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Mitochondria and Aging

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 October 2017) | Viewed by 111610

Special Issue Editors


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Guest Editor
Department of Biology, Northeastern University, Boston, MA 02115, USA
Interests: basic biology of aging; dynamics of intracellular mitochondrial population; nuclear pseudogenes of mtDNA - NUMTs; human evolution; somatic mitochondrial DNA mutations, their abundance and relevance to human aging and disease
Special Issues, Collections and Topics in MDPI journals
Department of Biology, Northeastern University, Boston, MA, USA
Interests: female germline stem cells; mitochondria in health and disease; aging; reproductive health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aging is a remarkably complex phenomenon. Some of us believe that this complexity is no coincidence, that evolution of longevity inevitably drives the aging process to be complex and redundant. We only start to appreciate this complexity.

The Mitochondrial Theory of Aging gives an example of this trend. The Theory has emerged from Dedham Harman’s idea that mitochondrial reactive oxygen species are the primary driver of aging. Today we appreciate that, first, ROS are not necessarily bad and may actually have ameliorating effect on the aging organism, e.g., during exercise. Second, detrimental processes in the mitochondria are not necessarily related to ROS production, e.g., clonally accumulating somatic mtDNA mutations that merely impede mitochondrial respiration. In fact, at present there are several independent theories relating processes in mitochondria to aging. The apparent complexity of aging implies that these theories need not be competitors, contending for the title of “the Correct Theory of Aging”. I fact many of them may be equally correct and reflect the different facets of the aging process.

In this Special Issue, we welcome reviews, new methods, and original articles covering many possible roles the mitochondria may play in the aging process. We look forward to your contributions.

Prof. Dr. Konstantin Khrapko
Prof. Dr. Dori Woods
Guest Editors

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Keywords

  • mutation
  • mtDNA
  • mitochondria
  • exercise
  • aging
  • mitochondrial dysfunction
  • mitochondrial theory of aging
  • energetics and aging
  • oxidative damage
  • oxidative stress
  • protein turnover
  • mitochondrial dynamics
  • aging of the germ line
  • lipid peroxidation
  • apoptosis
  • evolution of aging
  • neurodegeneration
  • Alzheimer disease
  • Parkinson disease
  • sarcopenia

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Published Papers (11 papers)

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Research

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21 pages, 4846 KiB  
Article
Mitochondrial HTRA2 Plays a Positive, Protective Role in Dictyostelium discoideum but Is Cytotoxic When Overexpressed
by Suwei Chen, Oana Sanislav, Sarah J. Annesley and Paul R. Fisher
Genes 2018, 9(7), 355; https://doi.org/10.3390/genes9070355 - 16 Jul 2018
Cited by 9 | Viewed by 4126
Abstract
HTRA2 is a mitochondrial protein, mutations in which are associated with autosomal dominant late-onset Parkinson’s disease (PD). The mechanisms by which HTRA2 mutations result in PD are poorly understood. HTRA2 is proposed to play a proteolytic role in protein quality control and homeostasis [...] Read more.
HTRA2 is a mitochondrial protein, mutations in which are associated with autosomal dominant late-onset Parkinson’s disease (PD). The mechanisms by which HTRA2 mutations result in PD are poorly understood. HTRA2 is proposed to play a proteolytic role in protein quality control and homeostasis in the mitochondrial intermembrane space. Its loss has been reported to result in accumulation of unfolded and misfolded proteins. However, in at least one case, PD-associated HTRA2 mutation can cause its hyperphosphorylation, possibly resulting in protease hyperactivity. The consequences of overactive mitochondrial HTRA2 are not clear. Dictyostelium discoideum provides a well-established model for studying mitochondrial dysfunction, such as has been implicated in the pathology of PD. We identified a single homologue of human HTRA2 encoded in the Dictyostelium discoideum genome and showed that it is localized to the mitochondria where it plays a cytoprotective role. Knockdown of HTRA2 expression caused defective morphogenesis in the multicellular phases of the Dictyostelium life cycle. In vegetative cells, it did not impair mitochondrial respiration but nonetheless caused slow growth (particularly when the cells were utilizing a bacterial food source), unaccompanied by significant defects in the requisite endocytic pathways. Despite its protective roles, we could not ectopically overexpress wild type HTRA2, suggesting that mitochondrial HTRA2 hyperactivity is lethal. This toxicity was abolished by replacing the essential catalytic serine S300 with alanine to ablate serine protease activity. Overexpression of protease-dead HTRA2 phenocopied the effects of knockdown, suggesting that the mutant protein competitively inhibits interactions between wild type HTRA2 and its binding partners. Our results show that cytopathological dysfunction can be caused either by too little or too much HTRA2 activity in the mitochondria and suggest that either could be a cause of PD. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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Figure 1

