Isolation and Characterization of Chloroplast DNA from the Marine Chromophyte, Olisthodiscus luteus: Electron Microscopic Visualization of Isomeric Molecular Forms

Inverted repeat of Olisthodiscus luteus chloroplast DNA contains genes for both subunits of ribulose-1,5-bisphosphate carboxylase and the 32,000-dalton Q(B) protein: Phylogenetic implications

The chloroplast DNA of the chromophytic alga Olisthodiscus luteus has been physically mapped with four restriction enzymes. An inverted repeat of 22 kilobase pairs is present in this 150-kilobase-pair plastid genome. The inverted repeat contains the genes for the large and small subunit polypeptides of ribulose-1,5-bisphosphate carboxylase (EC 4.1.1.39) and also codes for the 32,000-dalton Q(B) protein. These observations demonstrate that significant differences exist in chloroplast genome structure and organization among major plant taxa.

Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains

BACKGROUND

Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. Surprisingly, chloroplast genome sequences are available only for diatoms, representing two (Coscinodiscophyceae and Bacillariophyceae) of approximately 18 classes of algae that comprise this taxonomic cluster. A universal challenge to chloroplast genome sequencing studies is the retrieval of highly purified DNA in quantities sufficient for analytical processing. To circumvent this problem, we have developed a simplified method for sequencing chloroplast genomes, using fosmids selected from a total cellular DNA library. The technique has been used to sequence chloroplast DNA of two Heterosigma akashiwo strains. This raphidophyte has served as a model system for studies of stramenopile chloroplast biogenesis and evolution.

RESULTS

H. akashiwo strain CCMP452 (West Atlantic) chloroplast DNA is 160,149 bp in size with a 21,822-bp inverted repeat, whereas NIES293 (West Pacific) chloroplast DNA is 159,370 bp in size and has an inverted repeat of 21,665 bp. The fosmid cloning technique reveals that both strains contain an isomeric chloroplast DNA population resulting from an inversion of their single copy domains. Both strains contain multiple small inverted and tandem repeats, non-randomly distributed within the genomes. Although both CCMP452 and NIES293 chloroplast DNAs contains 197 genes, multiple nucleotide polymorphisms are present in both coding and intergenic regions. Several protein-coding genes contain large, in-frame inserts relative to orthologous genes in other plastids. These inserts are maintained in mRNA products. Two genes of interest in H. akashiwo, not previously reported in any chloroplast genome, include tyrC, a tyrosine recombinase, which we hypothesize may be a result of a lateral gene transfer event, and an unidentified 456 amino acid protein, which we hypothesize serves as a G-protein-coupled receptor. The H. akashiwo chloroplast genomes share little synteny with other algal chloroplast genomes sequenced to date.

CONCLUSION

The fosmid cloning technique eliminates chloroplast isolation, does not require chloroplast DNA purification, and reduces sequencing processing time. Application of this method has provided new insights into chloroplast genome architecture, gene content and evolution within the stramenopile cluster.

Chloroplast genome characterization in the red alga Griffithsia pacifica

It has been suggested that cyanobacteria served as the ancestors for rhodophytic algae whose chloroplasts contain chlorophyll a and phycobilins, and that a rodophyte served as the plastid source for chromophytic plants that contain chlorophylls a and c. Although organellar DNA has been used to assess phylogenetic relatedness among terrestrial plants and green algae whose chloroplasts contain chlorophylls a and b, few data are presently available on the molecular profile of plastid DNA in chromophytes or rhodophytes. In this study the chloroplast genome of the rhodophytic, filamentous alga Griffithsia pacifica has been characterized. DNA was purified from isolated chloroplasts using protease k treatment and sodium dodecyl sulfate lysis followed by density centrifugation in Hoechst-33258 dye-CsCl gradients. Single and double restriction enzyme digests demonstrate that the DNA prepared from purified chloroplasts has a genome size of about 178 kilobase pairs (kb). A restriction map of this chloroplast genome demonstrates that it is circular and, unlike the chloroplast DNA (cpDNA) in most other plants, contains only a single ribosomal DNA operon. DNA was also purified from the mitochondria that co-isolated with chloroplasts. Mitochondrial DNA consists of molecules that range in size from 27 to 350 kb based on restriction endonuclease digestion and electron microscopic analysis.

