Detection of deletions in the mitochondrial genome of Caenorhabditis elegans

Impact of Mitochondrial Architecture, Function, Redox Homeostasis, and Quality Control on Organismic Aging: Lessons from a Fungal Model System

Significance: Mitochondria are eukaryotic organelles with various essential functions. They are both the source and the targets of reactive oxygen species (ROS). Different branches of a mitochondrial quality control system (mQCS), such as ROS balancing, degradation of damaged proteins, or whole mitochondria, can mitigate the adverse effects of ROS stress. However, the capacity of mQCS is limited. Overwhelming this capacity leads to dysfunctions and aging. Strategies to interfere into mitochondria-dependent human aging with the aim to increase the healthy period of life, the health span, rely on the precise knowledge of mitochondrial functions. Experimental models such as Podospora anserina, a filamentous fungus with a clear mitochondrial aging etiology, proved to be instrumental to reach this goal. Recent Advances: Investigations of the P. anserina mQCS revealed that it is constituted by a complex network of different branches. Moreover, mitochondrial architecture and lipid homeostasis emerged to affect aging. Critical Issues: The regulation of the mQCS is only incompletely understood. Details about the involved signaling molecules and interacting pathways remain to be elucidated. Moreover, most of the currently generated experimental data were generated in well-controlled experiments that do not reflect the constantly changing natural life conditions and bear the danger to miss relevant aspects leading to incorrect conclusions. Future Directions: In P. anserina, the precise impact of redox signaling as well as of molecular damaging for aging remains to be defined. Moreover, natural fluctuation of environmental conditions needs to be considered to generate a realistic picture of aging mechanisms as they developed during evolution.

MtDNA deletions and aging

Aging is the major risk factor in most of the leading causes of mortality worldwide, yet its fundamental causes mostly remain unclear. One of the clear hallmarks of aging is mitochondrial dysfunction. Mitochondria are best known for their roles in cellular energy generation, but they are also critical biosynthetic and signaling organelles. They also undergo multiple changes with organismal age, including increased genetic errors in their independent, circular genome. A key group of studies looking at mice with increased mtDNA mutations showed that premature aging phenotypes correlated with increased deletions but not point mutations. This generated an interest in mitochondrial deletions as a potential fundamental cause of aging. However, subsequent studies in different models have yielded diverse results. This review summarizes the research on mitochondrial deletions in various organisms to understand their possible roles in causing aging while identifying the key complications in quantifying deletions across all models.

Non-coding Regions of Mitochondrial DNA and the cox1 Gene Reveal Genetic Variability Among Local Belarusian Populations of the Causative Agent of Cercarial Dermatitis, Bird Schistosome Trichobilharzia szidati (Digenea: Schistosomatidae)

INTRODUCTION

The cercariae of avian blood flukes Trichobilharzia szidati (Digenea, Schistosomatidae) are known to cause cercarial allergic dermatitis ("swimmer's itch") in humans. Global epidemics can have significant impacts on local tourism-related economies in recreational areas. Little is known about the genetic polymorphism of the parasite population, or about the variability of the non-coding regions of mitochondrial DNA (mtDNA) and the possibility of using this as a genetic marker.

MATERIALS AND METHODS

The T. szidati cercariae were collected over 7 years from 33 naturally infected Lymnaea stagnalis snails from five sites at two neighboring lakes in Belarus. We investigated the variability of the short (SNR) and long (LNR) non-coding regions of mt DNA and the genetic diversity within the 1125-bp sequences of the gene for subunit 1 of cytochrome c oxidase (cox1).

RESULTS

In the SNR sequences, we found only length variability caused by changes in the number of bases in the mononucleotide tracts T6-T8. LNR demonstrates high variability in nucleotide sequence length (182-260 bp) depending on the presence of two long deletions of 59 and 78 nucleotides. Both mitochondrial loci (LNR and cox1) are characterized by high haplotype diversity (H = 0.922 and H = 1.0, respectively); the nucleotide diversity is significantly higher for LNR (π = 1.926 ± 0.443) compared to cox1 (π = 0.704 ± 0.059). Phylogenetic reconstructions based on the variability of each of the loci (LNR and cox1) and their concatenated sequences revealed their shallow structure and the absence of a correlation between the distribution of single-nucleotide polymorphisms and the geographic origin of parasites from two Belarusian lakes. We identified at last four weakly sublineages in the phylogenetic pattern of T. szidati. The carriers of each deletion have specific patterns for each of the two loci and form their own phylogeographic sublineages. An association between two fixed LNR substitutions and a fixed non-synonymous substitution in cox1 was found in four representatives of one lineage that had a short deletion in the LNR.

CONCLUSIONS

This study clarified the phylogeographic structure of the Belarusian population of T. szidati. Our data provide the basis for the use two mt markers in large-scale population studies of the parasite, as well as for studying the molecular evolution of coding and non-coding mtDNA in trematodes.

Aging of Podospora anserina Leads to Alterations of OXPHOS and the Induction of Non-Mitochondrial Salvage Pathways

The accumulation of functionally impaired mitochondria is a key event in aging. Previous works with the fungal aging model Podospora anserina demonstrated pronounced age-dependent changes of mitochondrial morphology and ultrastructure, as well as alterations of transcript and protein levels, including individual proteins of the oxidative phosphorylation (OXPHOS). The identified protein changes do not reflect the level of the whole protein complexes as they function in-vivo. In the present study, we investigated in detail the age-dependent changes of assembled mitochondrial protein complexes, using complexome profiling. We observed pronounced age-depen-dent alterations of the OXPHOS complexes, including the loss of mitochondrial respiratory supercomplexes (mtRSCs) and a reduction in the abundance of complex I and complex IV. Additionally, we identified a switch from the standard complex IV-dependent respiration to an alternative respiration during the aging of the P. anserina wild type. Interestingly, we identified proteasome components, as well as endoplasmic reticulum (ER) proteins, for which the recruitment to mitochondria appeared to be increased in the mitochondria of older cultures. Overall, our data demonstrate pronounced age-dependent alterations of the protein complexes involved in energy transduction and suggest the induction of different non-mitochondrial salvage pathways, to counteract the age-dependent mitochondrial impairments which occur during aging.