Figure 1
<p>ClustalO sequence alignment of <span class="html-italic">Dictyostelium discoideum</span> and human HTRA2 sequences. The canonical HTRA2 protein in <span class="html-italic">Homo sapiens</span> contains 458 amino acids encoded by a gene 4152 bp long with eight exons and seven introns [<a href="#B33-genes-09-00355" class="html-bibr">33</a>], whereas in <span class="html-italic">D. discoideum</span>, it consists of 647 amino acids encoded by a 2023 bp gene with one intron. The three essential catalytic residues (the catalytic triad) are highlighted in red, including the conserved catalytic serine, substituted with alanine in this and previous work [<a href="#B33-genes-09-00355" class="html-bibr">33</a>]. The alignment was performed using ClustalO [<a href="#B34-genes-09-00355" class="html-bibr">34</a>], the mitochondrial leader peptide was predicted using Mitoprot II [<a href="#B35-genes-09-00355" class="html-bibr">35</a>] and the domains were identified using InterPro Scan [<a href="#B36-genes-09-00355" class="html-bibr">36</a>]. The human protein includes a propeptide that is removed during processing to form the mature protein [<a href="#B37-genes-09-00355" class="html-bibr">37</a>]. The <span class="html-italic">Dictyostelium</span> protein includes additional low complexity regions near the N- and C-termini. Such low complexity “additions” are common in <span class="html-italic">Dictyostelium</span> proteins.</p>
Full article ">Figure 2
<p><span class="html-italic">Dictyostelium</span> HTRA2 is located in the mitochondria. The top panels show live AX2 cells and the bottom panels are live transformants expressing HTRA2<sup>S300A</sup>:GFP, a GFP-tagged protease-dead mutant form of HTRA2. PH: phase contrast of the <span class="html-italic">D. discoideum</span> cells, DAPI: 4′, 6-diamidino-2-phenylindole, used to stain nuclei, GFP: green fluorescence protein, used to detect HTRA2<sup>S300A</sup>:GFP, Mitotracker: Mitotracker Red, used to stain mitochondria, Merge: the overlap of all the images. The differences in size and numbers of stained mitochondria between the wild type and transformed cells are coincidental—both of these features vary significantly from cell to cell even within the same preparation (see examples in [<a href="#B28-genes-09-00355" class="html-bibr">28</a>]).</p>
Full article ">Figure 3
<p>Expression of HTRA2 messenger RNA (mRNA) correlates with the copy numbers of the antisense-inhibition construct, pPROF689. The copy numbers of pPROF689 in HTRA2 antisense-inhibited transformants were measured by quantitative PCR (qPCR) and ranged from 28 to 252. The transcription of <span class="html-italic">htrA</span> was strongly correlated with the pPROF689 copy number (<span class="html-italic">p</span> = 6.2 × 10<sup>−5</sup>, quadratic regression, F test, <span class="html-italic">n</span> = 13). Error bars are standard errors from three independent experiments, each involving duplicate measurements. The previously established convention of using negative numbers for the antisense expression index was followed, so that <span class="html-italic">htrA</span> mRNA expression levels increase from left to right.</p>
Full article ">Figure 4
<p>Phenotypic consequences of reduced HTRA2 expression.</p>
Full article ">Figure 5
<p>Mitochondrial respiration is unaffected by HTRA2 knockdown. Seahorse respirometry was conducted in the indicated number (n) of independent experiments on wild type (AX2) cells and cells of four different HTRA2 knockdown strains (antisense construct copy numbers ranging from 96 to 163). Basal respiration (<b>a</b>) and its components attributable to adenosine triphosphate (ATP) synthesis (<b>c</b>) and “nonmitochondrial” respiration (<b>e</b>) were unaffected. The maximum respiration rate by carbonyl cyanide 3-chlorophenol hydrazone (CCCP)-uncoupled mitochondria (<b>b</b>) and its components attributable to Complex I (<b>d</b>) and Complex II activity (<b>f</b>) were not significantly affected. The copy number of the antisense construct had no significant effect on any of the parameters of respiration (Pearson correlation coefficient, n = 13, <span class="html-italic">p</span> &gt; 0.05).</p>
Full article ">Figure 6
<p>GFP mRNA is expressed in HTRA2: GFP fusion transformants, but the protein is not. HTRA2: GFP fusion transformants were isolated and shown to contain the full length <span class="html-italic">htrA</span> and GFP sequences (<a href="#app1-genes-09-00355" class="html-app">Figure S7</a>). The GFP mRNA was expressed in these transformants but the protein was not. (<b>a</b>) Transcription of GFP in DJ-1: GFP and HTRA2: GFP transformants. HPF1245 and HPF1246 are the DJ-1: GFP expression transformants and HPF1247, HPF1248 and HPF1249 are the HTRA2: GFP transformants. The GFP mRNA was measured and normalized against filamin. GFP coding sequence was transcribed in all GFP-tagged <span class="html-italic">D. discoideum</span> transformants. Error bars are standard errors of the mean from duplicate measurements. (<b>b</b>) Expression of GFP fusion protein in DJ-1:GFP and HTRA2:GFP transformants. The Western blot includes protein from AX2 (negative control), HPF1245 expressing GFP-tagged DJ-1 (52 kDa) (positive control), and HPF1247 and HPF1248 containing constructs for expressing GFP-tagged HTRA2. No GFP could be detected in the HTRA2:GFP transformants. The amount of protein loaded in each well was 300 μg (Bradford assay).</p>
Full article ">Figure 7
<p>Phenotypic consequences of protease-dead HTRA2<sup>S300A</sup> overexpression.</p>
Full article ">Figure 8
<p>Mitochondrial respiration is unaffected by overexpression of protease-dead HTRA2<sup>S300A</sup>. Seahorse respirometry was conducted in the indicated number (n) of independent experiments on wild type (AX2) cells and cells of four different HTRA2<sup>S300A</sup> overexpression strains (antisense construct copy numbers ranging from 90 to 312). Basal respiration <b>(a)</b> and its components attributable to ATP synthesis <b>(c)</b> and “non-mitochondrial” respiration <b>(e)</b> were unaffected. The maximum respiration rate by CCCP-uncoupled mitochondria <b>(b)</b> and its components attributable to Complex I <b>(d)</b> and Complex II <b>(f)</b> were also not significantly altered. The copy number of the HTRA2<sup>S300A</sup> overexpression construct had no significant effect on any of the parameters of respiration (Pearson correlation coefficient, n = 13, <span class="html-italic">p</span> &gt; 0.05).</p>
Full article ">Figure 8 Cont.
<p>Mitochondrial respiration is unaffected by overexpression of protease-dead HTRA2<sup>S300A</sup>. Seahorse respirometry was conducted in the indicated number (n) of independent experiments on wild type (AX2) cells and cells of four different HTRA2<sup>S300A</sup> overexpression strains (antisense construct copy numbers ranging from 90 to 312). Basal respiration <b>(a)</b> and its components attributable to ATP synthesis <b>(c)</b> and “non-mitochondrial” respiration <b>(e)</b> were unaffected. The maximum respiration rate by CCCP-uncoupled mitochondria <b>(b)</b> and its components attributable to Complex I <b>(d)</b> and Complex II <b>(f)</b> were also not significantly altered. The copy number of the HTRA2<sup>S300A</sup> overexpression construct had no significant effect on any of the parameters of respiration (Pearson correlation coefficient, n = 13, <span class="html-italic">p</span> &gt; 0.05).</p>
Full article ">
5712 KiB  
Article
Proliferation Cycle Causes Age Dependent Mitochondrial Deficiencies and Contributes to the Aging of Stem Cells
by Qiuting Ren, Fan Zhang and Hong Xu
Genes 2017, 8(12), 397; https://doi.org/10.3390/genes8120397 - 19 Dec 2017
Cited by 4 | Viewed by 5249
Abstract
In addition to chronological aging, stem cells are also subject to proliferative aging during the adult life span. However, the consequences of proliferative cycle and their contributions to stem cells aging have not been well investigated. Using Drosophila female germ line stem cells [...] Read more.
In addition to chronological aging, stem cells are also subject to proliferative aging during the adult life span. However, the consequences of proliferative cycle and their contributions to stem cells aging have not been well investigated. Using Drosophila female germ line stem cells as a model, we found that the replication cycle leads to the age dependent decline of female fecundity, and is a major factor causing developmental abnormalities in the progeny of old females. The proliferative aging does not cause telomere shortening, but causes an accumulation of mitochondrial DNA (mtDNA) mutations or rearrangements at the control region. We propose that damaging mutations on mtDNA caused by accumulation of proliferation cycles in aged stem cells may disrupt mitochondrial respiration chain and impair mtDNA replication and represent a conserved mechanism underlying stem cell aging. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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Figure 1

