Changes of mitochondrial DNA polymerase-gamma activity in synchronized mouse cell cultures

Effective differentiation of double negative thymocytes requires high fidelity replication of mitochondrial DNA in an age dependent manner

One of the most proliferative periods for T cells occurs during their development in the thymus. Increased DNA replication can result in increased DNA mutations in the nuclear genome, but also in mitochondrial genomes. A high frequency of mitochondrial DNA mutations can lead to abnormal mitochondrial function and have negative implications on human health. Furthermore, aging is accompanied by an increase in such mutations through oxidative damage and replication errors. Increased mitochondrial DNA mutations cause loss of mitochondrial protein function, and decrease energy production, substrates, and metabolites. Here we have evaluated the effect of increased mitochondrial DNA mutations on T cell development in the thymus. Using mice carrying a mutant mitochondrial DNA polymerase γ (PolG) that causes increased mitochondrial DNA mutations, we show that high fidelity replication of mitochondrial DNA is pivotal for proper T cell development. Reducing the fidelity of mitochondrial DNA replication results in a premature age-dependent reduction in the total number of CD4/CD8 double negative and double positive thymocytes. Analysis of mitochondrial density in thymocyte subpopulations suggests that this may be due to reduced proliferation in specific double negative stages. Taken together, this work suggests that T cell development is regulated by the ability of mitochondria to faithfully replicate their DNA.

A Genetic Bottleneck of Mitochondrial DNA During Human Lymphocyte Development

Mitochondria are essential organelles in eukaryotic cells that provide critical support for energetic and metabolic homeostasis. Although the elimination of pathogenic mitochondrial DNA (mtDNA) mutations in somatic cells has been observed, the mechanisms to maintain proper functions despite their mtDNA mutation load are poorly understood. In this study, we analyzed somatic mtDNA mutations in more than 30,000 single human peripheral and bone marrow mononuclear cells. We observed a significant overrepresentation of homoplasmic mtDNA mutations in B, T, and natural killer (NK) lymphocytes. Intriguingly, their overall mutational burden was lower than that in hematopoietic progenitors and myeloid cells. This characteristic mtDNA mutational landscape indicates a genetic bottleneck during lymphoid development, as confirmed with single-cell datasets from multiple platforms and individuals. We further demonstrated that mtDNA replication lags behind cell proliferation in both pro-B and pre-B progenitor cells, thus likely causing the genetic bottleneck by diluting mtDNA copies per cell. Through computational simulations and approximate Bayesian computation (ABC), we recapitulated this lymphocyte-specific mutational landscape and estimated the minimal mtDNA copies as <30 in T, B, and NK lineages. Our integrative analysis revealed a novel process of a lymphoid-specific mtDNA genetic bottleneck, thus illuminating a potential mechanism used by highly metabolically active immune cells to limit their mtDNA mutation load.

Prevalent coordination of mitochondrial DNA transcription and initiation of replication with the cell cycle

Nuclear (nDNA) and mitochondrial DNA (mtDNA) communication is essential for cell function, but it remains unclear whether the replication of these genomes is linked. We inspected human cells with a novel fluorescence in situ hybridization protocol (mitochondrial Transcription and Replication Imaging Protocol) that identifies mitochondrial structures engaged in initiation of mtDNA replication and unique transcript profiles, and reconstruct the temporal series of mitochondrial and nuclear events in single cells during the cell cycle. We show that mtDNA transcription and initiation of replication are prevalently coordinated with the cell cycle, preceding nuclear DNA synthesis, and being reactivated towards the end of S-phase. This coordination is achieved by modulating the fraction of mitochondrial structures that intiate mtDNA synthesis and/or contain transcript at a given time. Thus, although replication of the mitochondrial genome is active through the entire cell cycle, but in a limited fraction of mitochondrial structures, peaks of these activities are synchronized with nDNA synthesis. After release from blockage of mtDNA replication with either nocodazole or double thymidine treatment, prevalent mtDNA and nDNA synthesis occurred simultaneously, indicating that mitochondrial coordination with the nuclear phase can be adjusted in response to physiological alterations. These findings will help redefine other nuclear-mitochondrial links in cell function.

