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At least 19 recordsLinked to original sources

PubMed2002

Phycodnaviridae--large DNA algal viruses.

Members and prospective members of the family Phycodnaviridae are large icosahedral, dsDNA (180 to 560 kb) viruses that infect eukaryotic algae. The genomes of two phycodnaviruses have been sequenced: the 331 kb genome of Paramecium bursaria chlorella virus (PBCV-1) and more recently, the 336 kb genome of the Ectocarpus siliculosus virus (EsV-1). EsV-1 has approximately 231 protein-encoding genes whereas, the slightly smaller PBCV-1 genome has 11 tRNA genes and approximately 375 protein-encoding genes. Surprisingly, the two viruses only have 33 genes in common, of which 17 have no counterparts in the databases. The low number of homologous genes between the two viruses can probably be attributed to their different life styles. PBCV-1 is a lytic virus that infects a unicellular, endosymbiotic freshwater green alga whereas, EsV-1 is a lysogenic virus that infects a free-living filamentous marine brown alga. Furthermore, accumulating evidence indicates that the phycodnaviruses and their genes are ancient, thus allowing significant differences to have evolved. This review briefly describes some of the biological properties of the phycodnaviruses, focusing on PBCV-1 and EsV-1, and then compares their genomes.

Chlorella↗

PubMed1985

Isolation and purification of deoxyribonucleosides from 90% 13C-enriched DNA of algal cells and their characterization by 1H and 13C NMR.

13C-enriched deoxyribonucleosides have been isolated from the DNA of Algal cells grown in an atmosphere of 90% 13C-labelled carbon dioxide. The 13C enriched DNA was quantitatively hydrolysed with DNase I, snake venom phosphodiesterase I and alkaline phosphatase of intestinal mucosa. The resulting deoxyribonucleosides were separated by preparative reversed-phase high pressure liquid chromatography in 60 minutes with detection by ultraviolet absorption at 254 nm. The final products were obtained in milligram quantities in high purity and in high yield. The 1H resonances of the base and sugar protons of these deoxyribonucleosides appear as well resolved multiplets in the 600 MHz NMR spectrum, due to the extensive 1H-13C couplings. Similarly, the 13C resonances of these deoxyribonucleosides appear as multiplets in the 75.5 MHz 13C NMR spectrum, due to 13C-13C couplings. The 1H-13C and 13C-13C coupling constants were also measured and tabulated. The isotopic enrichment of 13C these deoxyribonucleosides was obtained by integration of the 1H and/or 13C NMR spectra. It was found that the enrichment varied from carbon to carbon and species to species in the range of 70-89%, suggesting differential uptake and assimilation of 90% 13CO2 during metabolism pathways. This protocol provides experimentally useful quantities of 13C-enriched deoxyribonucleosides, which may be incorporated into site-specifically labeled oligonucleotides by chemical synthesis.

Carbon Isotopes↗

PubMed1975

Ionic base radicals in gamma-irradiated oriented non-deuterated and fully deuterated DNA.

The free radicals induced by gamma-irradiation at 77 K in non-deuterated and fully deuterated oriented samples of moist algal DNA have been studied by electron paramagnetic resonance (e.p.r.). The e.p.r. spectra from the non-deuterated sample were found to be similar to those from calf-thymus DNA studied previously. Numerical spectra simulations were performed based on the previously proposed interpretation of the DNA spectra at 77 K in terms of a mixture of two spectral components arising from anionic and cationic base radicals (probably on thymine and guanine, respectively). The simulations were found to account satisfactorily for the main characteristics of the e.p.r. spectra from both the non-deuterated and the fully deuterated algal DNA sample.

Cobalt Radioisotopes↗

PubMed1996

A 5 S rRNA gene is present in the mitochondrial genome of the protist Reclinomonas americana but is absent from red algal mitochondrial DNA.

