Mitochondiral DNA from protozoa

The Cilioprotist Cytoskeleton , a Model for Understanding How Cell Architecture and Pattern Are Specified: Recent Discoveries from Ciliates and Comparable Model Systems

The cytoskeletons of eukaryotic, cilioprotist microorganisms are complex, highly patterned, and diverse, reflecting the varied and elaborate swimming, feeding, reproductive, and sensory behaviors of the multitude of cilioprotist species that inhabit the aquatic environment. In the past 10-20 years, many new discoveries and technologies have helped to advance our understanding of how cytoskeletal organelles are assembled in many different eukaryotic model systems, in relation to the construction and modification of overall cellular architecture and function. Microtubule organizing centers, particularly basal bodies and centrioles, have continued to reveal their central roles in architectural engineering of the eukaryotic cell, including in the cilioprotists. This review calls attention to (1) published resources that illuminate what is known of the cilioprotist cytoskeleton; (2) recent studies on cilioprotists and other model organisms that raise specific questions regarding whether basal body- and centriole-associated nucleic acids, both DNA and RNA, should continue to be considered when seeking to employ cilioprotists as model systems for cytoskeletal research; and (3) new, mainly imaging, technologies that have already proven useful for, but also promise to enhance, future cytoskeletal research on cilioprotists.

Sunlight radiation as a villain and hero: 60 years of illuminating research

In the 60 years since the inaugural edition of the International Journal of Radiation Biology, much of our understanding of the biological effects of solar radiation has changed. Earlier in the century, sunlight played a 'hero's' role in reducing disabling rickets, while today debate still continues on the amount of sun required before exposure reveals the 'villainous' side of solar radiation. Although knowledge of the ultra violet (UV) component of sunlight as a carcinogen has become widespread, skin cancer rates are still rising yearly. Twentieth century attitudes have seen an about-face in the field of dermatological sun protection, with sunscreens changing from recipes designed to promote a 'healthy tan' to formulations proven to block both ultraviolet B (UVB) and more recently, ultraviolet A (UVA), to minimize premature sun-aging and skin cancer risk. In the early 1960s, DNA was first found to exist within mitochondria, while recently the connections between mitochondrial changes and UV radiation exposure have been expanded. Sixty years ago, understanding of the endocrine systems of mammals was enjoying its infancy. Early discoveries that light, particularly natural light, could have profound effects on functions such as sleep patterns and hormonal balance were made, while today more advanced knowledge has led to lighting improvements having pronounced effects on human wellbeing. Photosensitization 60 years ago was a health concern for both humans and their domestic animals, while today chemically engineered photosensitizing drugs can be administered along with highly directed light to pinpoint delivery targets for drug action. Life on earth is inextricably bound up with solar radiation. This article attempts to outline many of the ways in which our opinions about solar radiation have changed since the journal's inception.

Distinct genomic copy number in mitochondria of different mammalian organs

This study shows that mitochondria in liver, kidney, heart, and brain of the mouse have a distinct mitochondrial density. It also demonstrates that the mtDNA copy number per mitochondrion is organ-specific. A reliable method of determining mitochondrial density per organ is by stereological analysis of tissue sections while mtDNA quantitation is by the use of radiolabelled mtDNA probe. This is the first study in which a comprehensive examination of mitochondrial density and quantitation of mitochondrial genomes in mouse organs have been done. In summary the variability is not only in mitochondrial density but also in genomic copy number in mitochondria of various tissues.