Impaired F1Fo-ATP-Synthase Dimerization Leads to the Induction of Cyclophilin D-Mediated Autophagy-Dependent Cell Death and Accelerated Aging

Mitochondrial F1Fo-ATP-synthase dimers play a critical role in shaping and maintenance of mitochondrial ultrastructure. Previous studies have revealed that ablation of the F1Fo-ATP-synthase assembly factor PaATPE of the ascomycete Podospora anserina strongly affects cristae formation, increases hydrogen peroxide levels, impairs mitochondrial function and leads to premature cell death. In the present study, we investigated the underlying mechanistic basis. Compared to the wild type, we observed a slight increase in non-selective and a pronounced increase in mitophagy, the selective vacuolar degradation of mitochondria. This effect depends on the availability of functional cyclophilin D (PaCYPD), the regulator of the mitochondrial permeability transition pore (mPTP). Simultaneous deletion of PaAtpe and PaAtg1, encoding a key component of the autophagy machinery or of PaCypD, led to a reduction of mitophagy and a partial restoration of the wild-type specific lifespan. The same effect was observed in the PaAtpe deletion strain after inhibition of PaCYPD by its specific inhibitor, cyclosporin A. Overall, our data identify autophagy-dependent cell death (ADCD) as part of the cellular response to impaired F1Fo-ATP-synthase dimerization, and emphasize the crucial role of functional mitochondria in aging.

Thermodynamic analysis of DNA hybridization signatures near mitochondrial DNA deletion breakpoints

Broad evidence in the literature supports double-strand breaks (DSBs) as initiators of mitochondrial DNA (mtDNA) deletion mutations. While DNA misalignment during DSB repair is commonly proposed as the mechanism by which DSBs cause deletion mutations, details such as the specific DNA repair errors are still lacking. Here, we used DNA hybridization thermodynamics to infer the sequence lengths of mtDNA misalignments that are associated with mtDNA deletions. We gathered and analyzed 9,921 previously reported mtDNA deletion breakpoints in human, rhesus monkey, mouse, rat, and Caenorhabditis elegans. Our analysis shows that a large fraction of mtDNA breakpoint positions can be explained by the thermodynamics of short ≤ 5-nt misalignments. The significance of short DNA misalignments supports an important role for erroneous non-homologous and micro-homology-dependent DSB repair in mtDNA deletion formation. The consistency of the results of our analysis across species further suggests a shared mode of mtDNA deletion mutagenesis.

Simultaneous Ablation of the Catalytic AMPK α-Subunit SNF1 and Mitochondrial Matrix Protease CLPP Results in Pronounced Lifespan Extension

Organismic aging is known to be controlled by genetic and environmental traits. Pathways involved in the control of cellular metabolism play a crucial role. Previously, we identified a role of PaCLPP, a mitochondrial matrix protease, in the control of the mitochondrial energy metabolism, aging, and lifespan of the fungal aging model Podospora anserina. Most surprisingly, we made the counterintuitive observation that the ablation of this component of the mitochondrial quality control network leads to lifespan extension. In the current study, we investigated the role of energy metabolism of P. anserina. An age-dependent metabolome analysis of the wild type and a PaClpP deletion strain verified differences and changes of various metabolites in cultures of the PaClpP mutant and the wild type. Based on these data, we generated and analyzed a PaSnf1 deletion mutant and a ΔPaSnf1/ΔPaClpP double mutant. In both mutants PaSNF1, the catalytic α-subunit of AMP-activated protein kinase (AMPK) is ablated. PaSNF1 was found to be required for the development of fruiting bodies and ascospores and the progeny of sexual reproduction of this ascomycete and impact mitochondrial dynamics and autophagy. Most interestingly, while the single PaSnf1 deletion mutant is characterized by a slight lifespan increase, simultaneous deletion of PaSnf1 and PaClpP leads to a pronounced lifespan extension. This synergistic effect is strongly reinforced in the presence of the mating-type "minus"-linked allele of the rmp1 gene. Compared to the wild type, culture temperature of 35°C instead of the standard laboratory temperature of 27°C leads to a short-lived phenotype of the ΔPaSnf1/ΔPaClpP double mutant. Overall, our study provides novel evidence for complex interactions of different molecular pathways involved in mitochondrial quality control, gene expression, and energy metabolism in the control of organismic aging.

Clonal expansion of mitochondrial DNA deletions is a private mechanism of aging in long-lived animals

Disruption of mitochondrial metabolism and loss of mitochondrial DNA (mtDNA) integrity are widely considered as evolutionarily conserved (public) mechanisms of aging (López-Otín et al., Cell, 153, 2013 and 1194). Human aging is associated with loss in skeletal muscle mass and function (Sarcopenia), contributing significantly to morbidity and mortality. Muscle aging is associated with loss of mtDNA integrity. In humans, clonally expanded mtDNA deletions colocalize with sites of fiber breakage and atrophy in skeletal muscle. mtDNA deletions may therefore play an important, possibly causal role in sarcopenia. The nematode Caenorhabditis elegans also exhibits age-dependent decline in mitochondrial function and a form of sarcopenia. However, it is unclear if mtDNA deletions play a role in C. elegans aging. Here, we report identification of 266 novel mtDNA deletions in aging nematodes. Analysis of the mtDNA mutation spectrum and quantification of mutation burden indicates that (a) mtDNA deletions in nematode are extremely rare, (b) there is no significant age-dependent increase in mtDNA deletions, and (c) there is little evidence for clonal expansion driving mtDNA deletion dynamics. Thus, mtDNA deletions are unlikely to drive the age-dependent functional decline commonly observed in C. elegans. Computational modeling of mtDNA dynamics in C. elegans indicates that the lifespan of short-lived animals such as C. elegans is likely too short to allow for significant clonal expansion of mtDNA deletions. Together, these findings suggest that clonal expansion of mtDNA deletions is likely a private mechanism of aging predominantly relevant in long-lived animals such as humans and rhesus monkey and possibly in rodents.

Caenorhabditis elegans: What We Can and Cannot Learn from Aging Worms

SIGNIFICANCE

The nematode Caenorhabditis elegans is a widely used model organism for research into aging. However, nematodes diverged from other animals between 600 and 1300 million years ago. Beyond the intuitive impression that some aspects of aging appear to be universal, is there evidence that insights into the aging process of nematodes may be applicable to humans?

RECENT ADVANCES

There have been a number of results in nematodes that appear to contradict long-held beliefs about mechanisms and causes of aging. For example, ablation of several key antioxidant systems has often failed to result in lifespan shortening in C. elegans.

CRITICAL ISSUES

While it is clear that some central signaling pathways controlling lifespan are broadly conserved across large evolutionary distances, it is less clear to what extent downstream molecular mechanisms of aging are conserved. In this review we discuss the biology of C. elegans and mammals in the context of aging and age-dependent diseases. We consider evidence from studies that attempt to investigate basic, possibly conserved mechanisms of aging especially in the context of the free radical theory of aging. Practical points, such as the need for blinding of lifespan studies and for appropriate biomarkers, are also considered.

FUTURE DIRECTIONS

As data on the aging process(es) in different organisms increase, it is becoming increasingly clear that there are both conserved (public) and private aspects to aging. It is important to explore the dividing lines between these two aspects and to be aware of the large gray areas in-between.

