tobacco-like (although abnormal) morphology, but were normally green, and sensitive to tentoxin, demonstrating chloroplast markers of the potato parent. Restriction enzyme analysis of the chloroplast DNA (cpDNA) revealed recombinant, nonparental patterns. A comparison with physical maps of the parental cpDNA demonstrated the presence of a considerable part of the potato plastome flanked by tobacco-specific regions. This "potacco" plastome proved to be stable in backcross and backfusion experiments, and normally functional in the presence solely of N. tabacum nucleus.

Mapping of chloroplast mutations conferring resistance to antibiotics in Chlamydomonas: evidence for a novel site of streptomycin resistance in the small subunit rRNA

A major obstacle to our understanding of the mechanisms governing the inheritance, recombination and segregation of chloroplast genes in Chlamydomonas is that the majority of antibiotic resistance mutations that have been used to gain insights into such mechanisms have not been physically localized on the chloroplast genome. We report here the physical mapping of two chloroplast antibiotic resistance mutations: one conferring cross-resistance to erythromycin and spiramycin in Chlamydomonas moewusii (er-nM1) and the other conferring resistance to streptomycin in the interfertile species C. eugametos (sr-2). The er-nM1 mutation results from a C to G transversion at a well-known site of macrolide resistance within the peptidyl transferase loop region of the large subunit rRNA gene. This locus, designated rib-2 in yeast mitochondrial DNA, corresponds to residue C-2611 in the 23 S rRNA of Escherichia coli. The sr-2 locus maps within the small subunit (SSU) rRNA gene at a site that has not been described previously. The mutation results from an A to C transversion at a position equivalent to residue A-523 in the E. coli 16 S rRNA. Although this region of the E. coli SSU rRNA has no binding affinity for streptomycin, it binds to ribosomal protein S4, a protein that has long been associated with the response of bacterial cells to this antibiotic. We propose that the sr-2 mutation indirectly affects the nearest streptomycin binding site through an altered interaction between a ribosomal protein and the SSU rRNA.

Rice mitochondrial genome contains a rearranged chloroplast gene cluster

We have previously reported the isolation and partial sequence analysis of a rice mitochondrial DNA fragment (6.9 kb) which contains a transferred copy of a chloroplast gene cluster coding for the large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL), beta and epsilon subunits of ATPase (atpB and atpE), methionine tRNA (trnM) and valine tRNA (trnV). We have now completely sequenced this 6.9 kb fragment and found it to also contain a sequence homologous to the chloroplast gene coding for the ribosomal protein L2 (rpl2), beginning at a site 430 bp downstream from the termination codon of rbcL. In the chloroplast genome, two copies of rpl2 are located at distances of 20 kb and 40 kb, respectively, from rbcL. We have sequenced these two copies of rice chloroplast rpl2 and found their sequences to be identical. In addition, a 151 bp sequence located upstream of the chloroplast rpl2 coding region is also found in the 3' noncoding region of chloroplast rbcL and other as yet undefined locations in the rice chloroplast genome. Hybridization analysis revealed that this 151 bp repeat sequence identified in rice is also present in several copies in 11 other plant species we have examined. Findings from these studies suggest that the translocation of rpl2 to the rbcL gene cluster found in the rice mitochondrial genome might have occurred through homologous recombination between the 151 bp repeat sequence present in both rpl2 and rbcL.

Nicotiana tabacum mutants with chloroplast encoded streptomycin resistance and pigment deficiency

Callus ofNicotiana tabacum SRI, a mutant with maternally inherited streptomycin resistance, was induced from leaf sections. Callus pieces were mutagenised with N-ethyl-N-nitrosourea and inoculated onto a shoot-induction medium on which calli are normally green. White callus sectors were observed in the mutagenised cultures, and white and variegated shoots were regenerated from these sectored calli. The SR1-A10 line regenerated a chimeric shoot with white leaf margins. The chimeric shoot was grafted onto a normal green rootstock, grown into a flowering plant in the greenhouse, and crosses were made. The SRI-A15 line was crossed using flowers formed on albino plants grown in sterile culture. Pigment deficiency was maternally inherited in both lines. Physical mapping of the chloroplast genome of the SR1-A15 mutant by SalI, PstI and BamHI restriction endonucleases did not reveal any difference between the SR1-A15 and the parental SRI chloroplast genomes.

