A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand

Abstract

The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria are responsible for aerobic respiration, it is expected that mtDNA mutational spectrum is affected by oxidative damage. Assuming that oxidative damage increases with age, we analyse mtDNA mutagenesis of different species in regards to their generation length. Analysing, (i) dozens of thousands of somatic mtDNA mutations in samples of different ages (ii) 70053 polymorphic synonymous mtDNA substitutions reconstructed in 424 mammalian species with different generation lengths and (iii) synonymous nucleotide content of 650 complete mitochondrial genomes of mammalian species we observed that the frequency of AH > GH substitutions (H: heavy strand notation) is twice bigger in species with high versus low generation length making their mtDNA more AH poor and GH rich. Considering that AH > GH substitutions are also sensitive to the time spent single-stranded (TSSS) during asynchronous mtDNA replication we demonstrated that AH > GH substitution rate is a function of both species-specific generation length and position-specific TSSS. We propose that AH > GH is a mitochondria-specific signature of oxidative damage associated with both aging and TSSS.

Mitochondrial mutation spectrum in Chordates: damage versus replication signatures, causes, and dynamics

“…The resulting spectrum reveals a notable predominance of transitions, with C H >T H and A H >G H being the most common ones. This mitochondrial mutagenesis pattern aligns with observations in mammalian germline mutations 5 , somatic mutations in human cancers 16 , and healthy tissues 17 . The complete 192-component mitochondrial mutational spectrum for chordates is available in numeric format, akin to a COSMIC database, in Supplementary Table 2.…”

“…If BER is deficient on a heavy strand of mtDNA we expect that some fraction of the most common C H >T H mutations can be driven by this deficiency. Additionally, C H >T H gradient in mtDNA connected with TSSS 5,38 probably can be the result of lagging NTHL1 activity. Interestingly, several NTHL1 variants demonstrate defective ability for the repair of the 5-hydroxyuracil, the most abundant oxidation product of cytosines 39 .…”

“…Traditionally, comparative species analyses employ the transitions to transversions ratio as a basic yet insightful characteristic of the mutational spectrum 6 . Availability of more sequence data, allowed researchers to use more complex 6-component (focusing only on pyrimidines in Watson-Crick base pairs: C>A, C>G, C>T, T>A, T>C, T>G, under the assumption of symmetrical mutagenesis on complementary strands) [7][8][9] and 12-component (doubling the 6-component spectrum to account for asymmetrical mutagenesis on complementary strands, inasmuch as it includes complementary substitutions, for instance, C>A and G>T as distinct events) 5 spectra in analyses for comparative studies. However, more comprehensive 96-component (expanding the 6-component spectrum with an inclusion of the nucleotide context -4 bases immediately 5' and 4 bases immediately 3' into spectra) and 192-component (a doubled version of the 96-component spectrum, assuming asymmetry between complementary strands) spectra, which consider adjacent nucleotide context, have been limited to extensively studied species such as humans and SARS-CoV-2.…”

The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging

“…We have previously used a subset of this dataset to demonstrate that a discontinuous strand-specific gradient of transitions exists across the mtDNA, consistent with deamination events arising from a long-lived single-stranded replication intermediate ( Sanchez-Contreras et al, 2021 ). The slope of this gradient increases with age, indicating that deamination is likely an active chemical process ( Mikhailova et al, 2022 ; Sanchez-Contreras et al, 2021 ). However, the underlying chemical mechanism behind these likely deaminations remains poorly understood and would impact its utility as a biomarker.…”

Secondary structure of the human mitochondrial genome affects formation of deletions

“…If the time being single-stranded is important for deletion formation, as it has been suggested for the mutagenesis of single-nucleotide substitutions [ 31 , 32 ], we can assume that the early-replicating region (~ 16.5 kb) may be more mutagenic as compared to the late-replicating region (~ 6 kb). The increased deletion mutagenicity of the early-replicating regions (16.5 kb, which corresponds to 3′ breakpoint) as compared to the late-replicating region (6 kb, which corresponds to 5′ breakpoint) can be realized in the fact that the early-replicating region is less selective: this region can associate with any other open regions of the major arc, meaning an increased variation in 5′ deletion breakpoint as compared to 3′ deletion breakpoint.…”