Figure 1
<p>Mitochondrial DNA (mtDNA) rearrangements and impaired mtDNA replication in ovaries of aged flies. (<b>A</b>) Schematic drawing of <span class="html-italic">Drosophila melanogaster</span> (Dm.) mtDNA. Enzyme sites of HindIII (H) and XhoI (X) are indicated. Sizes of digested fragments are also labelled. (<b>B</b>) Representative gel image of rolling cycle amplification of mtDNA (arrowhead) and DNA marker (M, kb). (<b>C</b>) Pattern of rolling cycle amplification (RCA) amplified mtDNA digested by XhoI and HindIII. The 5.8 kb fragment spanning the AT-rich region was recovered for restriction fragment length polymorphism (RFLP) analysis. (<b>D</b>) Schematic map of SspI site on 5.8 kb AT-rich region. (<b>E</b>) densitometry plot of SspI digestion pattern of 5.8 fragments spanning the AT-rich region from young (2-day-old) and old (60-day-old) ovaries, analyzed by Agilent Bioanalyzer 2100. Note the difference of bands (open arrowheads) demonstrating the rearrangements of AT-rich regions in aged ovaries. DNA dye standard (closed arrowheads) and DNA ladder are marked (M, bp). (<b>F</b>) Representative images showing 5-ethynyl-2’-deoxyuridine (EdU) incorporation into mtDNA (green puncta, arrowheads) in ovaries (dashed line, anterior toward left) from young (2-day-old) and old (40-day-old) female flies. Note that the number of EdU puncta was dramatically reduced in germarium from old fly. Arrowhead: mtDNA; arrow: nuclear DNA; scale bar: 10 µm.</p>
Full article ">Figure 2
<p>Germline stem cell (GSC) proliferation cycle contributes to the age dependent decline of female fecundity and progeny’s fitness. (<b>A</b>,<b>B</b>). Representative images of germarium from 1-week-old mated (<b>A</b>) or virgin (<b>B</b>) female, stained with anti-VASA (green) for germ line cells and anti- phosphorylated histone H3 (P-H3, red) for mitotic cells. In mated flies, dividing GSC (arrowhead) and germ cell cysts (arrows) are present. Scale bar: 10 µm. (<b>C</b>) Quantification of mitotic germ cells in germaria of mated and virgin female flies. No. (#) of mitotic germ cells flies is significantly less in virgin than mated flies (<span class="html-italic">n</span> = 100 germaria, <span class="html-italic">p</span> &lt; 0.001). We also counted the P-H3 positive GSCs. There were 13 dividing GSCs in total from 100 germaria of mated female flies, but only four out of 100 virgin females. (<b>D</b>) Female fecundity was assayed by calculating the average egg production per female per day over 40 days. (<b>E</b>) Egg hatching rates plotted over maternal age. Black line, mated female flies; red line, female flies maintained as virgins for two weeks after eclosion. A total of 150 female flies were used for each group in (<b>D</b>,<b>E</b>). Each group was assayed in 30 vials with five female flies in each vial. Arrowhead, time point when virgin flies were mated with males.</p>
Full article ">Figure 3
<p>Aging does not lead to telomere shortening in GSCs. (<b>A</b>) Total DNA from the ovaries of young (2-day-old) and old (60-day-old) females were prepared and the copy numbers of three telomeric transposons <span class="html-italic">Het-A</span>, <span class="html-italic">TARAE</span> and <span class="html-italic">TART-A1</span> were determined by real time PCR and plotted (<span class="html-italic">n</span> = 3). A non-telomeric transposon <span class="html-italic">Joecy</span> was used as an internal control. (<b>B</b>) Quantifications of telomere (tel.) DNA contents by normalizing fluorescence in situ hybridization (FISH) signal of telomere DNA with FISH signal of his4 locus in GSCs of young and old females. No significant difference between young and old GSCs (<span class="html-italic">n</span> = 100 for each group). (<b>C</b>,<b>D</b>) Representative images of two color FISH against telomere DNA (green, mix of three probes against all three telomeric transposons) and <span class="html-italic">his4</span> locus (red) in young ((<b>C</b>), 2-day-old) and old ((<b>D</b>), 60-day-old) germaria. Box regions were enlarged for better illustrations of telomere DNA (arrowheads) and <span class="html-italic">his4</span> locus (arrows). Scale bar: 5 µm.</p>
Full article ">Figure 4
<p>Aged GSCs have increased mtDNA mutation loads and defective electron transport chain complexes. (<b>A</b>) Cross scheme to assay the influence of maternal age (F0) on mtDNA mutation frequency in progeny (F1), as an indication of mtDNA mutation loads in F0 GSCs. (<b>B</b>) The different groups of F1 females expressing mitoXhoI in germ cells (<span class="html-italic">UASp-MitoXhoI/+; nanos-gal4/+, n</span> &gt; 100) were produced by the same group of F0 females (<span class="html-italic">nanos-gal4</span>) at different ages. The frequency of fertile F1 females, as an indication of mtDNA mutation frequency in F0 GSCs is plotted against age of F0 females. The positive correlation between the number of fertile F1 females and the age of F0 females suggests that there were more mtDNA mutations in older GSCs in F0 females. (<b>C</b>) Ovaries of young (2-day-old) or old (60-day-old) females that were either mated with males or maintained as virgins were stained for dual succinate dehydrogenase and cytochrome C oxidase (COX) activity. The representative images and their percentage (<span class="html-italic">n</span> = 20) for each group are shown. Nearly 100% of ovaries of young mated females, young virgins and old virgins displayed normal COX activity (brown color). Note that the anterior part of the germarium (boxed and enlarged view), the location of stem cells and early stage cysts are nearly colorless, showing that mitochondria are mostly inactive in this developmental stage. In addition, 55% of ovaries from old mated females were completely lacking in COX activity (blue color). Forty percent of ovaries from old mated flies (inserted panel) showed a mosaic pattern of normal and deficient COX activity (arrowheads), suggesting that COX is normal in one germ line stem cell, but disrupted in another one in the same ovariole.</p>
Full article ">