Except in the case of land plants, mitochondrial ribosomes apparently lack a 5 S rRNA species, even though this small RNA is a component of all prokaryotic, chloroplast and eukaryotic cytosol ribosomes. In plants, the mitochondrial 5 S rRNA is encoded by mtDNA and differs in sequence from the 5 S rRNA specified by plant nuclear and chloroplast genomes. A distinctive 5 S rRNA component has not been found in the mitochondrial ribosomes of non-plant eukaryotes and, with the notable exception of the chlorophycean alga, Prototheca wickerhamii, a 5 S rRNA gene has not been identified in those non-plant mtDNAs characterized to date. Here, we report the presence of a 5 S rRNA gene in the mtDNA of the heterotrophic flagellate Reclinomonas americana. This unicellular eukaryote is a member of the jakobid flagellates, an early-diverging group of protists that share ultrastructural characteristics with the retortamonads, primitive protists that lack mitochondria. We report sequence data from the mtDNAs of the red algae Porphyra purpurea and Gracilariopsis lemaneiformis, which we use to evaluate a recent claim that a 5 S rRNA gene exists in the mtDNA of a third rhodophyte alga, Chondrus crispus. Our results lead us to the opposite conclusion: that a 5 S rRNA gene is not encoded by red algal mtDNA. In view of the accumulating evidence favoring a monophyletic origin of the mitochondrial genome, it is likely that a 5 S rRNA gene was present in an ancestral proto-mitochondrial genome, and that contemporary mtDNA-encoded 5 S rRNA genes have all descended from this ancestral gene. Considering the highly restricted phylogenetic distribution of identified mtDNA-encoded 5 S rRNA genes, it follows that the mitochondrial 5 S rRNA gene must have been lost multiple times during evolutionary diversification of the eukaryotic lineage.

Animals↗

PubMed1990

Transcription and sequence studies of a 4.3-kbp fragment from a ds-DNA eukaryotic algal virus.

A 4.3-kbp portion of the genome from the Chlorella virus, PBCV-1, has been cloned and sequenced. Minimally, five open reading frames (ORFs) were identified on this fragment. Transcriptional analysis indicates that each ORF encodes complex patterns of RNA. The total length of transcribed RNA exceeds that of the ORF indicating either post-transcriptional modification or multiple transcriptional start/stop sites. The sequence TTTTTNT, previously described as the transcriptional stop site for the early genes of vaccinia virus, is also found downstream of each of our ORFs. The regions 5' to each ORF were very A + T-rich (approx 80%) but distinct promoter sequences were not unambiguously identified.

Base Sequence↗

PubMedDate not supplied

Method for rapid isolation and analysis of algal virus DNA.

A quick method has been developed for isolating viral DNA from small cultures of eukaryotic algae infected with PBCV-1 or similar viruses. The DNA preparations are virtually free of contaminating host DNA and are suitable substrates for restriction enzymes. 5 ml cultures yield 8-25 micrograms of viral DNA. Many plaque-purified isolates from environmental water samples can be analyzed in a day.

Chlorella↗

PubMed2004

Structure and expression of the ornithine decarboxylase gene of Chlamydomonas reinhardtii.

A cDNA was cloned encoding ornithine decarboxylase (ODC) of the unicellular green alga Chlamydomonas reinhardtii. The polypeptide consists of 396 amino acid residues with 35-37% sequence identity to other eukaryotic ODCs. As indicated by the phylogenetic tree calculated by neighbour joining analysis, the Chlamydomonas ODC has the same evolutionary distances to the ODCs of higher plants and mammalians. The Chlamydomonas ODC gene contains three introns of 222, 133, and 129bp, respectively. As revealed by Northern-blot analyses, expression of the Chlamydomonas ODC gene is neither altered throughout the vegetative cell cycle nor modulated by exogenous polyamines.

Amino Acid Sequence↗

PubMed1972

Studies with deoxyribonucleic Acid from blue-green algae.

DNA from two blue-green algae was isolated and characterized. The buoyant densities, thermal denaturation and renaturation, thermal melting values, base compositions, sedimentation coefficients, and molecular weights were determined. Blue-green algal DNA renatured extensively and at a comparable rate to that of bacterial DNA. The similarities among the kinds of DNA from bacteria and blue-green algae were interpreted to reflect a close relationship.

Journal Article↗

PubMed2005

Multiple independent losses of photosynthesis and differing evolutionary rates in the genus Cryptomonas (Cryptophyceae): combined phylogenetic analyses of DNA sequences of the nuclear and the nucleomorph ribosomal operons.

In this study, evidence for at least three independent losses of photosynthesis in the freshwater cryptophyte genus Cryptomonas is presented. The phylogeny of the genus was inferred by molecular phylogenetic analyses of the nuclear internal transcribed spacer 2 (nuclear ITS2), partial nuclear large subunit ribosomal DNA (LSU rDNA), and nucleomorph small subunit ribosomal DNA (SSU rDNA, NM). Both concatenated and single data sets were used. In all data sets, the colorless Cryptomonas strains formed three different lineages, always supported by high bootstrap values (maximum parsimony, neighbor joining and maximum likelihood) and posterior probabilities (Bayesian analyses). The three leukoplast-bearing lineages displayed differing degrees of accelerated evolutionary rates in nuclear and nucleomorph rDNA. Also an increase in A + T-content in highly variable regions of the nucleomorph SSU rDNA was observed in one of the leukoplast-bearing lineages.