Different faces of mitochondrial DNA mutators

A number of studies have shown that ageing is associated with increased amounts of mtDNA deletions and/or point mutations in a variety of species as diverse as Caenorhabditis elegans, Drosophila melanogaster, mice, rats, dogs, primates and humans. This detected vulnerability of mtDNA has led to the suggestion that the accumulation of somatic mtDNA mutations might arise from increased oxidative damage and could play an important role in the ageing process by producing cells with a decreased oxidative capacity. However, the vast majority of DNA polymorphisms and disease-causing base-substitution mutations and age-associated mutations that have been detected in human mtDNA are transition mutations. They are likely arising from the slight infidelity of the mitochondrial DNA polymerase. Indeed, transition mutations are also the predominant type of mutation found in mtDNA mutator mice, a model for premature ageing caused by increased mutation load due to the error prone mitochondrial DNA synthesis. These particular misincorporation events could also be exacerbated by dNTP pool imbalances. The role of different repair, replication and maintenance mechanisms that contribute to mtDNA integrity and mutagenesis will be discussed in details in this article. This article is part of a Special Issue entitled: Mitochondrial Dysfunction in Aging.

Control of mitochondrial integrity in ageing and disease

Various molecular and cellular pathways are active in eukaryotes to control the quality and integrity of mitochondria. These pathways are involved in keeping a 'healthy' population of this essential organelle during the lifetime of the organism. Quality control (QC) systems counteract processes that lead to organellar dysfunction manifesting as degenerative diseases and ageing. We discuss disease- and ageing-related pathways involved in mitochondrial QC: mtDNA repair and reorganization, regeneration of oxidized amino acids, refolding and degradation of severely damaged proteins, degradation of whole mitochondria by mitophagy and finally programmed cell death. The control of the integrity of mtDNA and regulation of its expression is essential to remodel single proteins as well as mitochondrial complexes that determine mitochondrial functions. The redundancy of components, such as proteases, and the hierarchies of the QC raise questions about crosstalk between systems and their precise regulation. The understanding of the underlying mechanisms on the genomic, proteomic, organellar and cellular levels holds the key for the development of interventions for mitochondrial dysfunctions, degenerative processes, ageing and age-related diseases resulting from impairments of mitochondria.

Deceleration of fusion-fission cycles improves mitochondrial quality control during aging

Mitochondrial dynamics and mitophagy play a key role in ensuring mitochondrial quality control. Impairment thereof was proposed to be causative to neurodegenerative diseases, diabetes, and cancer. Accumulation of mitochondrial dysfunction was further linked to aging. Here we applied a probabilistic modeling approach integrating our current knowledge on mitochondrial biology allowing us to simulate mitochondrial function and quality control during aging in silico. We demonstrate that cycles of fusion and fission and mitophagy indeed are essential for ensuring a high average quality of mitochondria, even under conditions in which random molecular damage is present. Prompted by earlier observations that mitochondrial fission itself can cause a partial drop in mitochondrial membrane potential, we tested the consequences of mitochondrial dynamics being harmful on its own. Next to directly impairing mitochondrial function, pre-existing molecular damage may be propagated and enhanced across the mitochondrial population by content mixing. In this situation, such an infection-like phenomenon impairs mitochondrial quality control progressively. However, when imposing an age-dependent deceleration of cycles of fusion and fission, we observe a delay in the loss of average quality of mitochondria. This provides a rational why fusion and fission rates are reduced during aging and why loss of a mitochondrial fission factor can extend life span in fungi. We propose the ‘mitochondrial infectious damage adaptation’ (MIDA) model according to which a deceleration of fusion–fission cycles reflects a systemic adaptation increasing life span.

Mitochondria are organelles that play a central role as ‘cellular power plants’. The cellular organization of these organelles involves a dynamic spatial network where mitochondria constantly undergo fusion and fission associated with the mixing of their molecular content. Together with the processes of mitophagy and biogenesis of mitochondrial mass, this results into a cellular surveillance system for maintaining their bioenergetic quality. The accumulation of molecular damage in mitochondria is associated with various human disorders and with aging. However, how these processes affect aging and how they can be reconciled with existing aging theories is just at the beginning to be considered. Mathematical modeling allows simulating the dynamics of mitochondrial quality control during aging in silico and leads to the ‘mitochondrial infectious damage adaptation’ (MIDA) model of aging. It reconciles a number of counterintuitive observations obtained during the last decade including infection-like processes of molecular damage spread, the reduction of fusion and fission rates during cellular aging, and observed life span extension for reduced mitochondrial fission. Interestingly, the MIDA model suggests that a reduction in mitochondrial dynamics rather than being merely a sign or even cause of aging, may actually reflect a systemic adaptation to prolong organismic life span.

The free-radical theory of ageing--older, wiser and still alive: modelling positional effects of the primary targets of ROS reveals new support

The continuing viability of the free-radical theory of ageing has been questioned following apparently incompatible recent results. We show by modelling positional effects of the generation and primary targets of reactive oxygen species that many of the apparently negative results are likely to be misleading. We conclude that there is instead a need to look more closely at the mechanisms by which free radicals contribute to age-related dysfunction in living systems. There also needs to be deeper understanding of the dynamics of accumulation and removal of the various kinds of molecular damage, in particular mtDNA mutations. Finally, the expectation that free-radical damage on its own might cause ageing needs to be relinquished in favour of the recognition that the free-radical theory is just one of the multiple mechanisms driving the ageing process.

Mitochondrial DNA mutations induce mitochondrial dysfunction, apoptosis and sarcopenia in skeletal muscle of mitochondrial DNA mutator mice

BACKGROUND

Aging results in a progressive loss of skeletal muscle, a condition known as sarcopenia. Mitochondrial DNA (mtDNA) mutations accumulate with aging in skeletal muscle and correlate with muscle loss, although no causal relationship has been established.

METHODOLOGY/PRINCIPAL FINDINGS

We investigated the relationship between mtDNA mutations and sarcopenia at the gene expression and biochemical levels using a mouse model that expresses a proofreading-deficient version (D257A) of the mitochondrial DNA Polymerase gamma, resulting in increased spontaneous mtDNA mutation rates. Gene expression profiling of D257A mice followed by Parametric Analysis of Gene Set Enrichment (PAGE) indicates that the D257A mutation is associated with a profound downregulation of gene sets associated with mitochondrial function. At the biochemical level, sarcopenia in D257A mice is associated with a marked reduction (35-50%) in the content of electron transport chain (ETC) complexes I, III and IV, all of which are partly encoded by mtDNA. D257A mice display impaired mitochondrial bioenergetics associated with compromised state-3 respiration, lower ATP content and a resulting decrease in mitochondrial membrane potential (Deltapsim). Surprisingly, mitochondrial dysfunction was not accompanied by an increase in mitochondrial reactive oxygen species (ROS) production or oxidative damage.