Review

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19 pages, 2457 KiB  
Review
Influence of Maternal Aging on Mitochondrial Heterogeneity, Inheritance, and Function in Oocytes and Preimplantation Embryos
by Dori C. Woods, Konstantin Khrapko and Jonathan L. Tilly
Genes 2018, 9(5), 265; https://doi.org/10.3390/genes9050265 - 21 May 2018
Cited by 38 | Viewed by 7620
Abstract
Contrasting the equal contribution of nuclear genetic material from maternal and paternal sources to offspring, passage of mitochondria, and thus mitochondrial DNA (mtDNA), is uniparental through the egg. Since mitochondria in eggs are ancestral to all somatic mitochondria of the next generation and [...] Read more.
Contrasting the equal contribution of nuclear genetic material from maternal and paternal sources to offspring, passage of mitochondria, and thus mitochondrial DNA (mtDNA), is uniparental through the egg. Since mitochondria in eggs are ancestral to all somatic mitochondria of the next generation and to all cells of future generations, oocytes must prepare for the high energetic demands of maturation, fertilization and embryogenesis while simultaneously ensuring that their mitochondrial genomes are inherited in an undamaged state. Although significant effort has been made to understand how the mtDNA bottleneck and purifying selection act coordinately to prevent silent and unchecked spreading of invisible mtDNA mutations through the female germ line across successive generations, it is unknown if and how somatic cells of the immediate next generation are spared from inheritance of detrimental mtDNA molecules. Here, we review unique aspects of mitochondrial activity and segregation in eggs and early embryos, and how these events play into embryonic developmental competency in the face of advancing maternal age. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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Figure 1