Base Composition↗

PubMed2005

A high frequency of overlapping gene expression in compacted eukaryotic genomes.

The gene density of eukaryotic nuclear genomes is generally low relative to prokaryotes, but several eukaryotic lineages (many parasites or endosymbionts) have independently evolved highly compacted, gene-dense genomes. The best studied of these are the microsporidia, highly adapted fungal parasites, and the nucleomorphs, relict nuclei of endosymbiotic algae found in cryptomonads and chlorarachniophytes. These systems are now models for the effects of compaction on the form and dynamics of the nuclear genome. Here we report a large-scale investigation of gene expression from compacted eukaryotic genomes. We have conducted EST surveys of the microsporidian Antonospora locustae and nucleomorphs of the cryptomonad Guillardia theta and the chlorarachniophyte Bigelowiella natans. In all three systems we find a high frequency of mRNA molecules that encode sequence from more than one gene. There is no bias for these genes to be on the same strand, so it is unlikely that these mRNAs represent operons. Instead, compaction appears to have reduced the intergenic regions to such an extent that control elements like promoters and terminators have been forced into or beyond adjacent genes, resulting in long untranslated regions that encode other genes. Normally, transcriptional overlap can interfere with expression of a gene, but these genomes cope with high frequencies of overlap and with termination signals within expressed genes. These findings also point to serious practical difficulties in studying expression in compacted genomes, because many techniques, such as arrays or serial analysis of gene expression will be misleading.

Animals↗

PubMed2005

Mating-induced shedding of cell walls, removal of walls from vegetative cells, and osmotic stress induce presumed cell wall genes in Chlamydomonas.

The first step in sexual differentiation of the unicellular green alga Chlamydomonas reinhardtii is the formation of gametes. Three genes, GAS28, GAS30, and GAS31, encoding Hyp-rich glycoproteins that presumably are cell wall constituents, are expressed in the late phase of gametogenesis. These genes, in addition, are activated by zygote formation and cell wall removal and by the application of osmotic stress. The induction by zygote formation could be traced to cell wall shedding prior to gamete fusion since it was seen in mutants defective in cell fusion. However, it was absent in mutants defective in the initial steps of mating, i.e. in flagellar agglutination and in accumulation of adenosine 3',5'-cyclic monophosphate in response to this agglutination. Induction of the three GAS genes was also observed when cultures were exposed to hypoosmotic or hyperosmotic stress. To address the question whether the induction seen upon cell wall removal from both gametes and vegetative cells was elicited by osmotic stress, cell wall removal was performed under isosmotic conditions. Also under such conditions an activation of the genes was observed, suggesting that the signaling pathway(s) is (are) activated by wall removal itself.

Amino Acid Sequence↗

PubMed2005

Subcellular localization and light-regulated expression of protoporphyrinogen IX oxidase and ferrochelatase in Chlamydomonas reinhardtii.

Protoporphyrinogen IX oxidase (PPO) catalyzes the last common step in chlorophyll and heme synthesis, and ferrochelatase (FeC) catalyzes the last step of the heme synthesis pathway. In plants, each of these two enzymes is encoded by two or more genes, and the enzymes have been reported to be located in the chloroplasts or in the mitochondria. We report that in the green alga Chlamydomonas reinhardtii, PPO and FeC are each encoded by a single gene. Phylogenetic analysis indicates that C. reinhardtii PPO and FeC are most closely related to plant counterparts that are located only in chloroplasts. Immunoblotting results suggest that C. reinhardtii PPO and FeC are targeted exclusively to the chloroplast, where they are associated with membranes. These results indicate that cellular needs for heme in this photosynthetic eukaryote can be met by heme that is synthesized in the chloroplast. It is proposed that the multiplicity of genes for PPO and FeC in higher plants could be related to differential expression in differently developing tissues rather than to targeting of different gene products to different organelles. The FeC content is higher in C. reinhardtii cells growing in continuous light than in cells growing in the dark, whereas the content of PPO does not significantly differ in light- and dark-grown cells. In cells synchronized to a light/dark cycle, the level of neither enzyme varied significantly with the phase of the cycle. These results indicate that heme synthesis is not directly regulated by the levels of PPO and FeC in C. reinhardtii.

Amino Acid Sequence↗

PubMed1987

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.

Chloroplasts↗

PubMed2006

Achlya abortispora, a new oomycete isolated from water samples taken from a water reservoir in Morocco.