'Empty' minicircles and petB/atpA and psbD/psbE (cytb559 alpha) genes in tandem in Amphidinium carterae plastid DNA

Amphidinium carterae minicircle chloroplast DNA was separated from total DNA by centrifugation through a sucrose/NaCl gradient. Sequences of minicircles with psbA and 23S rRNA contained a common region of 67 bp. Primers designed from this generated numerous polymerase chain reaction products of 1.5-2.6 kb. These contained psaA and psaB as one gene/circle, and petB/atpA and psbD/psbE as two genes/circle. 'Empty' minicircles of 1.7-2.5 kb containing no identifiable genes or parts of genes were more abundant than gene-containing circles. From 15 minicircles a minimum common region of 48 bp was identified, with little identity to that from other dinoflagellate minicircles.

Comparison of gene arrangements of chloroplasts between two centric diatoms, Skeletonema costatum and Odontella sinensis

We have cloned and sequenced 3.4 kbp, 2.5 kbp, 1.9 kbp, 1.6 kbp and 0.5 kbp segments of a marine centric diatom, Skeletonema costatum, chloroplast DNA. These segments contain 28 genes. The genes which are not encoded on chloroplast genomes of chlorophyll a+b plants are found such as the psaD, ycf33, ycf35 and ycf47 genes. The gene sequences were compared with that of Odontella sinensis. At nucleic acid level, the ycf genes have lower homologies (69-87%) with O. sinensis than the other genes (78-100%), and some differences in the gene arrangement are found between two centric diatoms, O. sinensis and S. costatum.

Cloning and characterization of the Chlamydomonas moewusii mitochondrial genome

We report that the mitochondrial genome of Chlamydomonas moewusii has a 22 kb circular map and thus contrasts with the mitochondrial genome of Chlamydomonas reinhardtii, which is linear and about 6 kb shorter. Overlapping restriction fragments spanning over 90% of the C. moewusii mitochondrial DNA (mtDNA) were identified in a clone bank constructed using a Sau3AI partial digest of a C. moewusii DNA fraction enriched for mtDNA by preparative CsCl density gradient centrifugation. Overlapping Sau3AI clones were identified by a chromosome walk initiated with a clone of C. moewusii mtDNA. The mtDNA map was completed by Southern blot analysis of the C. moewusii mtDNA fraction using isolated mtDNA clones. Regions that hybridized to C. reinhardtii or wheat mitochondrial gene probes for subunit I of cytochrome oxidase (cox1), apocytochrome b (cob), three subunits of NADH dehydrogenase (nad1, nad2 and nad5) and the small and the large ribosomal RNAs (rrnS and rrnL, respectively) were localized on the C. moewusii mtDNA map by Southern blot analysis. The results show that the order of genes in the mitochondrial genome of C. moewusii is completely rearranged relative to that of C. reinhardtii.

Characterization of Satellite DNA from Three Marine Dinoflagellates (Dinophyceae): Glenodinium sp. and Two Members of the Toxic Genus, Protogonyaulax

Using CsCl-Hoechst dye or CsCl-ethidium bromide gradients, satellite and nuclear DNAs were separated and characterized in three marine dinoflagellates: Glenodinium sp., and two toxic dinoflagellates, Protogonyaulax tamarensis and Protogonyaulax catenella. In all three dinoflagellates, the lowest density fraction, satellite DNA(1), hybridized to chloroplast genes derived from terrestrial plants and/or other algae. Dinoflagellate chloroplast DNAs exhibited molecular sizes of 114 to 125 kilobase pairs, which is consistent with plastid sizes determined for other chromophytic algae (120-150 kilobase pairs). Mitochondrial DNA was not resolved from nuclear DNA in this system. Two additional satellite DNAs, satellite DNA(2) and satellite DNA(3), recovered from P. tamarensis and P. catenella were similar to one another, both within and between species, when characterized by restriction enzyme analysis. These satellites were 85 to 95 kilobase pairs in size, and exhibited restriction fragments that hybridized to yeast nuclear ribosomal RNA genes. Restriction enzyme analyses and DNA hybridization studies of cpDNA document that the two Protogonyaulax isolates are not evolutionarily identical.