Figure 1
<p>Confocal photomicrographs of mitochondrial distribution patterns in mouse oocytes. Oocytes collected from adult female mice following hormone stimulation-induced superovulation were classified as metaphase-II (extruded first polar body), and then incubated with MitoTracker Red (Thermo Fisher Scientific, Waltham, MA). Oocytes were immediately coverslipped and imaged using a Zeiss laser scanning confocal microscope. Mitochondria are noticeably punctate and present throughout the oocyte. Examples demonstrate multiple focal planes, with perinuclear distribution (indicated by white asterisk), and a polar body (p) is visible in the top right panel. Scale bar = 15 μm.</p>
Full article ">Figure 2
<p>Mitochondrial ultrastructural features, as determined by transmission electron microscopy, in primary-stage oocytes contained within follicles of reproductive-age human ovaries: (<b>A</b>) Mitochondria are localized as clusters (mitochondrial clusters; mc) within oocytes. The oocyte-granulosa cell interface (i) is also depicted, and demonstrates areas of interdigitation between the oocyte and surrounding granulosa cells. Scale bar = 200 µm. (<b>B</b>,<b>C</b>) Mitochondrial morphology (m) depicted at two magnifications reveals that most mitochondria exhibit an ovoid morphology, dense matrices, and few cristae. However, a large variation in mitochondrial size can be observed, along with multiple examples of mitochondria that fall outside of the characteristic morphology described above. Tissues were collected and prepared for TEM by non-coagulative aldehyde fixation, followed by sectioning on an ultramicrotome. Images were acquired using a JEOL JEM-1010 transmission electron microscope.</p>
Full article ">
9 pages, 223 KiB  
Review
Brain Mitochondria, Aging, and Parkinson’s Disease
by Mario Rango and Nereo Bresolin
Genes 2018, 9(5), 250; https://doi.org/10.3390/genes9050250 - 11 May 2018
Cited by 61 | Viewed by 6847
Abstract
This paper reconsiders the role of mitochondria in aging and in Parkinson’s Disease (PD). The most important risk factor for PD is aging. Alterations in mitochondrial activity are typical of aging. Mitochondrial aging is characterized by decreased oxidative phosphorylation, proteasome activity decrease, altered [...] Read more.
This paper reconsiders the role of mitochondria in aging and in Parkinson’s Disease (PD). The most important risk factor for PD is aging. Alterations in mitochondrial activity are typical of aging. Mitochondrial aging is characterized by decreased oxidative phosphorylation, proteasome activity decrease, altered autophagy, and mitochondrial dysfunction. Beyond declined oxidative phosphorylation, mitochondrial dysfunction consists of a decline of beta-oxidation as well as of the Krebs cycle. Not inherited mitochondrial DNA (mtDNA) mutations are acquired over time and parallel the decrease in oxidative phosphorylation. Many of these mitochondrial alterations are also found in the PD brain specifically in the substantia nigra (SN). mtDNA deletions and development of respiratory chain deficiency in SN neurons of aged individuals as well as of individuals with PD converge towards a shared pathway, which leads to neuronal dysfunction and death. Finally, several nuclear genes that are mutated in hereditary PD are usually implicated in mitochondrial functioning to a various extent and their mutation may cause mitochondrial impairment. In conclusion, a tight link exists between mitochondria, aging, and PD. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
12 pages, 5971 KiB  
Review
Roles of Mitochondrial DNA Mutations in Stem Cell Ageing
by Tianhong Su, Doug M. Turnbull and Laura C. Greaves
Genes 2018, 9(4), 182; https://doi.org/10.3390/genes9040182 - 27 Mar 2018
Cited by 16 | Viewed by 9341
Abstract
Mitochondrial DNA (mtDNA) mutations accumulate in somatic stem cells during ageing and cause mitochondrial dysfunction. In this review, we summarize the studies that link mtDNA mutations to stem cell ageing. We discuss the age-related behaviours of the somatic mtDNA mutations in stem cell [...] Read more.
Mitochondrial DNA (mtDNA) mutations accumulate in somatic stem cells during ageing and cause mitochondrial dysfunction. In this review, we summarize the studies that link mtDNA mutations to stem cell ageing. We discuss the age-related behaviours of the somatic mtDNA mutations in stem cell populations and how they potentially contribute to stem cell ageing by altering mitochondrial properties in humans and in mtDNA-mutator mice. We also draw attention to the diverse fates of the mtDNA mutations with different origins during ageing, with potential selective pressures on the germline inherited but not the somatic mtDNA mutations. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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Figure 1

Figure 1
<p>Immunofluorescence images of the respiratory chain deficiency caused by the age-dependent accumulation of somatic mitochondrial DNA (mtDNA) mutations in the colon. Respiratory chain complex IV (marked by the COX1 antibody) is encoded by both mtDNA and nuclear DNA (nDNA), which is affected by the increased burden of mtDNA mutations. Complex II (labelled by the SDHA antibody) is entirely encoded by nDNA. The complex IV deficient colonic cells are indicated red in the merged picture. COX1, a key subunit of complex IV encoded by mtDNA. SDHA, one of the four nuclear encoded subunits of complex II. Scale bar: 50 µm.</p>
Full article ">Figure 2
<p>Schematic diagram of how the mitochondrial abnormalities caused by the age-dependent accumulation of somatic mtDNA mutations affect stem cell homeostasis in the mtDNA mutator mice. Mitochondrial DNA mutagenesis causes minor changes in reactive oxygen species (ROS)/redox level, which may alter stem cell identity (quiescence and regeneration). The somatic mtDNA mutation increases apoptosis and also shifts the level of mitophagy/autophagy in the stem cell population possibly through the loss of the mitochondrial membrane potential (MMP), which may eventually engender stem cell/progenitor depletion and accelerate stem cell senescence. Mitochondrial DNA mutagenesis imbalances mitochondrial dynamics towards fission independent of ATP production, which can affect stem cell self-renewal and differentiation. The amassing of somatic mtDNA mutations prevents stem cells from converting glycolysis to oxidative phosphorylation (OXPHOS) as they differentiate, resulting in cell death and failure to produce progenies. Normal mitochondria are coloured orange and dysfunctional mitochondria are in blue. Mutated mtDNA are red and the normal mtDNA are blue.</p>
Full article ">
13 pages, 1531 KiB  
Review
Is There Still Any Role for Oxidative Stress in Mitochondrial DNA-Dependent Aging?
by Gábor Zsurka, Viktoriya Peeva, Alexander Kotlyar and Wolfram S. Kunz
Genes 2018, 9(4), 175; https://doi.org/10.3390/genes9040175 - 21 Mar 2018
Cited by 46 | Viewed by 6533
Abstract
Recent deep sequencing data has provided compelling evidence that the spectrum of somatic point mutations in mitochondrial DNA (mtDNA) in aging tissues lacks G > T transversion mutations. This fact cannot, however, be used as an argument for the missing contribution of reactive [...] Read more.
Recent deep sequencing data has provided compelling evidence that the spectrum of somatic point mutations in mitochondrial DNA (mtDNA) in aging tissues lacks G > T transversion mutations. This fact cannot, however, be used as an argument for the missing contribution of reactive oxygen species (ROS) to mitochondria-related aging because it is probably caused by the nucleotide selectivity of mitochondrial DNA polymerase ? (POLG). In contrast to point mutations, the age-dependent accumulation of mitochondrial DNA deletions is, in light of recent experimental data, still explainable by the segregation of mutant molecules generated by the direct mutagenic effects of ROS (in particular, of HO· radicals formed from H2O2 by a Fenton reaction). The source of ROS remains controversial, because the mitochondrial contribution to tissue ROS production is probably lower than previously thought. Importantly, in the discussion about the potential role of oxidative stress in mitochondria-dependent aging, ROS generated by inflammation-linked processes and the distribution of free iron also require careful consideration. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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Figure 1