Achlya abortispora sp. nov. was found in water and floating organic matter taken form a dam near Rabat, Morocco. The new species is described and compared with other species of the genus. Distinguishing characteristics of A. abortispora are the production of long fusiform sporangia with achlyoid and aplanoid discharge of zoospores; smooth-walled spherical to club-shaped oogonia, which are usually lateral, but at times intercalary, containing 1 to 20 oospheres. The oogonia can also bear 1 to 5 appendages, which may indicate oogonial proliferation. Most of the oospheres do not mature and are thus abortive. The antheridial branches supplying the oogonia are predominantly diclinous, but at times these may be monoclinous and androgynous. Antheridial branches coil and wrap around the oogonia. Morphologic features of the oomycete and the sequence of the ITS region of its rDNA, as well as their comparison with related species, are discussed. This is the first report of the occurrence of a saprolegniaceous oomycete from Morocco.

Achlya↗

PubMed2005

Ergosterol from Phytophthora drechsleri, a unusual metabolite of a member of this genus.

Ergosterol was isolated from the plant pathogenic pseudofungus Phytophthora drechsleri grown on clarified V8 booth (CV8-B). Its structure was confirmed by comparison to an authentic sample. The species was identified by morphological analysis and molecular characterization by PCR: ITS (Internal transcribed spaces). This is the first report of this sterol in Phytophthora. This result is unusual because Phytophthora fungi were previously thought to be unable to synthesize sterols and the Oomycetes in general do not produce ergosterol.

Culture Media↗

PubMed2005

Shared molecular characteristics of successfully transformed mitochondrial genomes in Chlamydomonas reinhardtii.

Three types of respiratory deficient mitochondrial strains have been reported in Chlamydomonas reinhardtii: a deficiency due to (i) two base substitutions causing an amino acid change in the apocytochrome b (COB) gene (i.e., strain named dum-15), (ii) one base deletion in the COXI gene (dum-19), or (iii) a large deletion extending from the left terminus of the genome to somewhere in the COB gene (dum-1, -14, and -16). We found that these respiratory deficient strains of C. reinhardtii can be divided into two groups: strains that are constantly transformable and those could not be transformed in our experiments. All transformable mitochondrial strains were limited to the type that has a large deletion in the left arm of the genome. For these mitochondria, transformation was successful not only with purified intact mitochondrial genomes but also with DNA-constructs containing the compensating regions. In comparison, mitochondria of all the non-transformable strains have both of their genome termini intact, leading us to speculate that mitochondria lacking their left genome terminus have unstable genomes and might have a higher potential for recombination. Analysis of mitochondrial gene organization in the resulting respiratory active transformants was performed by DNA sequencing and restriction enzyme digestion. Such analysis showed that homologous recombination occurred at various regions between the mitochondrial genome and the artificial DNA-constructs. Further analysis by Southern hybridization showed that the wild-type genome rapidly replaces the respiratory deficient monomer and dimer mitochondrial genomes, while the E. coli vector region of the artificial DNA-construct likely does not remain in the mitochondria.

Animals↗

PubMed2004

Single-strand conformational polymorphism analysis of the ribosomal internal transcribed spacer 1 for rapid species identification within the genus Pythium.

Single-strand conformational polymorphism (SSCP) of the ribosomal internal transcribed spacer 1 (ITS-1) was characterized for 58 isolates of Pythium, representing 41 species from the five groups of Plaats-Niterink. Thirty-one species each produced a distinct SSCP pattern. Three species produced more than one unique pattern, corresponding to morphological subgrouping. The remaining seven species produced three distinct patterns with two or three morphologically similar species sharing a pattern. A successful blind test with four samples and the identification of eight previously unknown isolates from irrigation water demonstrated the reliability of this technique for species identification. Each SSCP pattern was defined and described by the positions of the top and bottom bands and the number of bands in between, which allows laboratories to use this technique without need to access the type isolates of Pythium species.

DNA, Algal↗

PubMed2005

Double hairpin elements and tandem repeats in the non-coding region of Adenoides eludens chloroplast gene minicircles.

Dinoflagellate plastid genomes are unique in having a reduced number of genes, most of which are found on unigenic minicircles of 2-3 kb. Although the dinoflagellate Adenoides eludens has larger minicircles of about 5 kb, they still carry only one gene. In addition, digenic circles of about 10 kb were detected and mapped by PCR. The non-coding regions of both unigenic and digenic circles share a number of common features including a pair of conserved cores in opposite orientation, four large families of tandem repeats and a number of double hairpin elements (DHEs). They most closely resemble the non-coding regions of the Symbiodinium psbA minicircles, but are much longer, less conserved and have an even greater variety of DHEs and tandem repeats. The presence of so many recombinogenic elements suggests models for the origin of minicircles from a multigenic ancestral chloroplast genome, and raises the possibility of recombination-directed replication rather than defined replication origins in the minicircles.

Animals↗