Isolation and characterization of DNA from the mitochondrial fraction of Euglena

Ribosomal RNA genes in Euglena gracilis mitochondrial DNA: fragmented genes in a seemingly fragmented genome

Because relatively little information is available about mtDNA in the euglenid protozoa, distant relatives of the kinetoplastid protozoa, we investigated mitochondrial genome structure and expression in Euglena gracilis. We found that isolated E. gracilis mtDNA comprises a heterodisperse collection of short molecules (modal size approximately 4 kbp) and that the mitochondrial large subunit (LSU) and small subunit (SSU) rRNAs are each split into two pieces. For the two halves of the SSU rRNA, we identified separate, non-contiguous coding modules that are flanked by a complex array of (primarily direct) A + T-rich repeats. The potential secondary structure of the bipartite SSU rRNA displays the expected conserved elements implicated in ribosome function. Label from [α-(32)P]GTP was incorporated in the presence of guanylyltransferase into each of the separate SSU and LSU rRNA fragments, confirming that these RNAs are primary transcripts, separately expressed from non-contiguous rRNA modules. In addition to authentic genes for SSU rRNA, we discovered numerous short fragments of protein-coding and rRNA genes dispersed throughout the E. gracilis mitochondrial genome. We propose that antisense transcripts of gene fragments of this type could have been the evolutionary precursors of the guide RNAs that mediate U insertion/deletion editing in the kinetoplastid relatives of the euglenids. To the extent that E. gracilis mtDNA is a representative euglenid mitochondrial genome, it differs radically in structure and organization from that of its kinetoplastid relatives, instead more closely resembling the mitochondrial genome of dinoflagellates in many of its features, an apparent evolutionary convergence.

Satellite-rich DNA in cucumber: hormonal enhancement of synthesis and subcellular identification

Cucumber hypocotyl DNA in neutral CsCl distributes into a mainband comprising 59% of the total, and two large satellite bands which contribute 41% to the DNA pattern. Organelle enrichment studies show that the densities of mitochondrial and chloroplast DNA coincide with those of the satellite bands. At least 12-19% of total cucumber DNA is associated with the cytoplasmic organelles. These values, which are several times larger than those usually quoted for higher plants, are correlated with an unusually low amount of DNA per haploid nucleus in cucumber. Synthesis of the satellite DNAs, as well as mainband DNA, is appreciably stimulated in vivo by application of the plant hormone, gibberellin. Endogenous and hormone-enhanced synthesis of the satellite DNAs is proportionately greater in target tissue showing a high rate of organelle synthetic activity.

Isolation of subcellular organelles and structures

One of the major challenges in functional proteomics is the separation of complex protein mixtures to allow detection of low abundance proteins and provide for reliable quantitative and qualitative analysis of proteins impacted by environmental parameters. Prerequisites for the success of such analyses are standardized and reproducible operating procedures for sample preparation prior to protein separation. Due to the complexity of total proteomes, especially of eukaryotic proteomes, and the divergence of protein properties, it is often beneficial to prepare standardized partial proteomes of a given organism to maximize the coverage of the proteome and to increase the chance to visualize low abundance proteins and make them accessible for subsequent analysis. In this chapter we will describe with detailed recipes procedures for the enrichment and isolation of the currently most investigated organelles and subcellular compartments in mammalian cells using classical centrifugation techniques to more sophisticated immunoaffinity-based procedures.

A possible ribosomal-directed regulatory system in Euglena gracilis. Chlorophyll synthesis

Cycloheximide at concentrations of 0.1-100mum stimulated chlorophyll synthesis when dark-grown cells of Euglena were illuminated. Chloramphenicol (1-4mm) inhibited chlorophyll synthesis. The effect of cycloheximide on the incorporation of [(14)C]leucine into material insoluble in trichloroacetic acid, and its failure to affect the incorporation of [(32)P]orthophosphate into such material in short incubations, are interpreted as evidence that cycloheximide specifically inhibits protein synthesis by 80S ribosomes. Since the inhibitory effect of chloramphenicol on chlorophyll synthesis is counteracted by the presence of cycloheximide, it is suggested that chlorophyll synthesis is subject to control by a cytoplasmic repressor synthesized on 80S ribosomes, and to a de-repressor synthesized on 70S ribosomes.

On the similarity between the tRNAs of organelles and prokaryotes

Fluorescence studies with organelle transfer RNAs separated from their cytoplasmic counterparts revealed that phenylalanine tRNA from Euglena chloroplasts or Neurospora mitochondria does not contain a fluorescent "base Y." In contrast, cytoplasmic phenylalanine tRNA from Euglena and cytoplasmic tRNA from Neurospora were found to contain fluorescent bases. The fluorescence-emission spectra of Neurospora cytoplasmic tRNAs and those of the related ascomycete Saccharomyces cerevisiue were observed to be quite different. The results support the generalization that eukaryotic tRNAs contain a fluorescent base, but indicate that their respective organelle tRNAs do not. They also indicate a striking parallelism between organelle and prokaryotic tRNAs.

Kinetic complexity of chloroplastal deoxyribonucleic acid and mitochondrial deoxyribonucleic acid from higher plants

1. Chloroplasts and mitochondria were isolated by aqueous and non-aqueous cell-fractionation techniques. In a variety of higher plants the mitochondrial DNA bands in a caesium chloride gradient at 1.706g.cm.(-3), whereas chloroplastal DNA has a buoyant density of 1.697g.cm.(-3). 2. In total cellular DNA of moderate molecular weight, the chloroplastal DNA is found within the Gaussian distribution of the nuclear DNA and is not resolved as a satellite. 3. Both chloroplastal DNA and mitochondrial DNA from lettuce renature rapidly. 4. The kinetic complexity of mitochondrial DNA is > 10(8) daltons. 5. Chloroplastal DNA is made up from fast and slow renaturing sequences with kinetic complexities of 3x10(6) and 1.2x10(8) daltons respectively. 6. From the discrepancy between analytical and kinetic complexity it is concluded that chloroplastal DNA is extensively reiterated.

Algae: amounts of DNA and organic carbon in single cells

An analysis of ten different unicellular algae, varying in size and containing from 10 to 6000 picograms of carbon per cell, indicates that the amount of DNA per cell is in direct proportion to cell size. The content of DNA is equal to approximately 1 to 3 percent af the cellular organic carbon.

Nucleotide composition of nuclear and mitochondrial deoxyribonucleic acid of fungi

The buoyant density of nuclear and mitochondrial deoxyribonucleic acid (DNA) from 14 species of fungi was determined by CsCl density gradient equilibrium centrifugation. The buoyant density of both types of DNA was the same for all three Mucorales analyzed. The buoyant density of mitochondrial DNA was significantly lower than that of the nuclear DNA for nine species of Ascomycetes and two species of Basidiomycetes. No simple correlation could be obtained from the comparison of the two types of DNA. Mitochondrial DNA represented a very small proportion of total DNA. Heat-denatured mitochondrial DNA renatured more readily than nuclear DNA.

A mutagenic effect of visible light mediated by endogenous pigments in Euglena gracilis

Mutant cells lackng chlorophyll, chloroplasts, and chloroplast DNA were produced by irradiating Euglena gracilis in aerobic conditions with visible or red light (greater than 610 nanometers) of an intensity equivalent to that of direct sunlight. The photosensitizer is apparently the endogenous chlorophyll present in the chloroplasts. These mutants are comparable to those induced by ultraviolet light, x-rays, heat, or streptomycin. Our findings indicate that visible light can serve as a mutagenic agent in the absence of exogenous photosensitizers, thus directly effecting the course of evolution of organisms containing chlorophyll.