Mitochondrial DNA replication‐related Nucleotide Patterns: Ancient ruins or living structures?
Authors: Franco Melissa , Fleischmann Zoe , Wasco Kevin , DeRosa Samantha , Payne Casey , Annis Sofia , Khrapko Konstantin 
Published: June 2021

Whether mtDNA replication occurs via strand‐symmetric or strand‐asymmetric mechanism has been a matter of controversy. The asymmetric model predicts special properties for the two origins of replication of mtDNA. In particular, it predicts characteristic discontinuity of mutational pressure,(high pressure 5’ and low pressure 3’ to each of the two origins), especially on guanine nucleotides We used the “sliding subtractive window”, to test the presence of the origins: for each position of the genome we subtracted the G‐density 5’ to that position from the 3’ G‐density, using adjacent sliding windows of variable length. This “sliding subtractive window” creates a characteristic profile as it moves along the genome, which is expected to peak around the origins of replication if the mode of replication is mostly asymmetric and origin‐dependent. Indeed, we found the expected pattern with peaks in both origins, thus corroborating the classical asymmetric mode of mtDNA replication. We found that this pattern was highly conserved as far as among the entire chordata (Fleischmann et al., in preparation).

In this study we asked whether this conservation is related to acute continuous mutational pressure (asymmetric replication is currently in use) or perhaps the pattern we observe is an ancient one, that's been created hundreds of millions years ago and was resistant to dissipation by random mutagenesis.

To test this hypothesis, we performed numerical simulations where the actual nucleotide differences between human mtDNA and various chordata species' genomes were introduced into human mtDNA at randomized positions to create “randomized species”. We measured whether the distances between the “subtractive window” profiles of the randomized species and human mtDNA were larger than those between real species and human mtDNA. The significance of the difference in distance was estimated by counting the proportion of simulated randomized species which were further from human mtDNA than the corresponding real species.

We demonstrate that the distances between subtractive window profiles of randomized species and human mtDNA are significantly larger than that from real species, i.e. chimpanzee. This implies that mutations are constrained is such a way that they change the subtractive window profile much less than random mutations would, and, because the profile reflects the mode of mtDNA replication, this confirms that keeping the profile stable is favored either by selection or by asymmetric mutational pressure. In either case this implies that the light origin of replication are currently of biological significance.

There is a possibility though that the role of exceptional profile with discontinuity precisely at light strand origin of replication has some other function that it acquired over millions of years of evolution, however, this should have happened independently in several highly divergent groups like mammals and lampreys, which is unlikely. Furthermore, it is possible that other parts of the profile drive the similarity rather the origin. We will repeat the simulation concentrating on progressively narrower area around the origin to determine which part of the profile caries most importance for it invariability.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.