CONCLUSIONS/SIGNIFICANCE

These findings demonstrate that mutations in mtDNA can be causal in sarcopenia by affecting the assembly of functional ETC complexes, the lack of which provokes a decrease in oxidative phosphorylation, without an increase in oxidative stress, and ultimately, skeletal muscle apoptosis and sarcopenia.

Apurinic/apyrimidinic endonuclease 1, p53, and thioredoxin are linked in control of aging in C. elegans

Deletions in mitochondrial DNA (mtDNA) accumulate during aging. Expression of the Caenorhabditis elegans apurinic/apyrimidinic endonuclease 1 (APE1) ortholog exo-3, involved in DNA repair, is reduced by 45% (P < 0.05) during aging of C. elegans. Suppression of exo-3 by treatment with RNAi resulted in a threefold increase in mtDNA deletions (P < 0.05), twofold enhanced generation of reactive oxygen species (ROS) (P < 0.01), distortion of the structural integrity of the nervous system, reduction of head motility by 43% (P < 0.01) and whole animal motility by 38% (P < 0.05). Suppression of exo-3 significantly reduced life span: mean life span decreased from 18.5 +/- 0.4 to 15.4 +/- 0.1 days (P < 0.001) and maximum life span from 25.9 +/- 0.4 to 23.2 +/- 0.1 days (P = 0.001). Additional treatment of exo-3-suppressed animals with a mitochondrial uncoupler decreased ROS levels, reduced neuronal damage, and increased motility and life span. Additional suppression of the C. elegans p53 ortholog cep-1 in exo-3 RNAi-treated animals similarly decreased ROS levels, preserved neuronal integrity, and increased motility and life span. In wild-type animals, suppression of cep-1, involved in downregulation of exo-3, increased expression of exo-3 without a significant effect on ROS levels, preserved neuronal integrity, and increased motility and life span. Suppression of the C. elegans thioredoxin orthologs trx-1 and trx-2, involved in the redox chaperone activity of exo-3, overrides the protective effect of cep-1 RNAi treatment on neuronal integrity, neuronal function, mean and maximum life span. These results show that APE1/EXO-3, p53/CEP-1, and thioredoxin affect each other and that these interactions determine aging as well as neuronal structure and function.

High rate of large deletions in Caenorhabditis briggsae mitochondrial genome mutation processes

Mitochondrial DNA (mtDNA) mutations underlie a variety of human genetic disorders and are associated with the aging process. mtDNA polymorphisms are widely used in a variety of evolutionary applications. Although mtDNA mutation spectra are known to differ between distantly related model organisms, the extent to which mtDNA mutation processes vary between more closely related species and within species remains enigmatic. We analyzed mtDNA divergence in two sets of 250-generation Caenorhabditis briggsae mutation-accumulation (MA) lines, each derived from a different natural isolate progenitor: strain HK104 from Okayama, Japan, and strain PB800 from Ohio, United States. Both sets of C. briggsae MA lines accumulated numerous large heteroplasmic mtDNA deletions, whereas only one similar event was observed in a previous analysis of Caenorhabditis elegans MA line mtDNA. Homopolymer length change mutations were frequent in both sets of C. briggsae MA lines and occurred in both intergenic and protein-coding gene regions. The spectrum of C. briggsae mtDNA base substitution mutations differed from the spectrum previously observed in C. elegans. In C. briggsae, the HK104 MA lines experienced many different base substitution types, whereas the PB800 lines displayed only C:G --> T:A transitions, although the difference was not significant. Over half of the mtDNA base substitutions detected in the C. briggsae MA lines were in a heteroplasmic state, whereas all those previously characterized in C. elegans MA line mtDNA were fixed changes, indicating a narrower mtDNA bottleneck in C. elegans as compared with C. briggsae. Our results show that C. briggsae mtDNA is highly susceptible to large deletions and that the mitochondrial mutation process varies between Caenorhabditis nematode species.

Molecular basis of and interference into degenerative processes in fungi: potential relevance for improving biotechnological performance of microorganisms

Biological systems, from simple microorganisms to humans, are characterized by time-dependent degenerative processes which lead to reduced fitness, disabilities, severe diseases, and, finally, death. These processes are under genetic control but also influenced by environmental conditions and by stochastic processes. Studying the mechanistic basis of degenerative processes in the filamentous ascomycete Podospora anserina and in other systems demonstrated that mitochondria play a key role in the expression of degenerative phenotypes and unraveled a number of underlying molecular pathways. Reactive oxygen species (ROS) which are mainly, but not exclusively, formed at the mitochondrial respiratory chain are crucial players in this network. While being essential for signaling processes and development, ROS are, at the same time, a potential danger because they lead to molecular damage and degeneration. Fortunately, a number of interacting pathways including ROS scavenging, DNA and protein repair, protein degradation, and mitochondrial fission and fusion are involved in keeping cellular damage low. If these pathways are overwhelmed by extensive damage, programmed cell death is induced. The current knowledge of this hierarchical system of mitochondrial quality control, although still incomplete, appears now to be ready for the development of strategies effective in interventions into those pathways leading to degeneration and loss of performance also in microorganisms used in biotechnology. Very promising interdisciplinary interactions and collaborations involving academic and industrial research teams can be envisioned to arise which bear a great potential, in particular, when system biology approaches are used to understand relevant networks of pathways in a holistic way.

Mitochondria and ageing in Drosophila

Studies in different organisms have revealed that ageing is a complex process involving a tight regulation of gene expression. Among other features, ageing organisms generally display an increased oxidative stress and a decreased mitochondrial function. The increase in oxidative stress can be attributable to reactive oxygen species, which are mainly produced by mitochondria as a by-product of energy metabolism. Consistent with these data, mitochondria have been suggested to play a significant role in lifespan determination. The fruitfly Drosophila melanogaster is a well-suited organism to study ageing as it is relatively short-lived, mainly composed of post-mitotic cells, has sequenced nuclear and mitochondrial genomes, and multiple genetic tools are available. It has been used in genome-wide studies to unveil the molecular signature of ageing, in different feeding and dietary restriction protocols and in overexpression and down-regulation studies to examine the effect of specific compounds or genes/proteins on lifespan. Here we review the various features linking mitochondria and ageing in Drosophila melanogaster.

Muller's Ratchet and compensatory mutation in Caenorhabditis briggsae mitochondrial genome evolution

Background

The theory of Muller' Ratchet predicts that small asexual populations are doomed to accumulate ever-increasing deleterious mutation loads as a consequence of the magnified power of genetic drift and mutation that accompanies small population size. Evidence for Muller's Ratchet and knowledge on its underlying molecular mechanisms, however, are lacking for natural populations.

