The significance of the structural and functional similarities of bacteria and mitochondria

The Mitochondrial Genome. The Nucleoid

Mitochondrial DNA (mtDNA) in cells is organized in nucleoids containing DNA and various proteins. This review discusses questions of organization and structural dynamics of nucleoids as well as their protein components. The structures of mt-nucleoid from different organisms are compared. The currently accepted model of nucleoid organization is described and questions needing answers for better understanding of the fine mechanisms of the mitochondrial genetic apparatus functioning are discussed.

The mitochondrial nucleoid: integrating mitochondrial DNA into cellular homeostasis

The packaging of mitochondrial DNA (mtDNA) into DNA-protein assemblies called nucleoids provides an efficient segregating unit of mtDNA, coordinating mtDNA's involvement in cellular metabolism. From the early discovery of mtDNA as "extranuclear" genetic material, its organization into nucleoids and integration into both the mitochondrial organellar network and the cell at large via a variety of signal transduction pathways, mtDNA is a crucial component of the cell's homeostatic network. The mitochondrial nucleoid is composed of a set of DNA-binding core proteins involved in mtDNA maintenance and transcription, and a range of peripheral factors, which are components of signaling pathways controlling mitochondrial biogenesis, metabolism, apoptosis, and retrograde mitochondria-to-nucleus signaling. The molecular interactions of nucleoid components with the organellar network and cellular signaling pathways provide exciting clues to the dynamic integration of mtDNA into cellular metabolic homeostasis.

Prokaryote or eukaryote? A unique microorganism from the deep sea

There are only two kinds of organisms on the Earth: prokaryotes and eukaryotes. Although eukaryotes are considered to have evolved from prokaryotes, there were no previously known intermediate forms between them. The differences in their cellular structures are so vast that the problem of how eukaryotes could have evolved from prokaryotes is one of the greatest enigmas in biology. Here, we report a unique organism with cellular structures appearing to have intermediate features between prokaryotes and eukaryotes, which was discovered in the deep sea off the coast of Japan using electron microscopy and structome analysis. The organism was 10 µm long and 3 µm in diameter, having >100 times the volume of Escherichia coli. It had a large 'nucleoid', consisting of naked DNA fibers, with a single nucleoid membrane and endosymbionts that resemble bacteria, but no mitochondria. Because this organism appears to be a life form distinct from both prokaryotes and eukaryotes but similar to eukaryotes, we named this unique microorganism the 'Myojin parakaryote' with the scientific name of Parakaryon myojinensis ('next to (eu)karyote from Myojin') after the discovery location and its intermediate morphology. The existence of this organism is an indication of a potential evolutionary path between prokaryotes and eukaryotes.

Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life

In 1977, Carl Woese and George Fox published a brief paper in PNAS that established, for the first time, that the overall phylogenetic structure of the living world is tripartite. We describe the way in which this monumental discovery was made, its context within the historical development of evolutionary thought, and how it has impacted our understanding of the emergence of life and the characterization of the evolutionary process in its most general form.

The roots of bioenergetics

Understanding metabolic energy transformation began with the realization of an 'intrusion' of phosphate into the mechanism of alcoholic fermentation. The discovery of an analogous participation of phosphate in muscle glycolysis connected the metabolic generation of energy-rich phosphate bonds fed into a common transmitter, adenosine triphosphate (ATP), with the production of mechanical energy through the finding that the phosphoryl group of creatine phosphate transferred to ATP could supply the energy for muscle contraction. In this way, a functional applicability of the energy of the phosphate bond was first shown. This observation was soon followed by the recognition that the phosphoanhydride bond of ATP provided the driving force in biosynthetic reactions; in this type of bond, metabolic energy apparently collects before it is transmitted for functional and biosynthetic use. The storage of energy in ATP was first detected in anaerobic energy-yielding reactions but soon was also found in respiratory and photosynthetic energy production. However, the mechanism by which energy derived from metabolites was converted into phosphate-bond energy in the latter processes appeared to differ from that of anaerobic energy transmission. Whereas phosphorylated compounds mediate the latter in homogeneous solutions, aerobic phosphorylation and photophosphorylation in prokaryotes seem to require special submembranous structures; and in eukaryotes, energy conversion is a function of special organelles, the mitochondria and chloroplasts. The evolutionary aspects of the transition from prokaryotes to eukaryotes are of considerable interest. In conclusion, the relevance of an apparent prokaryotic origin of the energy-transforming organelles in the eukaryotes will be commented on.

Lactic acidosis and other mitochondrial disorders

The ability of mitochondria to oxidize substrates and generate energy is integral to normal homeostasis and to the ability of cells to survive in the face of impending energy failure. Lactic acidosis is a common and readily apparent biochemical marker for mitochondrial dysfunction. However, lactic acidosis represents only the most obvious example in which acquired or congenital abnormalities of mitochondrial oxidative phosphorylating capacity contribute to the pathobiology and phenotypic expression of a broad spectrum of clinical disorders. Consequently, interventions that improve mitochondrial function or prevent mitochondrial energy failure may have widespread therapeutic implications.

