The ‘Stem’ and the ‘Workers’ of the mtDNA population of the cell. Evidence from mutational analysis

Abstract

Every cell in our body contains a vibrant population of mitochondria, or, more precisely, of mitochondrial DNA molecules (mtDNAs). Just like members of any population mtDNAs multiply (by replication) and die (i.e., are removed, either by degradation or by distribution into the sister cell in mitosis). An intriguing question is whether all mitochondria in this population are equal, especially whether some are responsible primarily for reproduction and some - for empowering the various jobs of the mitochondrion, oxidative phosphorylation in the first place. Importantly, because mtDNA is highly damaged such a separation of responsibilities could help greatly reduce the conversion of DNA damage into real inheritable mutations. An unexpected twist in the resolution of this problem has been brought about by a recent high-precision analysis of mtDNA mutations (Sanchez-Contreras et al. 2023). They discovered that certain transversion mutations, unlike more common transitions, are not accumulating with age in mice. We argue that this observation requires the existence of a permanent replicating subpopulation/lineage of mtDNA molecules, which are protected from DNA damage, a.k.a. the stem mtDNA. This also implies the existence of its antipode i.e., the worker mtDNA, which empowers OSPHOS, sustains damage and rarely replicates. The analysis of long HiFi reads of mtDNA performed by PacBio closed circular sequencing confirms this assertion.

Are some mutations more equal than others?

“…Consequently, transversions primarily occur on ‘worker’ mtDNA molecules which rarely replicate, which prevents these mutations from being able to clonally expand and accumulate with age. The model is supported by our analysis of HiFi sequencing data collected by Hon et al, 2020 , which shows mtDNA molecules falling into high- and low-damaged groups ( Cote-L’Heureu et al, 2023 ), and is also consistent with a functional study showing ‘replicating’ and ‘respiring’ subpopulations of mitochondria in the cell ( Döhla et al, 2022 ).…”

“…However, the transversion mutations – which are primarily caused by reactive oxygen species (ROS) – did not accumulate with age. Our own work ( Cote-L’Heureu et al, 2023 ) suggests that cells contain an actively replicating group of mtDNAs – termed the ‘stem’ subpopulation (green) – which are protected from ROS. ‘Stem’ mtDNAs renew themselves and also replenish another group of mtDNAs – termed the ‘worker’ subpopulation (blue) – which are involved in respiration and exposed to higher levels of ROS and therefore acquire more transversion mutations.…”

“…Work in this field should benefit from the use of single-cell duplex sequencing ( Arbeithuber et al, 2020 ), as well as newer, improved duplex sequencing approaches ( Abascal et al, 2021 ), and long-read mutational analysis ( Cote-L’Heureu et al, 2023 ). These methods could help to test if transversions are real mutations, and how the level of damage varies between mtDNA molecules.…”