Results

We characterized mitochondrial genome evolutionary processes in Caenorhabditis briggsae natural isolates to show that numerous lineages experience a high incidence of nonsynonymous substitutions in protein-coding genes and accumulate unusual deleterious noncoding DNA stretches with associated heteroplasmic function-disrupting genome deletions. Isolate-specific deletion proportions correlated negatively with nematode fecundity, suggesting that these deletions might negatively affect C. briggsae fitness. However, putative compensatory mutations were also observed that are predicted to reduce heteroplasmy levels of deleterious deletions. Paradoxically, compensatory mutations were observed in one major intraspecific C. briggsae clade where population sizes are estimated to be very small (and selection is predicted to be relatively weak), but not in a second major clade where population size estimates are much larger and selection is expected to be more efficient.

Conclusion

This study provides evidence that the mitochondrial genomes of animals evolving in nature are susceptible to Muller's Ratchet, suggests that context-dependent compensatory mutations can accumulate in small populations, and predicts that Muller's Ratchet can affect fundamental evolutionary forces such as the rate of mutation.

Accumulation of mitochondrial DNA deletion mutations in aged muscle fibers: evidence for a causal role in muscle fiber loss

Although mitochondrial mutation abundance has been recognized to increase in an age-dependent manner, the impact of mutation has been more difficult to establish. Using quantitative polymerase chain reaction, we measured the intracellular abundance of mutant and wild-type mitochondrial genomes along the length of individual laser-captured microdissected muscle fibers from aged rat quadriceps. Aged muscle fibers possessed segmental, clonal intracellular expansions of unique somatically derived mitochondrial DNA (mtDNA) deletion mutations. When the mutation abundance surpassed 90% of the total mitochondrial genomes, the fiber lost cytochrome c oxidase activity and exhibited an increase in succinate dehydrogenase activity. In addition to the mitochondrial enzymatic abnormalities, some fibers displayed abnormal morphology such as fiber splitting, atrophy, and breakage. Deletion mutation accumulation was linked to these aberrant morphologies with more severe cellular pathologies resulting from higher deletion mutation abundance. In summary, our measurements indicate that age-induced mtDNA deletion mutations expand within individual muscle fibers, eliciting fiber dysfunction and breakage.

Mitochondrial DNA Mutations and Aging

Mitochondria have been hypothesized to play a role in both aging and neurodegenerative diseases, such as Parkinson's disease (PD) and Alzheimer's disease. Many studies have shown the accumulation of mitochondrial DNA (mtDNA) mutations in post-mitotic tissues and more recent data have shown this also to be a feature of aging mitotic tissues. Much of this data has been correlative, until recently with the development of polymerase gamma deficient mice which accumulate high levels of mtDNA mutations and show a premature aging phenotype, that a more causative role has been proposed. This article focuses on recent developments in aging research into the role that mtDNA mutations play in the aging process.

Public and private mechanisms of life extension in Caenorhabditis elegans

Model organisms have been widely used to study the ageing phenomenon in order to learn about human ageing. Although the phylogenetic diversity between vertebrates and some of the most commonly used model systems could hardly be greater, several mechanisms of life extension are public (common characteristic in divergent species) and likely share a common ancestry. Dietary restriction, reduced IGF-signaling and, seemingly, reduced ROS-induced damage are the best known mechanisms for extending longevity in a variety of organisms. In this review, we summarize the knowledge of ageing in the nematode Caenorhabditis elegans and compare the mechanisms of life extension with knowledge from other model organisms.

Oxidative damage in mitochondrial DNA is not extensive

Since 1988 several research groups have reported greater levels of oxidative damage in mitochondrial DNA than in nuclear DNA, while others have suggested that the greater damage in mtDNA might be due to artifactual oxidation. The popular theory that mtDNA is more heavily damaged in vivo than nDNA does not stand on firm ground. Using an improved GC-MS method and pure mtDNA, our analyses revealed that the damage level in mtDNA is not higher, and may be somewhat lower, than that in nDNA.

Microarray analysis of variation in individual aging C. elegans: approaches and challenges

Aging is generally defined and studied as a population phenomenon. However, there is great interest, especially when discussing human aging, in the identification of factors that influence the life span of an individual organism. The nematode Caenorhabditis elegans provides an excellent model system for the study of aging at the level of the individual, since young nematodes are essentially clonal yet experience a large range of individual life spans. We are conducting gene expression profiling of individual nematodes, with the aim of discovering genes that vary stochastically in expression between individuals of the same age. Such genes are candidates to modulate the ultimate life span achieved by each individual. We here present statistical analysis of gene expression profiles of individual nematodes from two different microarray platforms, examining the issue of technical vs. biological variance as it pertains to uncovering genes of interest in this paradigm of individual aging.

Mitochondrial DNA and ageing

The accumulation of mitochondrial DNA mutations has been proposed as a potential mechanism in the physiological processes of ageing and age-related disease. Although mitochondria have long been anticipated as a perpetrator of ageing, there was little experimental evidence to link these changes directly with the cellular pathology of ageing. Recently, considerable progress in understanding basic mitochondrial genetics and in identifying acquired mtDNA mutations in ageing has been made. Furthermore, the creation of mtDNA-mutator mice has provided the first direct evidence that accelerating the mtDNA mutation rate can result in premature ageing, consistent with the view that loss of mitochondrial function is a major causal factor in ageing. This review will, therefore, focus on recent developments in ageing research related to the role played by mtDNA.

Detection of deletions flanked by short direct repeats in mitochondrial DNA of aging Drosophila

Cumulative damage due to reactive oxygen species (ROS) in mitochondria, especially in mitochondrial DNA (mtDNA), would result in a decrease in mitochondrial respiratory function and contributes to the age-related decline in the physiological functioning of organisms. Previously, we reported the tissue-specific accumulation of deleted mtDNA with age in Drosophila melanogaster. In the present study, to understand the mechanism by which mtDNA deletion is generated with age, nucleotide sequences of deleted mtDNA were determined. Consequently, 33 different sequences each containing a deletion were obtained from flies that were more than 55-day-old. Most of the deletions were found to be flanked by short direct repeats. The present results, together with those from other animals, suggest that there is a common mechanism generating mtDNA deletions through direct repeats.

Specific point mutations may not accumulate with aging in the mouse mitochondrial DNA control region

Increasing evidence suggests that mitochondrial function declines during aging in various tissues and in a wide range of organisms. This correlates with an age-dependent large accumulation of specific point mutations in the mtDNA control region that was reported recently in human fibroblast and skeletal muscle. However, evaluations of aging-related mtDNA mutations in other model animal systems. In this study, we analyzed mtDNA control regions of brain, skeletal muscle, heart, and other tissues from aged mice, in search of specific point mutations. A 948-bp fragment covering the entire mtDNA control region from various tissues of mice at the age of 25-26 months was sequenced. The sequence analysis was accomplished with a newly developed program Mutation Quantifier, which was able to accurately detect mutations with frequencies as low as 3%. Probably due to the relative shorter life-span, unlike what has been reported in human mtDNA, our results indicated there might be no significant accumulation of specific mutations in mouse mtDNA control region during aging.