Antineoplastic drug resistance and DNA repair

Important aspects of the DNA repair mechanisms in mammalian, and especially human, cells are reviewed. The DNA repair processes are essential in the maintenance of the integrity of the DNA and in the defense against cancer. It has recently been discovered that the DNA repair efficiency differs in different regions of the genome and that active genes are preferentially repaired. There is mounting evidence that DNA repair processes play a role in the development of drug resistance by tumor cells. We will discuss such data as well as further approaches to clarify the relationship between DNA repair and antineoplastic drug resistance. Specifically, there is an increasing need to investigate the intragenomic heterogeneity of DNA repair and correlate the repair efficiency in specific genes to aspects of drug resistance. We also discuss the therapeutic potential of inhibiting the DNA repair processes and thereby possibly overcoming drug resistance.

An improved method for estimating sequence divergence of DNA using restriction endonuclease mappings

The method proposed by Kaplan and Langley for estimating the extent of sequence divergence between related DNA's using restriction endonuclease maps is modified so that the estimates are easier to compute. In the two-species case, these modifications lead via a maximum likelihood approach to an estimate which is closely related to one recently suggested by Nei and Li (1979) and Gotoh et al. (1979). Simulation studies show that the modified estimates are comparable to those of Kaplan and Langley, providing that there is sufficient homology in the DNA segments of the related species. The M-species case, M greater than or equal to 3, is also discussed.

Covalent binding of polycyclic aromatic compounds to mitochondrial and nuclear DNA

Since the pioneering work of the Millers it has become clear that most chemical carcinogens require metabolism to reactive electrophiles and then exhibit their carcinogenic potential by reacting chemically with, and modifying, cellular macromolecules. At first modification of proteins was considered most likely to be of importance in carcinogenesis. Later, Brookes and Lawley demonstrated that the extent of binding of several polycyclic hydrocarbons to DNA, but not to RNA or protein isolated from the skin of mice treated topically with these compounds, correlated with their known carcinogenic potency to this tissue. Mammalian cells, particularly mouse embryo cells, treated with chemical carcinogens have often been used, and DNA has been involved almost exclusively from whole cells. However, mitochondria possess unique DNA which accounts for 0.1-1% of the total DNA present in mammalian cells, and three studies have shown that carcinogenic alkylating agents modify the michondrial DNA by a factor about five times greater than the nuclear DNA from the same cells. We demonstrate here that with six polycyclic aromatic compounds, all of which require metabolic activation and bind to DNA to a much smaller extent than direct than direct-acting alkylating agents, the binding to mitochondrial relative to DNA is dramatically increased by a factor of nearly 50 to over 500.

A new estimate of sequence divergence of mitochondrial DNA using restriction endonuclease mappings

A new estimate of the sequence divergence of mitochondrial DNA in related species using restriction enzyme maps is constructed. The estimate is derived assuming a simple Posisson-like model for the evolutionary process and is chosen to maximize an expression which is a reasonable approximation to the true likelihood of the restriction map data. Using this estimate, four sets of mitochondrial DNA data are analyzed and discussed.

The concept of cellular evolution

A central evolutionary question is whether the eucaryotic cytoplasm represents a line of descent that is separate from the typical bacterial line. It is argued on the basis of differences between their respective translation mechanisms that the two lines do represent separate phylogenetic trees in the sense that each line of descent independently evolved to a level of organization that could be called procaryotic. The two lines of descent, nevertheless shared a common ancestor, that was far simpler than the procaryote. This primitive entity is called a progenote, to recognize the possibility that it had not yet completed evolving the link between genotype and phenotype. This concept changes considerably the view one takes toward cellular evolution.

Symbiosis and the origin of life

The paper uses chemical kinetic arguments and illustrations by computer modelling to discuss the origin and evolution of life. Complex self-reproducing chemical systems cannot arise spontaneously, whereas simple auto-catalytic systems can, especially in an irradiated aqueous medium. Self-reproducing chemical particles of any complexity, in an appropriate environment, have a self-regulating property which permits long-term survival. However, loss of materials from the environment can lead to continuing decay which is circumvented by physical union between different kinds of self-reproducing particles. The increasing complexity produced by such unions (symbioses) is irreversible so that the chemical system evolves. It is suggested that evolution by successive symbioses brought about the change from simple, spontaneously arising, auto-catalytic particles to complex prokaryotic cells.

Mitochondrial genes and cell heredity

It is well known that mitochondria are only partly an autonomous system since they are subjected to nuclear control. For this reason, in studying mitochondrial genes one has to consider constantly the integration of mitochondrial and nuclear genetic systems. This fact makes experimental approaches still more sophisticated, especially, when one turns from individual genetic structures to mitochondrial heredity on the level of cells and multicellular organisms. Here we shall discuss some theoretical aspects of mitochondrial heredity that have been comparatively rarely dealt with in the literature.