Structural organization and transcription of plant mitochondrial and chloroplast genomes

Experimental evidence is presented showing that the plant mitochondrial and chloroplast genomes are multipartite and, that besides a large circular genomic DNA, they contain subgenomic minicircular and plasmid-like molecules. It is demonstrated that plant mitochondrial and chloroplast DNAs are packaged into deoxynucleoprotein fibrils comprising nucleosome-like and nucleomere-like globules; the fibrils form loops and rosette-like structures with central proteinaceous components. A similar structure is characteristic of the subgenomic DNAs. The basic proteins involved in the formation of nucleosome-like globules are quite different from the nuclear histones, indeed the basic proteins from plant mitochondria and chloroplasts are also distinct. Some of the basic proteins share common antigens with the E. coli HU protein. The genetic code for the mitochondrial and chloroplast genes is universal. The only codon now thought to be different from the universal in the mitochondrial genome is corrected during post-transcriptional mRNA editing. There are two hexanucleotides in the promoters of the chloroplast genes homologous to the sequences in -10 and -35 regions of the prokaryotic genes promoters requisite for transcription. Promoter sequences of the plant mitochondria genes responsible for transcription regulation were not identified. Immunoelectronmicroscopic evidence suggest that mitochondrial and chloroplast RNA polymerases have antigens in common with the beta-subunit of E. coli RNA polymerase. It is shown that the mitochondrial genes are intensely transcribed in the dark and repressed by illumination. Electron microscopy demonstrated that about 70% of plant mitochondria contain numerous RNA polymerase molecules in the dark, but this percentage falls to 10-15% after light exposure.

Chloroplast ribosomal DNA organization in the chromophytic alga Olisthodiscus luteus

There are almost no data describing chloroplast genome organization in chromophytic (chlorophyll a/c) plants. In this study chloroplast ribosomal operon placement and gene organization has been determined for the golden-brown alga Olisthodiscus luteus. Ribosomal RNA genes are located on the chloroplast DNA inverted repeat structure. Nucleotide sequence analysis, demonstrated that in contrast to the larger spacer regions in land plants, the 16S-23S rDNA spacer of O. luteus is only 265 bp in length. This spacer contains tRNA(Ile) and tRNA(Ala) genes which lack introns and are separated by only 3 bp. The sequences of the tRNA genes and 16S and 23S rDNA termini flanking the spacer were examined to determine homology between O. luteus, chlorophytic plant chloroplast DNA, and prokaryotes.

Structure of the mitochondrial genome of Beta vulgaris L

The structure of mitochondrial DNA (mt-DNA) from sugarbeet (Beta vulgaris L.) has been studied by biochemical methods and electron microscopy. It was found to be complex multipartite consisting of two main classes of molecules: high molecules weight (HMW) mtDNA and low molecular weight (LMW) mtDNA. The HMW mtDNA consists of rosette-like structures and globules resembling chromomeres (150-200nm). A typical rosette has a protein core and radially stemming closed DNA loops (from 0.6-1.5 μm). The number of loops in a rosette varies from 16-30. The bulk of HMW mtDNAs are represented by interconnected rosettes (total contour length about 130-160 μm, 403-496 kbp). Such large circular DNAs may be evidence of the master chromosome arrangement of the sugarbeet genome. Globules and rosettes are interconnected by thick and thin DNA fibrils, along which nucleosome- and nucleomere-like structures are distributed. The LWM mtDNA is composed of two groups of supercoiled circular molecules, 0,2-1.5 μm and 0.02-0.05 μm in size. Electrophoretic analysis demonstrated that LWM mtDNA is represented by minicircle plasmid-like DNA molecules of 1.3, 1.4 and 1.6 kbp.