Mitochondrial DNA polymerase editing mutation, PolgD257A, disturbs stem-progenitor cell cycling in the small intestine and restricts excess fat absorption

Changes in intestinal absorption of nutrients are important aspects of the aging process. To address this issue, we investigated the impact of accelerated mitochondrial DNA mutations on the stem/progenitor cells in the crypts of Lieberkühn in mice homozygous for a mitochondrial DNA polymerase gamma mutation, Polg(D257A), that exhibit accelerated aging phenotype. As early as 3-7 mo of age, the small intestine was significantly enlarged in the PolgD257A mice. The crypts of the PolgD257A mice contained 20% more cells than those of their wild-type littermates and exhibited a 10-fold increase in cellular apoptosis primarily in the stem/progenitor cell zones. Actively dividing cells were proportionally increased, yet a significantly smaller proportion of cells was in the S phase of the cell cycle. Stem cell-derived organoids from PolgD257A mice failed to develop fully in culture and exhibited fewer crypt units, indicating an impact of the mutation on the intestinal epithelial stem/progenitor cell maintenance. In addition, epithelial cell migration along the crypt-villus axis was slowed and less organized, and the ATP content in the villi was significantly reduced. On a high-fat, high-carbohydrate diet, PolgD257A mice showed significantly restricted absorption of excess lipids accompanied by an increase in fecal steatocrits. We conclude that the PolgD257A mutation causes cell cycle dysregulation in the crypts leading to the age-associated changes in the morphology of the small intestine and contributes to the restricted absorption of dietary lipids.

Crosstalk between mitochondrial (dys)function and mitochondrial abundance

A controlled regulation of mitochondrial mass through either the production (biogenesis) or the degradation (mitochondrial quality control) of the organelle represents a crucial step for proper mitochondrial and cell function. Key steps of mitochondrial biogenesis and quality control are overviewed, with an emphasis on the role of mitochondrial chaperones and proteases that keep mitochondria fully functional, provided the mitochondrial activity impairment is not excessive. In this case, the whole organelle is degraded by mitochondrial autophagy or "mitophagy." Beside the maintenance of adequate mitochondrial abundance and functions for cell homeostasis, mitochondrial biogenesis might be enhanced, through discussed signaling pathways, in response to various physiological stimuli, like contractile activity, exposure to low temperatures, caloric restriction, and stem cells differentiation. In addition, mitochondrial dysfunction might also initiate a retrograde response, enabling cell adaptation through increased mitochondrial biogenesis.

Biogenesis and dynamics of mitochondria during the cell cycle: significance of 3'UTRs

Nowadays, we are facing a renaissance of mitochondria in cancer biology. However, our knowledge of the basic cell biology and on the timing and mechanisms that control the biosynthesis of mitochondrial constituents during progression through the cell cycle of mammalian cells remain largely unknown. Herein, we document the in vivo changes on mitochondrial morphology and dynamics that accompany cellular mitosis, and illustrate the following key points of the biogenesis of mitochondria during progression of liver cells through the cycle: (i) the replication of nuclear and mitochondrial genomes is synchronized during cellular proliferation, (ii) the accretion of OXPHOS proteins is asynchronously regulated during proliferation being the synthesis of beta-F1-ATPase and Hsp60 carried out also at G2/M and, (iii) the biosynthesis of cardiolipin is achieved during the S phase, although full development of the mitochondrial membrane potential (DeltaPsim) is attained at G2/M. Furthermore, we demonstrate using reporter constructs that the mechanism regulating the accretion of beta-F1-ATPase during cellular proliferation is controlled at the level of mRNA translation by the 3'UTR of the transcript. The 3'UTR-driven synthesis of the protein at G2/M is essential for conferring to the daughter cells the original phenotype of the parental cell. Our findings suggest that alterations on this process may promote deregulated beta-F1-ATPase expression in human cancer.