Figure 1
<p>Atomic force microscopy (AFM) image of mitochondrial DNA (mtDNA) isolated from human skeletal muscle (essentially as described by [<a href="#B36-genes-09-00175" class="html-bibr">36</a>]) by phenol extraction. The DNA molecules (0.6 ng/mL) were deposited on freshly cleaved mica in 4 mM HEPES-K (pH 7.4), 2 mM MgCl<sub>2</sub>, and 10 mM NaCl for 5 min. The surface was rinsed with ultrapure distilled water and dried by blowing nitrogen gas. AFM imaging was performed on a Solver PRO AFM system (NT-MDT, Moscow, Russia), in a semicontact (tapping) mode, using Si-gold-coated cantilevers (NT-MDT) with a resonance frequency of 80–110 kHz. Molecules 1 and 2 are supercoiled and molecule 3 is linear mtDNA, all having a contour length of 5 µm.</p>
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<p>Southern blot showing the time course of native mtDNA damage caused by 1 mM H<sub>2</sub>O<sub>2</sub> and followed by the DNA repair by HEK293 cells. M: molecular weight marker; 0: control DNA (from untreated cells); The cells were exposed to 1 mM H<sub>2</sub>O<sub>2</sub> and harvested after 30 min, 2 h, 4 h, 6 h, 24 h, respectively. 1 µg of total DNA was loaded on a 0.6% agarose gel prepared in tris-borate-EDTA (TBE) buffer and was run in the presence of 0.5 µg/mL ethidium bromide overnight at 40 V. After alkaline treatment and re-neutralization of the gel, the DNA was blotted to a Zeta-Probe membrane (Bio-Rad, Hercules, CA, USA) and immobilized by baking at 80 °C for 30 min. The blot was hybridized with a MT-ND6 probe.</p>
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20 pages, 615 KiB  
Review
Targeting Mitochondria to Counteract Age-Related Cellular Dysfunction
by Corina T. Madreiter-Sokolowski, Armin A. Sokolowski, Markus Waldeck-Weiermair, Roland Malli and Wolfgang F. Graier
Genes 2018, 9(3), 165; https://doi.org/10.3390/genes9030165 - 16 Mar 2018
Cited by 43 | Viewed by 10649
Abstract
Senescence is related to the loss of cellular homeostasis and functions, which leads to a progressive decline in physiological ability and to aging-associated diseases. Since mitochondria are essential to energy supply, cell differentiation, cell cycle control, intracellular signaling and Ca2+ sequestration, fine-tuning [...] Read more.
Senescence is related to the loss of cellular homeostasis and functions, which leads to a progressive decline in physiological ability and to aging-associated diseases. Since mitochondria are essential to energy supply, cell differentiation, cell cycle control, intracellular signaling and Ca2+ sequestration, fine-tuning mitochondrial activity appropriately, is a tightrope walk during aging. For instance, the mitochondrial oxidative phosphorylation (OXPHOS) ensures a supply of adenosine triphosphate (ATP), but is also the main source of potentially harmful levels of reactive oxygen species (ROS). Moreover, mitochondrial function is strongly linked to mitochondrial Ca2+ homeostasis and mitochondrial shape, which undergo various alterations during aging. Since mitochondria play such a critical role in an organism’s process of aging, they also offer promising targets for manipulation of senescent cellular functions. Accordingly, interventions delaying the onset of age-associated disorders involve the manipulation of mitochondrial function, including caloric restriction (CR) or exercise, as well as drugs, such as metformin, aspirin, and polyphenols. In this review, we discuss mitochondria’s role in and impact on cellular aging and their potential to serve as a target for therapeutic interventions against age-related cellular dysfunction. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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<p>Biphasic alterations of mitochondrial function during aging. ETC: Electron transport chain, ROS: Reactive oxygen species, Mito: Mitochondrial, MtDNA: Mitochondrial desoxyribonucleic acid. Created using Servier Medical Art (Les Laboratoires Servier, Suresnes, France).</p>
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13 pages, 444 KiB  
Review
The Aging Mitochondria
by Pierre Theurey and Paola Pizzo
Genes 2018, 9(1), 22; https://doi.org/10.3390/genes9010022 - 9 Jan 2018
Cited by 74 | Viewed by 21994
Abstract
Mitochondrial dysfunction is a central event in many pathologies and contributes as well to age-related processes. However, distinguishing between primary mitochondrial dysfunction driving aging and a secondary mitochondrial impairment resulting from other cell alterations remains challenging. Indeed, even though mitochondria undeniably play a [...] Read more.
Mitochondrial dysfunction is a central event in many pathologies and contributes as well to age-related processes. However, distinguishing between primary mitochondrial dysfunction driving aging and a secondary mitochondrial impairment resulting from other cell alterations remains challenging. Indeed, even though mitochondria undeniably play a crucial role in aging pathways at the cellular and organismal level, the original hypothesis in which mitochondrial dysfunction and production of free radicals represent the main driving force of cell degeneration has been strongly challenged. In this review, we will first describe mitochondrial dysfunctions observed in aged tissue, and how these features have been linked to mitochondrial reactive oxygen species (ROS)–mediated cell damage and mitochondrial DNA (mtDNA) mutations. We will also discuss the clues that led to consider mitochondria as the starting point in the aging process, and how recent research has showed that the mitochondria aging axis represents instead a more complex and multifactorial signaling pathway. New working hypothesis will be also presented in which mitochondria are considered at the center of a complex web of cell dysfunctions that eventually leads to cell senescence and death. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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<p>Mitochondrial Health at the center of a Cause–Consequence cell crossroad. The original, simplistic view of the Mitochondrial Free Radical Theory of Aging (MFRTA), postulating a mitochondrial activity/ROS/mtDNA isolated interaction, was progressively replaced by a more integrative view in which healthy mitochondria are the result of multiple cellular pathways and activities, impacting different aspects of aging, in diverse tissues and in different manners. See text for details.</p>