Calcium-dependent and aspartyl proteases in neurodegeneration and ageing in C. elegans

Proteolytic mechanisms have been implicated in the process of ageing, and in many neurodegenerative disorders such as Alzheimer's, Parkinson's and Huntington's diseases, which are most prevalent in old age. Simple model organisms such as the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, which offer the prowess of sophisticated genetic approaches, have contributed to our understanding of ageing and neurodegeneration. Intensive research in these systems has resulted in detailed models of the ageing process, and also of several neurodegenerative diseases, which recapitulate same aspects of the human pathologies. Inappropriate cell death is a major component of these and other devastating conditions such as stroke. The dissection of the molecular mechanisms underlying the process of cell degeneration in ageing is of utmost importance. Evidence from investigations in C. elegans implicates deregulated proteolysis as one major determinant of cellular destruction in neurodegeneration and ageing, and suggests that the process depends critically on the activation of calcium-dependent, calpain proteases and lysosomal aspartyl proteases. Apart from shedding light on important but inadequately understood facets of such phenomena, these discoveries hold promise for developing novel, effective intervention strategies aiming to ameliorate or even counter inappropriate cell death.

The role of mitochondria in the life of the nematode, Caenorhabditis elegans

Mitochondria are essential organelles involved in energy metabolism via oxidative phosphorylation. They play a vital role in diverse biological processes such as aging and apoptosis. In humans, defects in the mitochondrial respiratory chain (MRC) are responsible for or associated with a bewildering variety of diseases. The nematode Caenorhabditis elegans is a simple animal and a powerful genetic and developmental model system. In this review, we discuss how the nematode model system has contributed to our understanding of mitochondrial dynamics, of the genetics and inheritance of the mitochondrial genome, and of the consequences of nuclear and mitochondrial DNA (mtDNA) mutations. Mitochondrial respiration is vital to energy metabolism but also to other aspects of multicellular life such as aging and development. We anticipate that further significant contributions to our understanding of mitochondrial function in animal biology are forthcoming with the C. elegans model system.

Accumulation of deleted mitochondrial DNA in aging Drosophila melanogaster

Cumulative damage in mitochondria by reactive oxygen species is thought to result in a decrease in mitochondrial respiratory function and to contribute to the age-related decline in the physiological function of organisms. The mitochondrial genome is also subjected to damage with age through deletions. The accumulation of deleted mitochondrial DNA (mtDNA) has been observed in various animals, but still remains unclear in insects. We examined the accumulation of deleted mtDNA in D. melanogaster at various ages from larvae to 65-day-old adults. When DNA extracted from whole bodies was examined by PCR and Southern hybridization, the age-related accumulation of deletions was not clear. However, when the accumulation of deleted mtDNA with age was examined separately in three parts of the body (head, thorax and abdomen), deleted mtDNA signals were detected more frequently in the thorax and the accumulation was age-dependent. Three of the deleted mtDNA were cloned, and the breakpoints of the deletions were identified. These results strongly suggest that deleted mtDNA accumulates in Drosophila with age in a tissue-specific manner.

Stable heteroplasmy but differential inheritance of a large mitochondrial DNA deletion in nematodes

Many human mitochondrial diseases are associated with defects in the mitochondrial DNA (mtDNA). Mutated and wild-type forms of mtDNA often coexist in the same cell in a state called heteroplasmy. Here, we report the isolation of a Caenorhabditis elegans strain bearing the 3.1-kb uaDf5 deletion that removes 11 genes from the mtDNA. The uaDf5 deletion is maternally transmitted and has been maintained for at least 100 generations in a stable heteroplasmic state in which it accounts for approximately 60% of the mtDNA content of each developmental stage. Heteroplasmy levels vary between individual animals (from approximately 20 to 80%), but no observable phenotype is detected. The total mtDNA copy number in the uaDf5 mutant is approximately twice that of the wild type. The maternal transmission of the uaDf5 mtDNA is controlled by at least two competing processes: one process promotes the increase in the average proportion of uaDf5 mtDNA in the offspring, while the second promotes a decrease. These two forces prevent the segregation of the mtDNAs to homoplasmy.

Mitochondrial mutagenesis in the brain in forensic and pathological research

Accumulation of alterations to the mitochondrial DNA (mtDNA) would be expected to significantly impair the bioenergetic function of mitochondria in the affected host cells. Many of these changes have been associated with several specific diseases and the process of aging. These mutations may be the result of mitochondrial oxidative stress, which is increased with age of individuals and specific degenerative diseases. Our aim with this review is to summarize the recent literature on the occurrence of mtDNA alterations and its possible relation to age-depending degenerative processes with special regards to the brain. Additionally, we show how these alterations could be used in fields of pathology and forensic medicine.

Caloric restriction and lifespan: a role for protein turnover?

Oxidative damage to cellular macromolecules has been postulated to be a major contributor to the ageing of diverse organisms. Oxidative damage can be limited by maintaining high anti-oxidant defenses and by clearing/repairing damage efficiently. Protein turnover is one of the main routes by which functional proteins are maintained and damaged proteins are removed. Protein turnover rates decline with age, which might contribute to the accumulation of damaged proteins in ageing cells. Interestingly, protein turnover rates are maintained at high levels in caloric restricted animals. Whether changes in protein turnover are a cause or a consequence of ageing is not clear, and this question has not been a focal point of modern ageing research. Here we survey work on protein turnover and ageing and suggest that powerful genetic models such as the nematode Caenorhabditis elegans are well suited for a thorough investigation of this long-standing question.

Longevity and heavy metal resistance in daf-2 and age-1 long-lived mutants of Caenorhabditis elegans

In the nematode Caenorhabditis elegans, dauer formation, stress resistance, and longevity are determined in part by DAF-2 (insulin receptor-like protein), AGE-1 (phosphatidylinositol-3-OH kinase catalytic subunit), and DAF-16 (forkhead transcription factor). Mutations in daf-2 and age-1 result in increased resistance to heat, oxidants, and UV. We have discovered that daf-2 and age-1 mutations result in increased Cd and Cu ion resistance in a 24 h toxicity assay. Lethal concentration (LC50) values for Cd and Cu ions in daf-2 and age-1 mutants were significantly (P<0.001) higher than in wild-type nematodes. However, LC50 values in daf-16;age-1 mutants were not significantly different, implying that metal resistance is influenced by a DAF-16-related function. As metallothionein (MT) proteins play a major role in metal detoxification, we examined the expression of MT genes both under noninducing conditions and after exposure to sublethal and acute heavy metal stress. MT1 mRNA levels were significantly (P<0.05) higher in daf-2 mutants compared to age-1 mutants and wild-type C. elegans under basal conditions. After 10 mM Cd treatment, induction of MT1 and MT2 mRNA was three- and twofold higher, respectively, in daf-2 mutant worms than in wild-type. However, a sublethal concentration of Cd (0.1 mM) resulted in even higher (three- to sevenfold) levels of both MT mRNAs in all strains. Cu did not induce MT1 or MT2 mRNAs. These results are consistent with a model in which the insulin-signaling pathway determines life span through regulation of stress protein genes

Peroxide accumulation without major mitochondrial alteration in replicative senescence

The aim of this work was to determine how ageing changes were related to each other by studying the establishment of a senescent state in cell culture, rabbit articular chondrocytes. A striking increase of the amount of peroxides appeared at 2/3 of the time of cell growth, which is responsible for an oxidative stress, as shown by the appearance of oxidized proteins, the overexpression of HSP27 gene and the accumulation of HSP27 protein. While no change of the mitochondrial membrane potential was observed all along the cell culture, p21, a protein overproduced in senescent cells, appeared with the peak of peroxides and accumulated.