Porin of Paramecium mitochondria isolation, characterization and ion selectivity of the closed state

Porin was isolated and purified from mitochondria of Paramecium tetraurelia. The protein showed a single band of apparent Mr 37,000 on sodium dodecyl sulfate polyacrylamide electrophoretograms. The reconstitution of the protein into artificial lipid bilayer membranes revealed it to be a porin giving pores with an average single-channel conductance of 0.26 nS in 0.1 M KCl. This conductance is about half of that of other eukaryotic porins studied to date. The pore formed by the mitochondrial porin of Paramecium was found to be voltage-dependent and switched to a defined substrate at membrane voltages larger than 20 mV. In the open state the pore exhibited the characteristics of a general diffusion pore because the mobility sequence of the ions inside the pore was similar to that in the bulk aqueous phase. The effective diameter was estimated to be about 1.3 nm. The properties of the low conductance state of the pore were studied in detail. In this state the pore favored the passage of cations, in contrast to the open state which favored anions slightly. The possible role of the low-conductance state in the regulation of transport processes across the outer mitochondrial membrane and in mitochondrial metabolism is discussed.

The cytochrome oxidase subunit I gene of Tetrahymena: a 57 amino acid NH2-terminal extension and a 108 amino acid insert

The gene sequence for cytochrome oxidase subunit I (COI) in the ciliate Tetrahymena mitochondrial DNA has been determined and shown to be coded by the same strand as codes the genes (in order) for 14S rRNA, tRNA(trp), tRNA(glu), 21S rRNA, tRNA(leu) and tRNA(met). The predicted protein has 698 amino acids, including an NH2-terminal 57 amino acid extension and a 108 amino acid insert originally found in Paramecium COI. These extension and insert segments are not highly hydrophobic but are relatively rich in lysine, arginine and serine. In analogy with the presequence of nuclear-encoded mitochondrial proteins, they might function as a transmembrane signal. The remaining polypeptide segments show a hydrophobicity characteristic of membrane spanning proteins. TCOI shows a 64% amino acid identity with Paramecium COI but less than a 38% amino acid conservation with human COI. The Tetrahymena mitochondrial code is analogous with the mammalian mitochondrial code; but differs from the Tetrahymena nuclear genetic code; TGA is exclusively translated as tryptophan; ATA is used as an initiation codon probably for methionine, and TAA as a stop codon; the arginine codons (CGN) are not used. The use of the leucine codon TTA in TCOI is contradictory to the codon recognition pattern previously obtained from the isolated tRNA(leu) isoacceptors recognizing only the CUN codons, but consistent with the tRNA(leu) (anticodon UAA) gene encoded in the genome. The reason for this inconsistency has not been resolved.

Unexpectedly long 14S ribosomal RNA gene in Tetrahymena mitochondria

Extraction of RNA from Tetrahymena mitochondrial ribosomes yields several RNA species, including a "large" 21S molecule, a "small" 14S molecule, a 7S molecule, and other smaller RNAs. The molecular weight of the 14S rRNA indicates that it is about 1,300 bases in length. We have sequenced the 14S rRNA gene and, by aligning our sequence with that of the corresponding small rRNA from E. coli, find that the 14S rDNA is at least 1,635 bases in length. We propose, based on the results of hybridization studies, that this unexpected length is due to the presence of 7S RNA sequence within the 14S gene sequence. The 7S region is apparently lost from the 14S rRNA, yet is still a component of the ribosome.

The telomeres of the linear mitochondrial DNA of Tetrahymena thermophila consist of 53 bp tandem repeats

We have cloned and sequenced the telomeric DNA of the linear mitochondrial DNA (mtDNA) of T. thermophila BVII. The mtDNA telomeres consist of a 53 bp sequence tandemly repeated from 4 to 30 times, with most molecules having 15 +/- 4 repetitions. The previously recognized terminal heterogeneity of the mtDNA is completely accounted for by the variability in the number of repeats. The 53 bp repeat does not resemble known telomeric DNA in sequence, repeat size, or number of repetitions. The termini occur at heterogeneous positions within the 53 bp repeat. The junction of the telomeric repeat with the internal DNA is at a different position within the telomeric repeat on each end of the mtDNA. We propose a model for the maintenance of the mtDNA ends involving unequal homologous recombination.