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1141 KiB  
Review
The Mitochondrial Basis of Aging and Age-Related Disorders
by Sarika Srivastava
Genes 2017, 8(12), 398; https://doi.org/10.3390/genes8120398 - 19 Dec 2017
Cited by 260 | Viewed by 24711
Abstract
Aging is a natural phenomenon characterized by progressive decline in tissue and organ function leading to increased risk of disease and mortality. Among diverse factors that contribute to human aging, the mitochondrial dysfunction has emerged as one of the key hallmarks of aging [...] Read more.
Aging is a natural phenomenon characterized by progressive decline in tissue and organ function leading to increased risk of disease and mortality. Among diverse factors that contribute to human aging, the mitochondrial dysfunction has emerged as one of the key hallmarks of aging process and is linked to the development of numerous age-related pathologies including metabolic syndrome, neurodegenerative disorders, cardiovascular diseases and cancer. Mitochondria are central in the regulation of energy and metabolic homeostasis, and harbor a complex quality control system that limits mitochondrial damage to ensure mitochondrial integrity and function. The intricate regulatory network that balances the generation of new and removal of damaged mitochondria forms the basis of aging and longevity. Here, I will review our current understanding on how mitochondrial functional decline contributes to aging, including the role of somatic mitochondrial DNA (mtDNA) mutations, reactive oxygen species (ROS), mitochondrial dynamics and quality control pathways. I will further discuss the emerging evidence on how dysregulated mitochondrial dynamics, mitochondrial biogenesis and turnover mechanisms contribute to the pathogenesis of age-related disorders. Strategies aimed to enhance mitochondrial function by targeting mitochondrial dynamics, quality control, and mitohormesis pathways might promote healthy aging, protect against age-related diseases, and mediate longevity. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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<p>Mitochondrial dysfunction during aging and age-related disorders. Aging is associated with progressive mitochondrial dysfunction that occurs due to accumulation of mitochondrial DNA (mtDNA) mutations and increased reactive oxygen species (ROS) production that causes oxidative damage to cellular macromolecules, thereby leading to reduced respiratory chain activity and adenosine triphosphate (ATP) generation. Mitochondrial fission and fusion play a vital role in the regulation of mitochondrial function, metabolism and quality control. Altered mitochondrial dynamics with chronological age can inhibit mitophagy leading to accumulation of damaged or dysfunctional mitochondria in cells. Moreover, decline in mitophagy with increasing age prevents clearance of dysfunctional mitochondria leading to further mitochondrial damage accrual and deterioration of cellular function. Genetic mutations or functional declines in mitochondrial dynamics and quality control are thus linked to pathogenesis of numerous age-related disorders including metabolic syndrome, neurodegenerative and cardiovascular diseases as well as cancer.</p>
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<p>Crosstalk between mitochondrial biogenesis and mitophagy. The crosstalk or coordination between the two opposing processes i.e., selective elimination of damaged or dysfunctional mitochondria by mitophagy and generation of newly synthesized mitochondria by mitochondrial biogenesis is pivotal for the maintenance of mitochondrial energy and cellular homeostasis in response to various physiological and environmental cues.</p>
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530 KiB  
Review
Mitochondria and ?-Synuclein: Friends or Foes in the Pathogenesis of Parkinson’s Disease?
by Gaia Faustini, Federica Bono, Alessandra Valerio, Marina Pizzi, PierFranco Spano and Arianna Bellucci
Genes 2017, 8(12), 377; https://doi.org/10.3390/genes8120377 - 8 Dec 2017
Cited by 53 | Viewed by 7923
Abstract
Parkinson’s disease (PD) is a movement disorder characterized by dopaminergic nigrostriatal neuron degeneration and the formation of Lewy bodies (LB), pathological inclusions containing fibrils that are mainly composed of ?-synuclein. Dopaminergic neurons, for their intrinsic characteristics, have a high energy demand that relies [...] Read more.