Variations in mitochondrial size and ultrastructure during germ cell development

Size variations and ultrastructural changes in mitochondria of developing germ cells of the female hamster were analyzed. Mitochondria in oogonia of foetus and newborn were elongate with transverse cristae. During pre-dictyate meiotic prophase they became small, rounded, and electron-dense with pleomorphic cristae. These changes were largely reversed when dictyate was reached. Maximum mitochondrial size and complexity of cristae were reached just at the beginning of the phase of rapid oocyte growth, and thereafter declined. As mitochondrial size and number of cristae decreased in the rapidly enlarging oocyte, the ratio of length to width increased, as did electron density of the matrix, until the formation of an antrum within the follicle. After antrum formation, the mitochondria again became more rounded and cristae were seldom seen. An attempt is made to correlate changes of mitochondrial morphology with other events occurring during oogenesis.

Phylogenetic origin of the chloroplast

The 16S ribosomal RNA of the chloroplast of Euglena gracilis strain Z has been characterized in terms of its 2-dimensional electrophoretic "fingerprint" (T1 ribonuclease). Over 100 spots were resolved on the "fingerprint" and each spot was characterized as to which RNA oligonucleotide fragment(s) is contained. When compared to similar analyses of prokaryotic 16S rRNAs and eukaryotic cytoplasmic 18S rRNAs, the chloroplast 16S rRNA was a typically prokaryotic RNA, but bore little if any relationship to eukaryotic 18S rRNAs. Therefore, the cistrons for chloroplast 16S rRNA are related to the equivalent prokaryotic cistrons, but, apparently, are not related to the equivalent eukaryotic cistrons. Among the organisms available for comparison, the Euglena chloroplast 16S rRNA appears most closely related to the 16S rRNA of the eukaryote, Porphyridium cruentum (a red alga), and at least distantly related to the 16S rRNAs of the blue-green algae and perhaps also to the bacilli.

The origin of mitochondria

The endosymbiont and episome theories about the origin of mitochondria are reviewed. Biochemical and genetic data, relevant to these theories are discussed. An alternative theory is also proposed; this theory is that nuclear and mitochondrial DNAs developed from compartmentalized duplicate prokaryote DNAs.

Characterization of the genome of Phycomyces blakesleeanus

DNA of Phycomyces blakesleeanus was extracted from whole mycelia and from nuclear and mitochondrial organelle fractions obtained from sporangiophores. DNA from all three sources exhibits one symmetrical band at p equals 1.688 g/ml in CsCl buoyant density gradients. Reassociation data are consistent with kinetic division of the DNA into three components: very rapidly renaturing (fraction I), rapidly reassociating (fraction II) and slowly reassociating (fraction III) base sequences. These components comprise approximately 10%, 20% and 64% of total cell DNA. Kinetic fractions were prepared from total cell DNA and reassociated separately. The corrected rate constant is 11.3 M-1-S-1 for the rapidly reassociating component and 0.055 M-1-S-1 for the slowly reassociating component. Based on these data and the data from unfractionated total cell DNA, the genome size of Phycomyces is approximately 1.9-10-10 daltons, 6.7 times that of Escherichia coli.

Alterations in mitochondria associated with cytoplasmic and nuclear genes concerned with male sterility in maize

Mitochondria isolated from etiolated shoots of a range of maize genotypes with the "Texas" cytoplasm conferring cytoplasmically-inherited male sterility, are sensitive to a pathotoxin isolated from Helmintho-sporium maydis, race T. The pathotoxin inhibits oxidation of α ketoglutarate and malate and stimulates NADH oxidation. The time taken for the pathotoxin to induce these changes is a measure of the sensitivity of the mitochondria to the pathotoxin. A range of nine different pairs of genotypes, each pair differing principally in the presence of nuclear male fertility restorer alleles has been compared in their sensitivity to pathotoxin. In every case the line carrying the restorer alleles is more resistant to the pathotoxin. The restored genotypes can be quantitatively arranged into groups which correspond to the four different sources of the restorer genes in these lines. It is suggested that the restorer genes cause changes in mitochondria, which modify the functional aberration introduced by the cytoplasmically-inherited mutation causing sterility.

Physicochemical characterization of mitochondrial DNA from pea leaves

The mitochondrial DNA from pea leaves exists in a circular conformation. 25% of the circular molecules exist as supercoils, and 10% of the molecules are dimers. The molecular weight of mitochondrial DNA is about 66 to 70 x 10(6) by electron microscopy, and 74 x 10(6) from its renaturation kinetics. No evidence for inter- and intramolecular heterogeneity is found.

Studies with cholroplast and mitochondrial DNA. I. Evidence of sequence homology between chloroplast and nuclear DNA (Broad Bean) and between mitochondrial and nuclear DNA (rat liver)

A mixture of broad bean chloroplast and nuclear DNA or rat liver mitochondrial and nuclear DNA was taken through a heating and annealing cycle, and examined by CsCl density gradient centrifugation. The formation of intermediates between the two DNAs during joint annealing was used as a method of detecting sequence homology in different DNA samples. Homology was found between chloroplast and nuclear DNA from broad bean and between mitochondrial and nuclear DNA from rat liver. Since this method produces only qualitative data no implication for possible nucleocytoplasmic relationship can be assessed.