Two dimensional polyacrylamide gel electrophoresis analysis of Tetrahymena mitochondrial tRNA

Two dimensional (2D) urea-polyacrylamide gel electrophoresis of tRNA isolated from Tetrahymena mitochondria separated at least 36 spots, while more than 45 major and minor spots were resolved with cytosolic tRNA. Co-electrophoresis of mitochondrial and cytosolic tRNAs revealed that many spots co-migrate. When radioactive mitochondrial tRNA was hybridized to mtDNA under various conditions and tRNA melted from the hybrid was analyzed by 2D gel electrophoresis, only 10 tRNA spots were found. Identified as mtDNA-encoded were 2 spots for tRNA(leu), 2 for tRNA(met), and 1 each for tRNA(phe), tRNA(trp) and tRNA(tyr). The remaining three were unidentified. Mitochondrial tRNA spots that correspond to the tRNAs for arg, gly, ile, lys, ser, and val do not hybridize with mtDNA, and in gel positions they correspond to the cytoplasmic tRNA spots for the same respective amino acids. These mitochondrial tRNAs isolated from the gel can be acylated either by the mitochondrial or cytosolic enzymes. Mitochondrial tRNA isolated from a Tetrahymena cell homogenate which was pretreated with RNase A and Micrococcus nuclease exhibited the same 2D gel pattern as a non-treated control. Mitochondrial tRNAs from old and young cells showed generally similar tRNA spots in 2D gels, though more variable spots were seen with old cells. 3H-labeled whole-cell tRNA added to the cell homogenate prior to the mitochondrial isolation procedure did not remain associated with the final mitochondrial tRNA preparation. The present studies also showed mitochondrial tRNAs bound to the mitochondrial 80S monosome and polysome fractions. Radioactive tRNA added to the mitochondrial lysate does not adhere to the ribosomes, suggesting that the ribosome-bound tRNAs are not contaminating cytoplasmic tRNAs. These results are generally in good agreement with our previous data showing that only a small number of tRNAs are coded for by the mitochondrial DNA, while the others are a selected set of imported cytoplasmic tRNAs.

A fine restriction map of the linear mitochondrial DNA of Tetrahymena pyriformis: genome size, map locations of rRNA and tRNA genes, terminal inversion repeat, and restriction site polymorphism

A fine restriction map of the linear mitochondrial DNA of Tetrahymena pyriformis strain ST is presented. 1. Based on agarose gel electrophoresis data together with limited nucleotide sequences available on some restriction fragments, we estimate the actual size of this genome to be about 55,000 base pairs. 2. Seven tRNA gene locations have been assigned, which are scattered along the genome length. Six of these locations encode the genes for tRNA(phe), tRNA(his), tRNA(trp), and tRNA(glu), and the duplicate tRNA(tyr) genes which are located at the inverted terminal repeat segments. The tRNA gene(s) encoded in one location has not been identified. We have not yet found the tRNA(leu) and tRNA(met) genes, which were previously shown to be encoded in the genome (Chiu et al. 1974; Suyama 1982). 3. We have mapped the 14S rRNA gene by sequencing the 170 bp segment of EcoRI fragment 8 and by aligning its sequence with E. coli 16S rRNA. From our recent complete sequence data the gene size was found to be about 1,650 bp, which is unexpectedly large for the 14S rRNA which has an estimated size of 1,300 bp. The 14S rRNA is probably a cleavage product of the larger primary transcript of which 200-300 bases of the 5' end are missing. 4. The duplicate copies of the 21S rRNA gene at the terminal duplication inversion segments were analyzed. ClaI fragment 7 (1,500 bp) corresponds in sequence from base position 850 to 2,390 of the 20S rRNA gene of Paramecium mitochondrial DNA (Seilhamer et al. 1984b). The 21S gene is approximately 2,500 bp long. The presence of some restriction site polymorphism is apparent in this segment. 5. Each of the 21S gene copies precedes the tRNA(tyr) gene, but the space flanking one tRNA(tyr) gene differs in size and restriction sites from the space flanking another tRNA(tyr) gene. Thus, this space corresponds to the segment of an imperfect match in the terminal duplication inversion of Goldbach et al. (1978a). 6. Saccharomyces cerevisiae mitochondrial probes including Cob, ATPase VI and IX, and cytochrome oxidase I gene sequences, 21S and 15S rRNAs, and mouse mitochondrial DNA showed no significant hybridization with any restriction fragments of Tetrahymena mitochondrial DNA. The results are in accordance with an extensive sequence divergence previously found in the Tetrahymena mitochondrial genome (Goldbach et al. 1977).