Co-localization of mitochondrial and double minute DNA in the nuclei of HL-60 cells but not normal cells

In an attempt to isolate genes located on double minute (Dmin) DNA in HL-60 cells, we prepared DNA probe from purified micronuclei. Micronucleation was induced in HL-60 cells by treatment with hydroxyurea. Screening of a cDNA library unexpectedly produced a number of clones containing mitochondrial DNA (mtDNA) sequences. Here, we show that amplified mtDNA sequences were localized in nuclei and micronuclei of HL-60 and COLO 320DM cells, but not in nuclei of WI-38 normal human fibroblasts or peripheral blood T-cells. To unequivocally demonstrate the presence of mtDNA inside of nuclei and micronuclei, we obtained tomographic fluorescence in situ hybridization (FISH) images of mtDNA by confocal microscopy of consecutive sections of paraformaldehyde (PFA)-fixed material. We also located mtDNA in nuclear buds and purified micronuclei. Dmin DNA and mtDNA were always located at similar sites. The mechanisms of nuclear retention of mtDNA and Dmin DNA and the resulting influence on tumorigenesis are discussed.

DNA polymerase alpha-primase complex from the silk glands of the non-mulberry silkworm Philosamia ricini

The DNA content in the silk glands of the non-mulberry silkworm Philosamia ricini increases continuously during the fourth and fifth instars of larval development indicating high levels of DNA replication in this terminally differentiated tissue. Concomitantly, the DNA polymerase alpha activity also increases in the middle and the posterior silk glands during development, reaching maximal levels in the middle of the fifth larval instar. A comparable level of DNA polymerase delta/epsilon was also observed in this highly replicative tissue. The DNA polymerase alpha-primase complex from the silk glands of P. ricini has been purified to homogeneity by conventional column chromatography as well as by immunoaffinity techniques. The molecular mass of the native enzyme is 560 kDa and the enzyme comprises six non-identical subunits. The identity of the enzyme as DNA polymerase alpha has been established by its sensitivity to inhibitors such as aphidicolin, N-ethylmaleimide, butylphenyl-dGTP, butylanilino-dATP and antibodies to polymerase alpha. The enzyme possesses primase activity capable of initiating DNA synthesis on single-stranded DNA templates. The tight association of polymerase and primase activities at a constant ratio of 6:1 is observed through all the purification steps. The 180 kDa subunit harbours the polymerase activity, while the primase activity is associated with the 45 kDa subunit.

DNA polymerase-beta from the pupal ovaries of Bombyx mori

The silk glands of Bombyx mori, a highly replicative tissue contains high levels of DNA polymerases alpha, delta and epsilon but not DNA polymerase-beta. However, we detected the latter activity in the gonadal tissues, viz. the pupal ovaries and testes of B. mori. The enzyme has been purified to homogeneity from the pupal ovaries by a series of column chromatographic and affinity purification steps. The enzyme satisfied the criteria to be designated as DNA polymerase-beta based on its small size, requirement for high concentration of monovalent cations for catalytic activity, sensitivity to ddTTP and insensitivity to aphidicolin. It is a monomeric polypeptide of M(r) 40 kDa, and the Km for dNTPs ranges between 8-20 microM. DNA polymerase-beta is biochemically and immunologically distinct from DNA polymerase-alpha from the silk glands of B. mori. The enzyme showed a preference for gapped DNA, and could not elongate ultraviolet irradiated template beyond the pyrimidine dimers. The absence of any associated primase and exonuclease activities from this enzyme, and its conspicuous absence in the highly replicative tissue, imply that it is unlikely to participate in the DNA endoreplication process.

