Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000263

Natalya P. Degtyareva, Natalie Saini, Joan F. Sterling, Victoria C. Placentra, Leszek J. Klimczak, Dmitry A. Gordenin, Paul W. Doetsch

• The authors report on the mutational spectra of redox stress in single-stranded DNA of budding yeast and in human mitochondrial DNA in the context of healthy aging, finding that the predominance of C>T transitions is a predominant feature in both.
• The authors find that the frequencies of hydrogen peroxide-induced mutations in proof-reading deficient yeast mutants supports the conclusion that this form of mutagenesis is the result of direct damage to DNA, rather than misincorporation errors.
• They propose that mutations may occur to the heavy strand of mtDNA when DNA replication starts at the light chain, temporarily making the displaced, heavy strand more vulnerable to damage.

An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482013/pdf/aav1110.pdf

John U, Lu Y, Wohlrab S, Groth M, Janouškovec J, Kohli GS, Mark FC, Bickmeyer U, Farhat S, Felder M, Frickenhaus S, Guillou L, Keeling PJ, Moustafa A, Porcel BM, Valentin K, Glöckner G

• A long-standing debate in the field of mitochondrial physiology is the purpose of mitochondrial DNA. The "co-location for redox regulation" (CoRR) hypothesis states that mitochondrial genomes are necessary to provide local control of the electron transport chain.
• The authors describe an aerobic eukaryotic parasite (Amoebophyra ceratii) with functional mitochondria, but have completely lost their mitochondrial genome, finding that all mitochondrial proteins appear to be lost or encoded in the nucleus. 
• This finding challenges the CoRR hypothesis, and potentially suggests the possibility of complete transfer of the mitochondrial genome into the nuclear genome for more complex organisms.

Mitochondrial fragmentation drives selective removal of deleterious mtDNA in the germline

https://www.nature.com/articles/s41586-019-1213-4

Toby Lieber, Swathi P. Jeedigunta, Jonathan M. Palozzi, Ruth Lehmann & Thomas R. Hurd

• The authors generate mutated fruit flies by transfering mitochondria from a wild-type strain of Drosophila yakuba into a strain of Drosophila melanogaster in which the mtDNA contain a temperature-sensitive mutation in Complex IV of the electron transport chain.
• The authors designed fluorescent probes to specifically bind to the D-loop of either D. yakuba or D. melanogaster, allowing them to visualise heteroplasmy.
• At 18C, the point mutation does not affect Complex IV activity, whereas at the inhibitory temperature of 29C, Complex IV activity is greatly reduced and is selected against 
• Selection first manifests during oogenesis, where a reduction in mitofusins causes fragmentation of the mitochondrial network
• The authors identify the proteins Atg1 and BNIP3  as necessary for the selective removal of mitochondria with mutated mtDNAs
• A reduction in Atg1 or BNIP3 decreases the amount of wild-type mtDNA, suggesting a link between mitochondrial degradation and replication
• At the restrictive temperature, selection occured in the germline but not in the somatic cells which surround the germline in the ovariole, and was largely absent in the male germ line (possibly because only female mtDNA is inherited)
• Inhibiting cell death through over-expression of the cell-death inhibitor p35 did not block selection
• Expression of the alternative oxidase protein (AOX) bypasses the function of complex IV and partially blocked selection, suggesting that the selection process senses defects in oxidative phosphorylation
• The authors observed greater fragmentation in the germline mitochondria relative to the soma. Using photoactivatable GFP, the authors show that mitochondrial contents rarely pass from one mitochondrion to another, suggesting that the purpose of fragmentation is to reduce complementation so that the genotype of individual mitochondria may be sensed through their phenotype.
• Reducing Mitofusin expression in somatic cells also induced selection
• The authors inhibited the protein IF1, to allow ATP synthase to run in reverse and maintain mitochondrial membrane potential by burning ATP. In doing so, the authors did not observe statistically significant selection, which may suggest that membrane potential sensing is the mechanism by which mitochondria are selected.
• Expression of a dominant-negative form of ATP synthase caused a reduction in mtDNA copy number of both mutants and wild-types

Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single cell resolution: a focus on aging and cancer

https://www.biorxiv.org/content/biorxiv/early/2019/03/16/579789.full.pdf

Ryan O’Hara, Enzo Tedone,, Andrew Ludlow, Ejun Huang, Beatrice Arosio, Daniela Mari, Jerry W. Shay

• The authors develop a protocol to measure single-cell mtDNA copy number using digital droplet PCR
• The authors find ~10-fold inter-cellular variability in mtDNA copy number (in an immortalised human cell line, H1299), which could not be fully explained by cell cycle variations.
• The authors investigated how mtDNA copy number changes after stimulation of peripheral blood mononuclear cells (PBMCs, a heterogeneous cellular population largely consisting of T cells). Previous studies have shown a decline in mtDNA copy number with ageing in this cell population. The authors studied stimulated PBMCs in young, old, and healthy/frail centenarians. Healthy centenarians tended to have higher mtDNA copy number than frail, or ~70 year old, individuals.