Nucleotide sequences of three tRNA genes encoded in Tetrahymena mitochondrial DNA

Nucleotide sequences of three cloned restriction fragments of Tetrahymena mtDNA which showed hybridization with mitochondrial tRNA have been determined. EcoRI fragment 5 (4.1 kbp) contains the tRNAphe gene sequence with anticodon GAA; Hind III fragment 6 (2.0 kbp) the tRNAhis with anticodon GTG; and EcoRI fragment 7 (1.9 kbp) the tRNAtrp with anticodon TCA. The CCA end is not encoded. All three tRNAs show usual features with common invariant and semi-invariant bases and can be folded into a cloverleaf structure with standard loops and regular base pairs in the stems. However, some minor irregular features are present including several GT pairs and an unmatched TT in the stems, and TCC instead of T psi C. All exhibit high G+C contents (about 50%); in contrast, the flanking regions are extremely A+T rich (about 80%). Several short coding frames can be deduced in these sequences, but their significance is not known.

Structure of mitochondrial DNA from Paramecium tetraurelia

Mitochondrial DNA (mtDNA) from endosymbiote-free stocks of Paramecium tetraurelia was isolated by 2 procedures. The buoyant density of the mtDNA in neutral CsCl was 1.702 gm/cm3, a value consistent with the melting temperature of the mtDNA. Only linear molecules were observed by electron microscopy. These molecules were homogeneous in size with a monomer molecular weight of 25.6 x 10(6) daltons. The size of the mtDNA determined after digestion with the restriction endonucleases EcoRI or Hind III agreed with the value obtained by electron microscopy. These studies also revealed that the digestion pattern of mtDNA from stock 172 differed from that of other 3 stocks (51, 127, 203) examined. Some mtDNA molecules exhibited snapback reassociation following denaturation.

Free ribosomal RNA genes in Paramecium are tandemly repeated

The genes coding for 17S and 25S rRNA in Paramecium tetraurealia were isolated. The macronuclear ribosomal DNA (rDNA) exists as relatively small, extrachromosomal molecules with both linear and circular forms. Electron microscopy and restriction endonuclease analysis revealed that the rDNA is arranged as tandem repeats with an average repeat size of 5.5 X 10(6) daltons. Some heterogeneity of repeat lengths was found both by electron microscopy and by restriction enzyme analysis. The rDNA does not snap back after denaturation. This study provides additional evidence that extrachromosomal rDNA may be a common feature among lower eukaryotes. However, in contrast to several other cases, the rDNA of Paramecium is not palindromic, but occurs as tandem repeats as in higher eukaryotes.

Covalently closed, circular DNA in kappa endosymbionts of Paramecium

Caedobacter taeniospiralis(kappa), a bacterial endosymbiont isolated fromParamecium tetraureliastock 51, contains, in addition to the bacterial chromosome, covalently closed circular DNA molecules as shown by isolation on dye-buoyant-density gradients. The closed circular molecule has a contour length of 13·75 ± 0·04 µm with a buoyant density of 1·698 g/cm3. The buoyant density of the bacterial chromosome is 1·700–1·701 g/cm3. Kappa of the 51 group isolated from stock 298 and stock 6g2,P. tetraurelia, also contain the closed circular DNA. Two forms of kappa coexist in paramecia: brights and nonbrights. Examination by density-gradient centrifugation of the DNA of brights and nonbrights shows the extrachromosomal DNA to be associated mainly with brights. It is suggested that the extrachromosomal DNA might be the determinant for the refractile bodies and the helical phage-like structures found in brights.