Purification and characterization of an inducible mitochondrial DNA polymerase from Tetrahymena thermophila

Treatment of the eukaryotic organism Tetrahymena with various types of DNA-damaging agents has been reported to cause a 35-fold induction of a mitochondrial DNA polymerase. We here report that the enzyme can be induced in large-scale cultures by exposure of the cells to thymine starvation and/or intercalating agents. The induced DNA polymerase has been purified to near homogeneity, with a specific activity of approx. 300,000 units/mg protein. The relative molecular mass of the active form of the enzyme is approx. 100,000, as determined by glycerol gradient sedimentation. The subunit structure has been analysed by SDS polyacrylamide gel electrophoresis of the highly purified preparation and by immunoprecipitation with a monoclonal antibody directed to the DNA polymerase. A polypeptide of Mr 47,000 has been observed to be a subunit of the enzyme. This corresponds to the size of the subunits suggested for mitochondrial DNA polymerase from chicken embryos and mouse myeloma cells.

Kinetics of DNA replication in C3H 10T1/2 cells synchronized by aphidicolin

Aphidicolin is an inhibitor of DNA polymerase alpha and blocks nuclear DNA replication without interfering with mitochondrial DNA synthesis. The efficacy of this mycotoxin as a tool in cell synchronization was evaluated in C3H 10T1/2 clone 8 cells. At concentrations of 1-2 micrograms/mL, aphidicolin quickly reduced the [3H]thymidine uptake to less than 5% of control levels in the first 5 min of incubation. This inhibition was easily reversed by washing and refeeding cells with fresh medium. The synchronization protocol consisted of first blocking cells by confluence arrest, replating them at lower density, and then treating the cells with aphidicolin for 24 h. Once the inhibitor was removed, DNA replication started without any delay. The cell population traversed the S phase in about 8 h and synchronously doubled in cell number. Autoradiography studies revealed a labeling index of 89-93% during the S phase. However, it was also observed that 10T1/2 cells were able to enter S phase in the presence of aphidicolin. The extent of the ensuing replication in the nucleus was dependent on the time that cells remained arrested in early S phase. Analyses of the newly replicated DNA in alkaline sucrose gradients revealed a fairly homogeneous distribution of sizes of nascent DNA in synchronized cells pulse-labeled at the beginning of the S phase. Upon chase in nonradioactive medium, the average molecular weight of the nascent DNA increased linearly with time of DNA synthesis for 2 h. The apparent rate of DNA chain growth determined from pulse and chase experiments was 1.2 micron/min. This rate was strongly inhibited (93%) by aphidicolin at a concentration of 2 micrograms/mL.

The effect of retroviral transformation on DNA replication and DNA polymerase-gamma activity in chick embryo fibroblast mitochondria

The effect of transformation by oncogenic Rous sarcoma viruses on the replication of mitochondrial DNA (mtDNA) in chick embryo fibroblasts (CEF) was investigated, extending our previous report of a three- to five-fold increase in the rate of mtDNA replication, which is strictly linked to the expression of the transformed state, is mitochondria-specific, and is not attributable to virus production per se or different growth rates between normal and transformed CEF. In this paper, in vivo pulse-label and pulse-chase analysis shows an increased specific activity in all the replicative and topological forms of transformed cell mtDNA I, labeled within a 10-min pulse, 30-min chase period, reflecting about the same proportion of total label incorporated into D-loop strands (approximately 9S) relative to full-length closed circular forms (approximately 37S) of mtDNA from both cell types. In contrast to the concomitant changes observed in many other systems with elevated DNA synthesis, neither the estimated intramitochondrial pool size of the labeled DNA precursor (dTTP), nor the total level of the mtDNA-replicating enzyme (mt gamma-polymerase) is increased in the transformed cells. Notably, however, in both cell types the mitochondrial dTTP pools relative to the mtDNA complement are significantly larger than whole-cell pools relative to the nuclear DNA complement, confirming recent reports in HeLa cells. The solubilized mt gamma-polymerases from normal and transformed CEF, respectively, are both precipitated by 50% ammonium sulfate, inhibited by N-ethylmaleimide, have similar sedimentation coefficients, and exhibit optimal activity when poly(rA) . d(pT)10 is used as the template-primer. On the other hand, the transformed cell enzyme demonstrates an altered response to thiol compounds, a decreased tendency to aggregate during sedimentation, and is significantly less tightly attached to the mitochondria than the normal cell enzyme. We conclude that, as a result of transformation, an increased fraction of mtDNA molecules replicate at a given time, and that this increased replication rate in vivo is correlated with the expression of several altered endogenous properties, which possibly include a modified intramitochondrial structural attachment of the mt gamma-polymerase in situ. This experimental system may be well suitable for use in the identification of regulatory factors which function during the replication of the mitochondrial genome in vivo.

