The structural basis for substrate specificity in DNA topoisomerase IV

Most bacteria possess two type IIA topoisomerases, DNA gyrase and topo IV, that together help manage chromosome integrity and topology. Gyrase primarily introduces negative supercoils into DNA, an activity mediated by the C-terminal domain of its DNA binding subunit (GyrA). Although closely related to gyrase, topo IV preferentially decatenates DNA and relaxes positive supercoils. Here we report the structure of the full-length Escherichia coli ParC dimer at 3.0 A resolution. The N-terminal DNA binding region of ParC is highly similar to that of GyrA, but the ParC dimer adopts a markedly different conformation. The C-terminal domain (CTD) of ParC is revealed to be a degenerate form of the homologous GyrA CTD, and is anchored to the top of the N-terminal domains in a configuration different from that thought to occur in gyrase. Biochemical assays show that the ParC CTD controls the substrate specificity of topo IV, likely by capturing DNA segments of certain crossover geometries. This work delineates strong mechanistic parallels between topo IV and gyrase, while explaining how structural differences between the two enzyme families have led to distinct activity profiles. These findings in turn explain how the structures and functions of bacterial type IIA topoisomerases have evolved to meet specific needs of different bacterial families for the control of chromosome superstructure.     

Elongation factor 1a mediates the specificity of mitochondrial tRNA import in T. brucei

Mitochondrial tRNA import is widespread in eukaryotes. Yet, the mechanism that determines its specificity is unknown. Previous in vivo experiments using the tRNAs(Met), tRNA(Ile) and tRNA(Lys) have suggested that the T-stem nucleotide pair 51:63 is the main localization determinant of tRNAs in Trypanosoma brucei. In the cytosol-specific initiator tRNA(Met), this nucleotide pair is identical to the main antideterminant that prevents interaction with cytosolic elongation factor (eEF1a). Here we show that ablation of cytosolic eEF1a, but not of initiation factor 2, inhibits mitochondrial import of newly synthesized tRNAs well before translation or growth is affected. tRNA(Sec) is the only other cytosol-specific tRNA in T. brucei. It has its own elongation factor and does not bind eEF1a. However, a mutant of the tRNA(Sec) expected to bind to eEF1a is imported into mitochondria. This import requires eEF1a and aminoacylation of the tRNA. Thus, for a tRNA to be imported into the mitochondrion of T. brucei, it needs to bind eEF1a, and it is this interaction that mediates the import specificity.     

Development and characterization of continuous avian cell lines depleted of mitochondrial DNA

Summary Populations of quail and chicken cells were treated with ethidium bromide, an inhibitor of mitochondrial DNA replication. After long-term exposure to the drug, the cell populations were transferred to ethidium bromide (EtdBr)-free medium, and cloned. Clones HCF7 (quail) and DUS-3 (chicken) were propagated for more than a year, and then characterized. Analysis of total cellular DNA extracted from these cells revealed no characteristic mitochondrial DNA molecule by Southern blot hybridization of HindIII- or AvaI-digested total cellular DNA probed with cloned mitochondrial DNA fragments. Reconstruction experiments, where a small number of parental cells was mixed with HCF7 cells and DUS-3 cells before extraction of total cellular DNA, further strengthen the notion that the drug-treated cells are devoid of mitochondrial DNA molecules. The cell populations were found to proliferate at a moderately reduced growth rate as compared to their respective parents, to be auxotrophic for uridine, and to be stably resistant to the growth inhibitory effect of EtdBr and chloramphenicol. At the ultrastructural level, mitochondria were considerably enlarged and there was a severe reduction in the number of cristae within the organelles and loss of cristae orientation. Morphometric analysis revealed a fourfold increase of the mitochondrial profile area along with a twofold decrease of the numerical mitochondrial profiles. Analysis of biochemical parameters indicated that the cells grew with mitochondria devoid of a functional respiratory chain. The activity of the mitochondrial enzyme dihydroorotate dehydrogenase was decreased by 95% and presumably accounted for uridine auxotrophy. This work was supported by a grant from the Medical Research Council of Canada.     

