Screen for mitochondrial DNA copy number maintenance genes reveals essential role for ATP synthase

The machinery of mitochondrial DNA (mtDNA) maintenance is only partially characterized and is of wide interest due to its involvement in disease. To identify novel components of this machinery, plus other cellular pathways required for mtDNA viability, we implemented a genome‐wide RNAi screen in Drosophila S2 cells, assaying for loss of fluorescence of mtDNA nucleoids stained with the DNA‐intercalating agent PicoGreen. In addition to previously characterized components of the mtDNA replication and transcription machineries, positives included many proteins of the cytosolic proteasome and ribosome (but not the mitoribosome), three proteins involved in vesicle transport, some other factors involved in mitochondrial biogenesis or nuclear gene expression, > 30 mainly uncharacterized proteins and most subunits of ATP synthase (but no other OXPHOS complex). ATP synthase knockdown precipitated a burst of mitochondrial ROS production, followed by copy number depletion involving increased mitochondrial turnover, not dependent on the canonical autophagy machinery. Our findings will inform future studies of the apparatus and regulation of mtDNA maintenance, and the role of mitochondrial bioenergetics and signaling in modulating mtDNA copy number.

• Publication year

  2014

• Venue

  Molecular Systems Biology

• Publication date

  2014-06-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.15252/msb.20145117PMID 24952591PMCID 4265055
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2014cited by this paper
• To be or not to be a nucleoid protein: a comparison of mass-spectrometry based approaches in the identification of potential mtDNA-nucleoid associated proteins.

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• Mitochondrial Fusion Proteins and Human Diseases

  2013cited by this paper
• Tissue‐specific oxidative stress and loss of mitochondria in CoQ‐deficient Pdss2 mutant mice

  2013cited by this paper
• Replicating animal mitochondrial DNA

  2013cited by this paper
• Negative regulation of NF-κB signaling in T lymphocytes by the ubiquitin-specific protease USP34

  2013cited by this paper
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  2013cited by this paper
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  2013cited by this paper
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  2013cited by this paper
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  2013cited by this paper
• REXO2 Is an Oligoribonuclease Active in Human Mitochondria

  2013cited by this paper
• The maintenance of mitochondrial DNA integrity--critical analysis and update.

  2013cited by this paper
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  2013cited by this paper
• The role of mitochondria in aging.

  2013cited by this paper
• Declining NAD(+) induces a pseudohypoxic state disrupting nuclear-mitochondrial communication during aging.

  2013cited by this paper
• Mutations in FBXL4 cause mitochondrial encephalopathy and a disorder of mitochondrial DNA maintenance.

  2013cited by this paper
• Mitonuclear protein imbalance as a conserved longevity mechanism

  2013cited by this paper
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  2013cited by this paper
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  2013cited by this paper
• Mitochondrial Transcription Terminator Family Members mTTF and mTerf5 Have Opposing Roles in Coordination of mtDNA Synthesis

  2013influential reference
• Persistent damage induces mitochondrial DNA degradation.

  2013influential reference
• Loss-of-function mutations in MGME1 impair mtDNA replication and cause multisystemic mitochondrial disease

  2013influential reference
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  2012cited by this paper
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  2012cited by this paper
• A Deubiquitylating Complex Required for Neosynthesis of a Yeast Mitochondrial ATP Synthase Subunit

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• Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis

  2012cited by this paper
• A fresh start – but business as usual

  2012cited by this paper
• Mechanisms of mitochondrial diseases

  2012cited by this paper
• Mitochondrial DNA nucleoid structure.

  2012cited by this paper
• Glucose Modulates Respiratory Complex I Activity in Response to Acute Mitochondrial Dysfunction

  2012influential reference
• The impact of aging on mitochondrial function and biogenesis pathways in skeletal muscle of sedentary high‐ and low‐functioning elderly individuals

  2012cited by this paper
• Mitochondrial quality control mediated by PINK1 and Parkin: links to parkinsonism.

  2012cited by this paper
• Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number.

  2012influential reference
• MICS-1 interacts with mitochondrial ATAD-3 and modulates lifespan in C. elegans.

  2012cited by this paper
• Oligomycin frames a common drug-binding site in the ATP synthase

  2012cited by this paper
• LRPPRC/SLIRP suppresses PNPase-mediated mRNA decay and promotes polyadenylation in human mitochondria

  2012cited by this paper
• Identification of deubiquitinating enzymes involved in methylmercury toxicity in Saccharomyces cerevisiae.

  2012cited by this paper
• Loss of OPA1 disturbs cellular calcium homeostasis and sensitizes for excitotoxicity

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  2012cited by this paper
• Alternative oxidase rescues mitochondria-mediated dopaminergic cell loss in Drosophila.