DNA polymerases alpha and gamma during pre-emergence and early larval development of Artemia

DNA polymerases alpha and gamma have been studied in cryptobiotic cysts and developing embryos and larvae of the brine shrimp Artemia. The two enzymes readily separate on Cibacron blue 3-GA Matrex gel. Assay requirements with activated DNA as primer-template are pH 8.0, 1 mM Mg2+, 50 mM K+ for DNA polymerase alpha and pH 8.4, 10 mM Mg2+, 80 mM K+ for DNA polymerase gamma. DNA polymerase alpha is inhibited by N-ethylmaleimide (94% and 100% at 1 mM and 10 mM respectively) and aphidicolin (96% at 60 microM). DNA polymerase gamma is also sensitive to N-ethylmaleimide (83% and 100% inhibition at 1 mM and 10 mM respectively) but is resistant to aphidicolin. 2',3'-Dideoxythymidine 5'-triphosphate (ddTTP) inhibits the gamma polymerase by 88% when in fivefold excess over dTTP whereas the alpha polymerase is unaffected by this compound. DNA polymerase alpha has a sedimentation coefficient of 7.6 S which is reduced to 6.2 S by a phenylmethylsulphonyl fluoride-sensitive proteinase. The gamma polymerase sediments at 8.3 S. No DNA polymerase beta activity could be detected. After the reinitiation of development both activities increased twofold up to 8 h (gamma polymerase) and 16 h (alpha polymerase), then declined before the onset of nuclear DNA replication after hatching. Thymidine kinase activity increased over 200-fold up to the time of replication. Analysis on Percoll density gradients of the intracellular distribution of both polymerases during development suggests that the changes in their activities may be due to migration from storage sites to replication complexes in the nuclei and mitochondria. The content of the mitochondrial DNA polymerase gamma in different batches of cysts may reflect the relative viabilities of the cysts.

Effects of DNA polymerase inhibitors on replicative and repair DNA synthesis in ultraviolet-irradiated HeLa cells

Aphidicolin specifically inhibits eukaryotic DNA polymerase alpha, while 2',3'-dideoxythymidine 5'-triphosphate (d2TTP) inhibits DNA polymerase beta and gamma but not alpha. 1-beta-D-Arabinofuranosylcytosine 5'-triphosphate (araCTP) inhibits both DNA polymerase alpha and beta although to a different extent. Here we measured the effects of these inhibitors on repair DNA synthesis of U.V.-irradiated HeLa cells by two different methods. Firstly, aphidicolin, 1-beta-D-arabinofuranosylcytosine (araC, a precursor of araCTP) and 2',3'-dideoxythimidine (d2Thd, a precursor of d2TTP) were added directly to the culture medium. In this case, aphidicolin and araC strongly inhibited replicative DNA synthesis of HeLa cells, and they also inhibited repair synthesis after U.V.-irradiation but to a much lesser extent. In contrast, high concentrations of d2Thd inhibited repair DNA synthesis to a higher extent than replicative DNA synthesis. Secondly, the active form of inhibitor, d2TTP, was microinjection directly into cytoplasm or nuclei or U.V.-irradiated HeLa cells. Microinjection of d2TTP effectively inhibited repair synthesis. The microinjection of d2TTP, into either cytoplasm or nucleus, strongly inhibited replicative synthesis. These results might indicate that multiple DNA polymerases are involved in repair synthesis as well as in replicative synthesis.