Effects of a 300 mT static magnetic field on human umbilical vein endothelial cells

This study describes the effects of a static magnetic field (SMF) on cell growth and DNA integrity of human umbilical vein endothelial cells (HUVECs). Fast halo assay was used to investigate nuclear damage; quantitative polymerase chain reaction (QPCR), standard PCR, and real‐time PCR were used to evaluate mitochondrial DNA integrity, content, and gene expression. HUVECs were continually exposed to a 300 mT SMF for 4, 24, 48, and 72 h. Compared to control samples (unexposed cultures) the SMF‐exposed cells did not show a statistically significant change in their viability. Conversely, the static field was shown to be significant after 4 h of exposure, inducing damage on both the nuclear and mitochondrial levels, reducing mitochondrial content and increasing reactive oxygen species. Twenty‐four hours of exposure increased mitochondrial DNA content as well as expression of one of the main genes related to mitochondrial biogenesis. No significant differences between exposed and sham cultures were found after 48 and 72 h of exposure. The results suggest that a 300 mT SMF does not cause permanent DNA damage in HUVECs and stimulates a transient mitochondrial biogenesis. Bioelectromagnetics 31:630–639, 2010. © 2010 Wiley‐Liss, Inc.     

Structure-Function Relationships in Cellular Organelles Introductory Remarks by the Convener

Cells of the order Kinetoplastida possess a single mitochondrion which contains a large amount of a uniquely organized DNA. This kinetoplastic DNA (K-DNA), representing 10–20% of the total cell DNA in different species, has as its major molecular component a small closed circular molecule present in large numbers. The size and thereby the amount of genetic information carried by the minicircles varies from species to species: Leishmania tarentolae and the Salivarian trypanosomes have the smallest, the Stercorarian trypanosomes Trypanosoma lewisi and Trypanosoma cruzi intermediate, and Crithidia and also Trypanosoma mega the largest minicircles. In L. tarentolae, purified minicircles, which are the size of 1 gene, have been shown by renaturation kinetics to consist of only 1 or 2 classes. L. tarentolae K-DNA also contains another molecular species—a long molecule which may represent up to 30% of the total K-DNA. The minicircles, nevertheless, represent a gene amplification of the order of 10⁴. In all species that have been examined so far, the K-DNA consists of a single sheet of interlocked closed circular molecules which can be isolated in an intact form because of its resistance to shear forces and its high molecular weight. In addition, at least in L. tarentolae, 6–9% of the K-DNA is either free in the mitochondrion or loosely bound. The main K-DNA structure has been termed a “network” and can be seen in the light microscope after staining in solution with acridine orange or after fixing and staining with Giemsa's, or in the electron microscope. The quaternary structure of such networks in terms of the organization of minicircles and long molecules is not understood. Controlled breakdown of networks from L. tarentolae was achieved by sonication, and the release of open and closed monomeric minicircles, catenated dimers, trimers and higher oligomers, and short linear fragments was measured. A maximum of 43% of the total network DNA was released in the form of closed monomers, dimers, and trimers, thus providing a minimal estimate for the percentage of minicircles in K-DNA from this species. K-DNA replicates fairly synchronously with nuclear DNA in all species that have been examined. Replication of DNA molecules in the kinetoplast networks is limited to the periphery, as seen in autoradiographs of networks isolated from cells (L. tarentolae, Crithidia fasciculata) pulsed with ³H-thymidine. The molecular implications of this unusual replication pattern remain an open question, as does the genetic function of the K-DNA itself.     

Hypervariability in Gene Copy Number for the Glucose Transporter Genes in Trypanosomes

The copy number of the gene encoding the carrier protein responsible for the uptake of glucose in bloodstream form Trypanosoma brucei (THT1) was investigated in the genome of 55 different members of the subgenus Trypanozoon. The gene is present in multiple copies in tandem arrays on two homologous chromosomes in these organisms, and copy number varies both intra- and interspecifically. Variability is also apparent in the number of genes encoding a second hexose transporter (THT2) which is the only isoform expressed in procyclic organisms. Multiple copies of THT2 are conserved in representatives of the non-tsetse transmitted species, Trypanosoma evansi and Trypanosoma equiperdum.     