Mitochondrial DNA rearrangements in aging human brain and in situ PCR of mtDNA

Deletions of the mitochondrial DNA (mtDNA) have been shown to accumulate with age in a variety of species regardless of mean or maximal life span. This implies that such mutations are either a molecular biomarker of senescence or that they are more causally linked to senescence itself. One assay that can be used to detect these mtDNA mutations is the long-extension polymerase chain reaction assay. This assay amplifies approximately 16 kb of the mtDNA in mammalian mitochondria and preferentially amplifies mtDNAs that are either deleted or duplicated. We have applied this assay to the aging human brain and found a heterogeneous array of rearranged mtDNAs. In addition, we have developed in situ polymerase chain reaction to detect mtDNA within individual cells of both the mouse and the human brain as a first step in identifying and enumerating cells containing mutant mtDNAs in situ.

Mitochondria in organismal aging and degeneration

Several lines of experimentation support the view that the genetic, biochemical and bioenergetic functions of somatic mitochondria deteriorate during normal aging. Deletion mutations of the mitochondrial genome accumulate exponentially with age in nerve and muscle tissue of humans and multiple other species. In muscle, a tissue that undergoes age-related fiber loss and atrophy in humans, there is an exponential rise in the number of cytochrome-oxidase-deficient fibers, which is first detectable in the fourth decile of age. Most biochemical studies of animal mitochondrial activity indicate a decline in electron transport activity with age, as well as decreased bioenergetic capacity with age, as measured by mitochondrial membrane potential. Mitochondrial mutations may be both the result of mitochondrial oxidative stress, and cells bearing pure populations of pathogenic mitochondrial mutations are sensitized to oxidant stress. Oxidant stress to mitochondria is known to induce the mitochondrial permeability transition, which has recently been implicated in the release of cytochrome c and the initiation of apoptosis. Thus several lines of evidence support a contribution of mitochondrial dysfunction to the phenotypic changes associated with aging.

Mitochondrial DNA rearrangements, including partial duplications, occur in young and old rat tissues

Using polymerase chain reaction (PCR) with back-to-back primers, 85 different mitochondrial DNA (mtDNA) rearrangements, consisting of partial duplications or mini-circles, were detected in brain, liver, and heart tissue from Fischer 344 rats. The regions around the mitochondrial tRNALeu(UUR) gene, the cluster of three tRNA genes [His, Ser(AGY), Leu(UUC)], as well as the region of the displacement loop were analyzed separately with different primer sets. Rearrangements were detected in all regions analyzed in samples taken throughout the animal life span, ranging from 1 day old to 33 months of age (senescent). Two-thirds of the rearrangements terminated at short (3-9-bp) direct repeats. Three of the different rearrangements were detected in more than one animal; the most common rearrangement was found in nine different template preparations. Two loci (hot spots) were found to be particularly susceptible to rearrangement, and both were located at sequences that exhibited highly conserved potential for secondary structure formation. The displacement loop region of 10 samples exhibited the presence of multiple tandem duplications ranging between 324 and 449 bp in length. One of these consisted of heterologous, but overlapping, repeating units. Identical PCR protocols were carried out in control experiments using a cloned fragment of mtDNA that encompassed the most common hot spot sequence. The results showed that this fragment did not artifactually generate a rearrangement junction under our PCR conditions and suggested that this sequence does not promote rearrangement mutations in bacteria during the cloning process.

Analysis of oxygen consumption and mitochondrial permeability with age in mice

Biochemical and physiological parameters have been investigated in purified liver mitochondria from C57BL/6J mice of relatively young and old age, 1 month vs. 36 months. Under identical purification conditions, mitochondria from old animals consumed significantly less O2 under state 3 conditions (i.e. with saturating ADP stimulation), consistent with a lower activity of the electron transport chain. In the absence of ADP (i.e. state 4 conditions), old mitochondria consumed significantly more O2 than young mitochondria; one possible explanation was increased mitochondrial permeability as a result of induction of the mitochondrial permeability transition (MPT), and this was investigated by the mitochondrial swelling assay. In response to induction by 20 microM Ca2+, MPT rates were observed to be variable, but significantly faster in old mitochondria (t1/2 = 105 s) than in young mitochondria (t1/2 = 155 s), and in all cases MPT was inhibitable by cyclosporin A (CsA). The implications of lower state 3 respiration, higher state 4 respiration and increased rate of MPT in old mitochondria are discussed.

The rate of mitochondrial mutagenesis is faster in mice than humans

We have investigated mitochondrial DNA (mtDNA) mutagenesis in the laboratory mouse. Using a nested PCR method for quantification, the absolute frequency, tissue distribution and rate of increase of mitochondrial deletion mutations was determined. Multiple deletions arise in brain, cardiac muscle and kidney tissues: deletions occur most frequently at regions of directly repeated mtDNA homology. Deletion frequencies rose by 2.5 x 10(5), 6300- and 4000-fold in heart, brain and kidney, respectively, between young and old mice. The rates of mtDNA mutation accumulation in mouse and human hearts are modeled well by exponential equations, with r-values of 0.96 and 0.97, and mutations rose much faster in mouse than human mtDNA per unit time. Thus, maintenance of the human mitochondrial genome is much better than that of mice, consistent with the higher rate and final extent of total DNA repair in humans than mice, that has been observed by others and consistent with the predictions of the disposable soma model of aging. A comparison of mtDNA mutagenesis from cardiocytes vs. whole heart tissue was undertaken. Deletion mutations were observed to be 100-fold lower in DNA prepared from isolated cardiocytes than from whole heart homogenates, consistent with a model of uneven mtDNA mutation accumulation.