Mitochondrial DNA of Tetrahymena pyriformis strain ST contains a long terminal duplication-inversion

1. We have studied denatured Tetrahymena mtDNA by electron microscopy using the formamide technique. 2. After denaturation all DNA is single stranded, but within a few minutes single-stranded circles with a duplex tail are formed. 3. The duplex tail is 1.3 mum long, i.e. 8 percent of the length of native mtDNA, and it often contains a small single-stranded eye. 4. Digestion of the duplex DNA with exonuclease III of Escherichia coli abolishes its ability to form circles and duplex tails after denaturation. 5. Renaturation of denatured mtDNA leads to the formation of duplex circles with single-stranded section and/or duplex tails. In addition, a minority of duplex circles without apparent tails is formed, but these circles contain a small ambiguous section. 6. We conclude that this mtDNA contains a long terminal duplication-inversion, that could be involved in the replication of this linear mtDNA.

Effect of chloramphenicol on replication of mitochondria in Tetrahymena

Tetrahymena pyriformis ST (3 X 10-4 cells/ml) was treated with 0.1 mg/ml chloramphenicol (CAP). Cell division ceased after 1.5 divisions with no decreased viability. Total mitochondrial volume and succinic dehydrogenase (SDH) activity/liter increased 1.7-fold and 3-fold, respectively. SDH activity/cell decreased whereas malate dehydrogenase activity/cell and respiratory control ratios and P:O ratios of isolated mitochondria were unchanged in treated cells. During 12 hours of growth in CAP the total surface area of mitochondrial inner and outer membrane was essentially unchanged or increased 4-fold, respectively. Mitochondria from cells treated with chloramphenicol had decreased size, buoyant density and protein:lipid ratio in the membranes. The membrane ubiquinone:protein ratio was unchanged. Tetrahymena cells contained 3.6 X 10-minus 12 g of mitochondrial DNA and 6,800 mitochondria in a volume of 41,000 mu-3. A 4-hour treatment with CAP caused a 4-fold increase in the number of mitochondria/cell and a 10-fold increase in mitochondria/liter in contrast to a 4-fold increase in number of mitochondria/liter in control cells. Thus CAP stimulated division of mitochondria. Individual mitochondria of treated cells had one-tenth the volume of control mitochondria. The rate of increase of mitochondrial DNA/liter was the same in control and CAP-treated cultures. The amount of DNA/mitochondrion decreased 75% in CAP-treated cells due to the rapid division of mitochondria. The cell volume, cell protein content and mitochondrial DNA content/cell decreased with growth of control cultures.

Sequence homology of nuclear and mitochondrial DNAs of different yeasts

1. Both nuclear and mtDNA of four different yeasts show approximately 10% homology as measured by DNA-DNA filter hybridization. These homologous sequences are mainly attributable to the ribosomal cistrons. 2. Melting curve analysis shows that the heterologous mitochondrial DNA-DNA hybrids contain several times more mismatching than the nuclear DNA-DNA hybrids. 3. DNA-rRNA hybridization shows that the sequences of the ribosomal cistrons in both the nuclear and the mitochondrial genome have been conserved during evolution. 4. However, melting curve analysis of the DNA-RNA hybrids shows that the sequence of the nuclear ribosomal cistrons have undergone considerable fewer nucleotide substitutions than their mitochondrial counterparts. 5. The results suggest that the mitochondrial ribosomal cistrons have evolved more rapidly than the nuclear cistrons. This is discussed in the light of theories on the rat of molecular evolutin.

Kappa and other endosymbionts in Paramecium aurelia

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