The plastome of a brown alga,Dictyota dichotoma : I. Physical properties and the Bam HI/Sal I/Bgl II cleavage site map

Plastids of the brown algaDictyota dichotoma contain a single homogeneous DNA species which bands at a buoyant density of 1.693 g/cm(3) in neutral CsCl equilibrium density gradients. The corresponding nuclear DNA has a density of 1.715 g/cm(3). The molecular size of the plastid DNA is 123 kbp as calculated by both electron microscopy of spread intact circular molecules and gel electrophoresis following single and double digestions with various restriction enzymes. A restriction map has been constructed using the endonucleases Sal I, Bam HI, and Bgl II which cleave theDictyota plastome into 6, 12, and 17 fragments, respectively. No large repeated regions, as found in chlorophycean andEuglena plastid DNAs, were detected.Dictyota dichotoma is the first member from the chlorophyll c-line of the algal pedigree for which a physical map of plastid DNA has been established.

Chloroplast Protein Synthesis in the Chromophytic Alga Olisthodiscus luteus: Cell Cycle Analysis

This study represents the first report on chloroplast protein synthesis during the synchronous cell growth of a chromophytic (chlorophyll a,c) plant. When the unicellular alga Olisthodiscus luteus is maintained on a 12-hour light:12-hour dark cycle, cell and chloroplast number double every 24 hours. A temporal separation between these two events occurs. Measurements of chloroplast and total cellular protein values suggest that polypeptide synthesis occurs mainly in the light portion of the cell cycle, and pulse chase studies demonstrate that chloroplast proteins made in the light are not degraded in the dark. Data support the following conclusions: (a) a similar complement of chloroplast DNA coded proteins is made at all phases of the light portion of the cell cycle, and (b) chloroplast protein synthesis is a light rather than a cell cycle mediated response.

Chloroplast biosystematics: chloroplast DNA as a molecular probe

The classification of plants has traditionally been dependent upon the comparative analysis of morphological and biochemical data. In this paper the use of molecular probe analysis of chloroplast DNA (ctDNA) is used to expand the data base used in taxonomic studies. Chloroplast DNA size, homogeneity, the global arrangement of ctDNA structure, gene content, gene cluster array and gene sequence determination are discussed as useful criteria in the analysis of phylogenetic relationships.

Extranuclear DNA of a Marine Chromophytic Alga : RESTRICTION ENDONUCLEASE ANALYSIS

Two extranuclear DNA species have been isolated from the marine alga Olisthodiscus luteus. Rapid lysis of cells followed by the immediate addition of CsCl to the lysate was critical to the preservation of these satellite DNA species. Restriction endonuclease analysis demonstrates a molecular weight of 99 x 10(6) for chloroplast DNA and 23 x 10(6) for a second satellite species. The origin of the second satellite is not known. However, this smaller satellite DNA which originates from a nonnuclear, DNAse insensitive cellular component, displays no sequence homology with ctDNA by hybridization experiments. Constancy of restriction endonuclease fragment patterns of chloroplast and second satellite species during all phases of the growth cycle, whether cultures were maintained synchronously or asynchronously, was demonstrated.

Kinetic Complexity, Homogeneity, and Copy Number of Chloroplast DNA from the Marine Alga Olisthodiscus luteus

The kinetic complexity of chloroplast DNA isolated from the chromophytic alga Olisthodiscus luteus has been determined. Using optical reassociation techniques, it was shown that the plastid DNA of this alga reacted as a single component with a second order rate constant of 4.1 molar(-1) and second(-1) (Cot((1/2)) 0.24 molar second) under conditions equivalent to 180 millimolar Na(+) and 60 degrees C. Given the 92 x 10(5) dalton complexity calculated for this chloroplast genome, an Olisthodiscus cell contains 650 plastome copies. Although this complement remains constant throughout the growth cycle of the organism, the ploidy level of an individual chloroplast shows significant plasticity and is dependent upon the number of chloroplasts present per cell. Experiments with the DNA fluorochrome Hoechst dye 33258 (bisbenzimide) demonstrate that plastids isolated from all phases of cell growth each possess a ring-shaped nucleoid containing detectable DNA. Olisthodiscus chloroplast DNA showed no sequence mismatch when thermal denaturation profiles of reassociated chloroplast DNA were examined, thus all plastome copies are essentially identical. Finally, reassociation studies demonstrated that no foldback (short inverted repeat) sequences were present in the plastid genome although significant hairpin loop structures were observed in control nuclear DNA samples.