Recombinant DNA analysis indicates that the multiple chromosomes of maize mitochondria contain different sequences

Twenty-eight Bam H 1 restriction fragments were isolated from normal mitochondrial DNA of maize by recombinant DNA techniques to investigate the organization of the mitochondrial genome. Each cloned fragment was tested by molecular hybridization against a Bam digest of total mitochondrial DNA. Using Southern transfers, we identified the normal fragment of origin for d each clone. Twenty-three of the tested clones hybridized only to the fragment from which the clone was derived. In five cases, labeling of an additional band indicated some sequence repetition in the mitochondrial genome. Four clones from normal mitochondrial DNA were found which share sequences with the plasmid-like DNAs, S-1 and S-2, found in S male sterile cytoplasm. The total sequence complexity of the clones tested is 121×10⁶ d (daltons), which approximates two thirds of the total mitochondrial genome (estimated at 183×10⁶ d). Most fragments do not share homology with other fragments, and the total length of unique fragments exceeds that of the largest circular molecules observed. Therefore, the different size classes of circular molecules most likely represent genetically discrete chromosomes in a complex organelle genome. The variable abundance of different mitochondrial chromosomes is of special interest because it represents an unusual mechanism for the control of gene expression by regulation of gene copy number. This mechanism may play an important role in metabolism or biogenesis of mitochondria in the development of higher plants.     

Reactive oxygen species, mitochondria, apoptosis and aging

In this paper, we shall review various antioxygen defense systems of the cell paying particular attention to those that prevent superoxide formation rather than scavenge already formed superoxide and its products. The role of uncoupled, decoupled and non-coupled respiration, mitochondrial pore, mitochondrion-linked apoptosis will be considered. Mitochondrial theory of aging will be regarded in context of reactive oxygen species-induced damage of mitochondrial DNA. (Mol Cell Biochem 174: 305–319, 1997)     

Silver Carp, Hypophthalmichthys molitrix, in the Poyang Lake belong to the Ganjiang River Population Rather than the Changjiang River Population

The Poyang Lake is the largest lake and the main nursery area in the middle basin of the Changjiang (Yangtze) River. We compared molecular genetic markers of silver carp among populations of the Changjiang River, the Ganjiang River and the Poyang Lake using the ND5/6 region of mtDNA. Analysis of restriction fragment length polymorphisms (RFLPs) of this region revealed distinct variation between the Ganjiang River and the Changjiang River populations. The Poyang Lake is linked with the Ganjiang River and the Changjiang River. Shared RFLP fragments between the Ganjiang River population and the Poyang Lake population are as high as 61.4%. The value is 47.74% between the populations of the Changjiang River and that of the Poyang Lake. Frequencies of bands peculiar to the Ganjiang River population are the same as in the Poyang Lake population. We conclude that the Poyang Lake silver carp population consists mainly of the Ganjiang River population. The water level of the Poyang Lake outlet, which is higher than that of the Changjiang River in the silver carp spawning season, supports this conclusion.     

DNA and recent human evolution

The study of recent human evolution, or the origin of modern humans, is currently dominated by two theories. The recent African origin hypothesis holds that there was a single origin of modern humans in Africa about 100,000 years ago, after which these humans dispersed throughout the rest of the world, mixing little or not at all with nonmodern populations. The multiregional evolution hypothesis holds that there was no single origin of modern humans but, instead, that the mutations and other traits that led to modern humans were spread in concert throughout the old world by gene flow, leading to genetic continuity among old world populations during the past million years. Although both of these theories are based on observations stemming from the fossil record, much discussion and controversy during the past six years has focused on the application and interpretation of studies of DNA variation, particularly mitochondrial DNA (mtDNA). The past year, especially, has brought new data, interpretations, and controversies. Indeed, I initially resisted writing this review, on the grounds that new information would be likely to render it obsolete by the time it was published. However, now that the dust is starting to settle, it seems timely to review various investigations and interpretations and where they are likely to lead. While the focus of this review is the mtDNA story, brief mention is made of studies of nuclear DNA variation (both autosomal and Y-chromosome DNA) and the implications of the genetic data with regard to the fossil record and our understanding of recent human evolution.     