  2012cited by this paper
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  2012cited by this paper
• APOPTOSIS INDUCED BY PERSISTENT SINGLE-STRAND BREAKS IN THE MITOCHONDRIAL GENOME: CRITICAL ROLE OF EXOG (5’ EXO/ENDONUCLEASE) IN THEIR REPAIR

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  2011cited by this paper
• NARP mutation and mtDNA depletion trigger mitochondrial biogenesis which can be modulated by selenite supplementation.

  2011cited by this paper
• Human papillomavirus infection and expression of ATPase family AAA domain containing 3A, a novel anti-autophagy factor, in uterine cervical cancer.

  2011cited by this paper
• In vivo protein-interaction mapping of a mitochondrial translocator protein Tom22 at work

  2011cited by this paper
• Involvement of DNA ligase III and ribonuclease H1 in mitochondrial DNA replication in cultured human cells

  2011cited by this paper
• OPA1 links human mitochondrial genome maintenance to mtDNA replication and distribution.

  2011cited by this paper
• Rhomboid-7 over-expression results in Opa1-like processing and malfunctioning mitochondria.

  2011cited by this paper
• Evolution Meets Disease: Penetrance and Functional Epistasis of Mitochondrial tRNA Mutations

  2011cited by this paper
• Actin and myosin contribute to mammalian mitochondrial DNA maintenance

  2011cited by this paper
• Regulation of mitochondrial protein import by cytosolic kinases.

  2011cited by this paper
• ATPase family AAA domain containing 3A is an anti-apoptotic factor and a secretion regulator of PSA in prostate cancer.

  2011cited by this paper
• Biochemical characterization of a multidomain deubiquitinating enzyme Ubp15 and the regulatory role of its terminal domains.

  2011cited by this paper
• Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function

  2011cited by this paper
• DNA Ligase III is critical for mtDNA integrity but not Xrcc1-mediated nuclear DNA repair

  2011cited by this paper
• Ubp15p, a Ubiquitin Hydrolase Associated with the Peroxisomal Export Machinery*

  2011cited by this paper
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  2010cited by this paper
• Yeast Exonuclease 5 Is Essential for Mitochondrial Genome Maintenance

  2010cited by this paper
• A stress-responsive system for mitochondrial protein degradation.

  2010cited by this paper
• Antioxidant defence systems and generation of reactive oxygen species in osteosarcoma cells with defective mitochondria: effect of selenium.

  2010cited by this paper
• The increase in the number of subunits in eukaryotic RNA polymerase III relative to RNA polymerase II is due to the permanent recruitment of general transcription factors.

  2010cited by this paper
• Mitochondrial Lon protease regulates mitochondrial DNA copy number and transcription by selective degradation of mitochondrial transcription factor A (TFAM)

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• Defects in mitochondrial DNA replication and human disease

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• The AAA+ ATPase ATAD3A Controls Mitochondrial Dynamics at the Interface of the Inner and Outer Membranes

  2010cited by this paper
• Emerging roles of mitochondrial proteases in neurodegeneration.

  2010cited by this paper
• Mitochondrial RNA polymerase is needed for activation of the origin of light-strand DNA replication.

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• LRPPRC and SLIRP Interact in a Ribonucleoprotein Complex That Regulates Posttranscriptional Gene Expression in Mitochondria

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• The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L

  2010cited by this paper
• Animal models of mitochondrial DNA transactions in disease and ageing.

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• Functional organization of mammalian mitochondrial DNA in nucleoids: History, recent developments, and future challenges

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  2008cited by this paper
• Ubiquitin-proteasome-dependent degradation of a mitofusin, a critical regulator of mitochondrial fusion.

  2008cited by this paper
• Structure of eukaryotic RNA polymerases.

  2008cited by this paper
• Mitochondrial Genome Integrity Mutations Uncouple the Yeast Saccharomyces cerevisiae ATP Synthase*

  2007cited by this paper
• OPA1 processing controls mitochondrial fusion and is regulated by mRNA splicing, membrane potential, and Yme1L

  2007cited by this paper
• Biochemical phenotypes associated with the mitochondrial ATP6 gene mutations at nt8993.

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  2007influential reference
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• A novel mitochondrial ubiquitin ligase plays a critical role in mitochondrial dynamics

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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2019influential citation
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  2019cites this paper
• Mitochondrial DNA alterations in aged macrophage migration inhibitory factor-knockout mice.

  2019cites this paper
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  2019cites this paper
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  2018cites this paper
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  2018cites this paper
• Mitochondria, its DNA and telomeres in ageing and human population

  2018cites this paper
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  2018cites this paper
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  2018cites this paper
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  2017cites this paper
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  2017cites this paper
• Animal Mitochondrial DNA Replication.

  2016cites this paper
• Familial longevity study reveals a significant association of mitochondrial DNA copy number between centenarians and their offspring.

  2016cites this paper
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  2015cites this paper
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  2015cites this paper
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  2015cites this paper
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  2015cites this paper
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