Electron microscopic localization of the chloroplast DNA replicative origins in Chlamydomonas reinhardii

Chloroplast DNA, isolated from a synchronized culture of Chlamydomonas reinhardii, was digested with restriction endonucleases and examined in the electron microscope. Restriction fragments containing displacement loops (D-loop) were photographed and measured to determine the position of replicated sequences in relation to the restriction enzyme sites. D-loops were located at two positions on the physical map of chloroplast DNA. One replication origin was mapped at about 10 kb upstream of the 5' end of a 16s rRNA gene. The second origin was spaced 6. 5kb apart from the first origin and was about 16.5 kb upstream of the same 16s rRNA. Initiations at those two sites were not always synchronized. Replication initiated with the formation of a D-loop resulting from the synthesis of one daughter strand. After a short initial lag phase, corresponding to the synthesis of 350 +/- 130 bp of one daughter strand, DNA synthesis then proceeded in both directions. Both D-loop regions were preferred binding sites of undetermined protein complexes.

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.

Regulation of the Chlamydomonas cell cycle by light and dark

By growing cells in alternating periods of light and darkness, we have found that the synchronization of phototrophically grown Chlamydomonas populations is regulated at two specific points in the cell cycle: the primary arrest (A) point, located in early G1, and the transition (T) point, located in mid-G1. At the A point, cell cycle progression becomes light dependent. At the T point, completion of the cycle becomes independent of light. Cells transferred from light to dark at cell cycle position between the two regulatory points enter a reversible resting state in which they remain viable and metabolically active, but do not progress through their cycles. The photosystem II inhibitor dichlorophenyldimethylurea (DCMU) mimics the A point block induced by darkness. This finding indicates that the A point block is mediated by a signal that operates through photosynthetic electron transport. Cells short of the T point will arrest in darkness although they contain considerable carbohydrate reserves. After the T point, a sharp increase occurs in starch degradation and in the endogenous respiration rate, indicating that some internal block to the availability of stored energy reserves has now been released, permitting cell cycle progression.

Deoxyribonucleic acid methyltransferase from the eukaryote, Chlamydomonas reinhardi

DNA methyltransferase was purified 310-fold from a green alga, Chlamydomonas reinhardi vegetative cells. The native enzyme of molecular weight 55 000--58 000 catalyzed the transfer of methyl groups from S-adenosylmethionine to the 5 position of cytosine in DNA. Native DNA accepted methyl groups 10-fold more than did denatured DNA. The sequence specificity analysis of methylated deoxycytidine in vitro revealed that the enzyme introduces methyl groups preferentially into sequences containing 5'd(T-mC-R)3'. Kinetic analysis of the reaction indicated that the enzyme obeys a random sequential mechanism. The extent of saturation with methyl groups depends upon the species from which the DNA was obtained. Kinetic analysis of the reaction catalyzed by RNA polymerase II has indicated that DNA methylation decreases the rate of initiation of RNA synthesis, but does not affect the rate of RNA chain elongation.

The non-reciprocality of organelle gene recombination in Chlamydomonas reinhardtii and Saccharomyces cerevisiae: some new observations and a restatement of some old problems

Organelle recombinant genotype frequencies, derived from analysis of individual mitotic zygote clones of Chlamydomonas reinhardtii and Saccharomyces cerevisiae, were subjected to two types of statistical tests in an attempt to detect the occurrence of reciprocal recombination: (i) calculation of correlation coefficients for the frequencies of two recombinant genotypes (reciprocal or non-reciprocal pairs) within individual zygote clones, and (ii) application of the chi-square test for independence to the frequencies of zygotes yielding one or the other, neither, or both of a given recombinant pair. Applying test (i), the strongest correlations are found for non-reciprocal rather than reciprocal pairs. When the data are analyzed by method (ii), some reciprocal as well as non-reciprocal pairs appear to be produced concurrently in zygote clones. However, such deviations from independence are greatest for non-reciprocal pairs. These tests yield comparable results for yeast mitochondrial and Chlamydomonas chloroplast gene recombination, and provide no convincing evidence for reciprocal genetic exchange. Explanations for the observed lack of reciprocality are discussed with reference both to our present understanding of the molecular events responsible for genetic recombination, and to the problems which may be unique to the analysis of organelle gene recombination.