Mitochondrial DNA variation in Spanish populations of Ceratitis capitata (Wiedemann) (Tephritidae) and the colonization process

Abstract: Mitochondrial DNA variation in the Mediterranean fruit fly Ceratitis capitata (Wiedemann, Diptera: Tephritidae) was studied in three natural populations from southern, central and eastern Spain by means of restriction fragment length polymorphisms using 22 restriction endonucleases. Nine different haplotypes were found based upon the restriction patterns of the seven polymorphic endonucleases, providing a measure of discrimination between populations (N_ST = 0.2462, F_ST = 0.154). The observed distribution of haplotypes, corroborated by a parsimonious unrooted tree, suggests an ancient origin for haplotype VII, and a first step in the colonization of the Iberian Peninsula and subsequently the northern and eastern Mediterranean basin, through the Straits of Gibraltar. No relationship can be established between the colonization process for Europe and America.     

Prehistorical East–West admixture of maternal lineages in a 2,500‐year‐old population in Xinjiang

As an area of contact between Asia and Europe, Central Asia witnessed a scenario of complex cultural developments, extensive migratory movements, and biological admixture between West and East Eurasians. However, the detanglement of this complexity of diversity requires an understanding of prehistoric contacts of the people from the West and the East on the Eurasia continent. We demonstrated the presence of genetic admixture of West and East in a population of 35 inhabitants excavated in Gavaerk in southern Xinjiang and dated 2,800–2,100 years before present by analyzing their mitochondrial DNA variations. This result indicates that the initial contact of the East and the West Eurasians occurred further east than Central Asia as early as 2,500 years ago. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.     

Development of Mitochondrial Gene Replacement Therapy

Many "classic" mitochondrial diseases have been described that arise from single homoplasmic mutations in mitochondrial DNA (mtDNA). These diseases typically affect nonmitotic tissues (brain, retina, muscle), present with variable phenotypes, can appear sporadically, and are untreatable. Evolving evidence implicates mtDNA abnormalities in diseases such as Alzheimer's, Parkinson's, and type II diabetes, but specific causal mutations for these conditions remain to be defined. Understanding the mtDNA genotype-phenotype relationships and developing specific treatment for mtDNA-based diseases is hampered by inability to manipulate the mitochondrial genome. We present a novel protein transduction technology ("protofection") that allows insertion and expression of the human mitochondrial genome into mitochondria of living cells. With protofection, the mitochondrial genotype can be altered, or exogenous genes can be introduced to be expressed and either retained in mitochondria or be directed to other organelles. Protofection also delivers mtDNA in vivo, opening the way to rational development of mitochondrial gene replacement therapy of mtDNA-based diseases.     

Mitochondrial DNA and RNA isolation from small amounts of potato tissue

We present a fast and simple protocol for purification of mitochondrial DNA and RNA from small amounts of potato tissue including tubers, leaves, flowers, and flower buds. This method uses a high ionic strength medium to isolate mitochondria and extract mitochondrial DNA and RNA from a single preparation and is easily adaptable to other plant species. The mitochondrial DNA was not contaminated by plastid DNA, was fully restrictable and was successfully used for PCR, cloning and Southern analyses. Similarly, the isolated mitochondrial RNA was not contaminated (flower buds) or only slightly contaminated (leaves) by plastid RNA. RNA prepared according to our method was acceptable for northern and RT-PCR analyses.     

Organization of mitochondrial DNA in normal and texas male sterile cytoplasms of maize

Recombinant DNA and hybridization techniques have been used to compare the organization of mitochondrial DNA (mtDNA) from normal (N) and Texas male sterile (T) cytoplasms of maize. Bam H1 restriction fragments of normal mtDNA were cloned and used in molecular hybridizations against Southern blots of Bam H1 digested N and T mtDNA. Fifteen of the 35 fragments were conserved in both N and T as indicated by hybridization to comigrating bands in their restriction patterns. Only three fragments produced autoradiographs whose differences could reasonably be attributed to single changes in the cleavage site of the enzyme while approximately half (17/35) of the clones resulted in more complicated differences between N and T. The autoradiographs produced by these 17 clones indicated multiple cleavage site changes and/or sequence rearrangements of the mtDNA. Patterns of six of these 17 clones indicated partial duplication of the sequence and two showed variation in the intensity of hybridization between N and T, which may be related to the molecular heterogeneity phenomenon found in maize mitochondrial genomes. The large proportion of changes observed between N and T mtDNA indicates that rearrangements may have played an important role in the evolution of the maize mitochondrial genome.