Age-associated alterations of the mitochondrial genome

Age-associated alterations of the mitochondrial genome occur in several different species; however, their physiological relevance remains unclear. The age-associated changes of mitochondrial DNA (mtDNA) include nucleotide point mutations and modifications, as well as deletions. In this review, we summarize the current literature on age-associated mtDNA mutations and deletions and comment on their abundance. A clear need exists for a more thorough evaluation of the total damage to the mitochondrial genome that accumulates in aged tissues.

Premature death in Podospora anserina: sporadic accumulation of the deleted mitochondrial genome, translational parameters and innocuity of the mating types

The Podospora anserina premature death syndrome was described as early growth arrest caused by a site-specific deletion of the mitochondrial genome (mtDNA) and occurring in strains displaying the genotype AS1-4 mat-. The AS1-4 mutation lies in a gene encoding a cytosolic ribosomal protein, while mat- is one of the two forms (mat- and mat+) of the mating-type locus. Here we show that, depending on culture conditions, death due to the accumulation of the deleted mtDNA molecule can occur in the AS1-4 mat+ context and can be delayed in the AS1-4 mat- background. Furthermore, we show that premature death and the classical senescence process are mutually exclusive. Several approaches permit the identification of the mat-linked gene involved in the appearance of premature death. This gene, rmp, exhibits two natural alleles, rmp- linked to mat- and rmp+ linked to mat+. The first is probably functional while the second probably carries a nonsense mutation and is sporadically expressed through natural suppression. A model is proposed that emphasizes the roles played by the AS1-4 mutation, the rmp gene, and environmental conditions in the accumulation of the deleted mitochondrial genome characteristic of this syndrome.

Invertebrate gerontology: the age mutations of Caenorhabditis elegans

Ageing is a complex phenomenon which remains a major challenge to modern biology. Although the evolutionary biology of ageing is well understood, the mechanisms that limit lifespan are unknown. The isolation and analysis of single-gene mutations which extend lifespan (Age mutations) is likely to reveal processes which influence ageing. Caenorhabditis elegans is the only metazoan in which Age mutations have been identified. The Age mutations not only prolong life, but also confer a complex array of other phenotypes. Some of these phenotypes provide clues to the evolutionary origins of these genes while others allude to mechanisms of lifespan-extension. Many of the Age genes interact and share a second common phenotype, that of stress resistance. Rather than invertebrate ageing being determined by a 'clock mechanism', a picture is emerging of ageing as a non-adaptive process determined, in part, by resistance to intrinsic stress mediated by stress-response genes.

Rearrangements in the shorter arc of rat mitochondrial DNA involving the region of the heavy and light strand promoters

Brain mtDNA from rats ranging in age from 1 day to 33 months were analyzed for large-scale rearrangements using nested PCR. The region of the mtDNA targeted by the primers was the shorter are between the two origins of replication and encompassed the heavy (H) and light (L) strand promoters (HSP) and (LSP). Rearrangements lacking 4 to 5 kb of genomic sequence were found in animals of all ages. Twenty-two different rearrangements were sequenced; two of these were found replicated in several different animals. All the rearrangements identified lacked an HSP and six lacked an LSP as well. The end points of each rearrangement had short direct repeats of 9 bp or less, but repeats of 4 bp or less were the most common. The mode of involvement of the direct repeats in the rearrangement mechanism varied since in some cases a sequence precisely equivalent to one member of the paired repeats was found at the junction; whereas in other cases, more or less than one complete member was found. Sixteen of the 22 rearrangements terminated on one side within a 22-bp locus, or hot spot, located at a potential stem-loop structure midway between the HSP and LSP. The other ends of these rearrangements were at different sites. In addition, a secondary hot spot was found near the junction between the tRNA(Ala) and tRNA(Asn) genes, which lie in a cluster of five tRNA genes that surround the stem-loop structure of the L-strand origin of replication. The data suggest a link between secondary structure and short direct repeats and the rearrangement mechanism(s). The results of this study, in conjunction with out previous study of the longer arc of rat mtDNA (Van Tuyle, G.C., J.P. Gudikote, V.H. Hurt, B.B. Miller and C.A. Moore (1996) Multiple, Large deletions in rat mitochondrial DNA: Evidence for a major hot spot, Mutation Res., 349, 95-107), indicate that nearly the entire mitochondrial genome is subject to rearrangement mutations that are detectable in brain tissue throughout an animal's life span.

Mitochondrial electron transport chain activities and DNA deletions in regions of the rat brain

Deletions in human mitochondrial DNA cause various mitochondrial myopathies and increase markedly with age in highly oxidative tissues, but exhibit a differential distribution in the brain. In order to determine whether a similar pattern occurs in rat brain the levels of a 4.8 kb deletion and electron transport complex activities were measured in the striatum, hippocampus, cerebellum, and cerebral cortex of young adult and senescent male Wistar rats. Deletion-containing mtDNA was present at relatively similar levels (0.0003%) in all regions in 6 mo rats, but increased 25-, 7-, 3-, and 2-fold in the striatum, hippocampus, cerebral cortex, and cerebellum, respectively, of 22-23 mo old rats. To assess the relationship between fractional occurrence of a deletion and oxidative phosphorylation capacity, the activities of mitochondrial respiratory chain complexes I, III, IV and V, the mitochondrial ATP-ase, each of which contains subunits encoded in mtDNA, were determined in homogenates. No age-related decrements in activity were observed in any of the brain regions. Thus, while mtDNA deletions increase with age and to a large extent mirror the pattern observed in the human brain, they appear to have no effect on capacity for oxidative phosphorylation of distinct brain regions. Any reductions in capacity that may be present are likely to occur only at the level of individual cells.

Multiple, large deletions in rat mitochondrial DNA: evidence for a major hot spot

This study identified 33 different deletions in mitochondrial DNA from four aging Fischer-344 rat brains and from a cultured rat lymphoma cell line (Nb2 cells). The deletions were located in the longer arc between the heavy and light strand origins of replication. PCR products that spanned across the deleted regions were sequenced, and deletions ranging between 6548 bp and 9977 bp in length were identified. Short direct repeats of < or = 8 bp were present at the end points of all but one of the deletions. The remaining deletion contained, instead, a near-perfect direct repeat (9/10 bp) within two base pairs of its end points. In 24 of the deletions, a sequence equivalent to one member of the paired direct repeats was lost with the deleted segment. In the remaining nine, either more or less of the base pairs of a single repeat were lost. Twelve of the 33 different deletions terminated on one side at a common locus (major hot spot) of 5 bp in length, located at the 5' end of the tRNAThr gene. The opposite ends of these 12 deletions were at different sites. The hot spot was located in a region of the mtDNA with strong potential for secondary structure and was flanked by a pair of AT-rich sequences. The utilization of the hot spot as an end point for deletions appeared to be widespread in that it was represented in 1/3-1/2 of the deletions characterized in each of the five mtDNA sources examined. In addition, several minor hot spots, where one end of two or three different deletions coincided, were also identified.