Parkinson’s disease (PD) is a movement disorder characterized by dopaminergic nigrostriatal neuron degeneration and the formation of Lewy bodies (LB), pathological inclusions containing fibrils that are mainly composed of ?-synuclein. Dopaminergic neurons, for their intrinsic characteristics, have a high energy demand that relies on the efficiency of the mitochondria respiratory chain. Dysregulations of mitochondria, deriving from alterations of complex I protein or oxidative DNA damage, change the trafficking, size and morphology of these organelles. Of note, these mitochondrial bioenergetics defects have been related to PD. A series of experimental evidence supports that ?-synuclein physiological action is relevant for mitochondrial homeostasis, while its pathological aggregation can negatively impinge on mitochondrial function. It thus appears that imbalances in the equilibrium between the reciprocal modulatory action of mitochondria and ?-synuclein can contribute to PD onset by inducing neuronal impairment. This review will try to highlight the role of physiological and pathological ?-synuclein in the modulation of mitochondrial functions. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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<p>Effects of physiological and aggregated α-synuclein on mitochondria. (<b>A</b>) <b>1:</b> α-Synuclein controls protein targeting and mitochondrial morphology. <b>2:</b> Interaction with mitochondria-associated ER membranes (MAM). <b>3:</b> Interaction with adenosine triphosphate (ATP) synthase. (<b>B</b>) <b>4:</b> Inhibitory action of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and Rotenone on complex I is fostered by α-synuclein. <b>5:</b> Complex I dysfunction. <b>6:</b> Impaired mitochondrial protein import. <b>7:</b> Mitochondrial fragmentation and mitophagy. <b>8:</b> Release of cytochrome C. <b>9:</b> Upregulation of inducible nitric oxide synthase (iNOS) and nitric oxide generation.</p>
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12 pages, 1243 KiB  
Perspective
Resolving the Enigma of the Clonal Expansion of mtDNA Deletions
by Axel Kowald and Thomas B.L. Kirkwood
Genes 2018, 9(3), 126; https://doi.org/10.3390/genes9030126 - 27 Feb 2018
Cited by 29 | Viewed by 5497
Abstract
Mitochondria are cell organelles that are special since they contain their own genetic material in the form of mitochondrial DNA (mtDNA). Damage and mutations of mtDNA are not only involved in several inherited human diseases but are also widely thought to play an [...] Read more.
Mitochondria are cell organelles that are special since they contain their own genetic material in the form of mitochondrial DNA (mtDNA). Damage and mutations of mtDNA are not only involved in several inherited human diseases but are also widely thought to play an important role during aging. In both cases, point mutations or large deletions accumulate inside cells, leading to functional impairment once a certain threshold has been surpassed. In most cases, it is a single type of mutant that clonally expands and out-competes the wild type mtDNA, with different mutant molecules being amplified in different cells. The challenge is to explain where the selection advantage for the accumulation comes from, why such a large range of different deletions seem to possess this advantage, and how this process can scale to species with different lifespans such as those of rats and man. From this perspective, we provide an overview of current ideas, present an update of our own proposal, and discuss the wider relevance of the phenomenon for aging. Full article
(This article belongs to the Special Issue Mitochondria and Aging)
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<p>The replication of mitochondrial DNA (mtDNA) in vertebrates is primed via processed mRNA molecules [<a href="#B22-genes-09-00126" class="html-bibr">22</a>,<a href="#B23-genes-09-00126" class="html-bibr">23</a>]. We propose that a product inhibition exists that diminishes transcription (−), and thus replication, if sufficient proteins are available. If a deletion event eliminates the genes for proteins that participate in this feedback, transcription and also replication will not be downregulated in such mutants, resulting in a replication advantage (+).</p>
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<p>Locations of mtDNA deletions found in rats [<a href="#B2-genes-09-00126" class="html-bibr">2</a>] (top left), rhesus monkeys [<a href="#B3-genes-09-00126" class="html-bibr">3</a>] (top right), and humans [<a href="#B27-genes-09-00126" class="html-bibr">27</a>,<a href="#B28-genes-09-00126" class="html-bibr">28</a>] (bottom). The highlighted area indicates a stretch of mtDNA that is common to all 30 deletions in rat, 38 of 39 deletions in rhesus monkey, all 89 deletions in human neurons (left bottom), and 46 of 48 deletions in human muscle (right bottom). Redrawn from [<a href="#B10-genes-09-00126" class="html-bibr">10</a>].</p>
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<p>Deletion spectrum of mtDNA deletions found in mice, taken from the MitoBreak database [<a href="#B25-genes-09-00126" class="html-bibr">25</a>]. The data come from 24 publications that studied various tissues using different techniques. The highlighted area indicates a stretch of mtDNA deleted in a total of 236 of the 245 mice samples around the nicotinamide adenine dinucleotide dehydrogenase (NADH) subunit 4 gene (<span class="html-italic">ND4</span>) and <span class="html-italic">ND5</span> genes. The remaining nine deletions are shown in red.</p>
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<p>Results of computer simulations of the proposed feedback mechanism for the accumulation of mtDNA deletion mutants. It shows the timespan required from the occurrence of the deletion mutant until the complete takeover of the mitochondrial population depending on the ratio of the transcription rates. Wild type; wt.</p>
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<p>Results of stochastic computer simulations for different species lifespans and different hypotheses (filled circles: random drift, open circles: smaller genome size, filled triangles: replication via transcription) explaining the accumulation of deletion mutants. Only the idea that replication is controlled via a transcriptional feedback leads to the low level of heteroplasmy observed in short lived species. Modified from [<a href="#B10-genes-09-00126" class="html-bibr">10</a>].</p>
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