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Why Do Some Mitochondrial Mutations Expand to Overtake All Mitochondria in a Cell?

There is a constantly replicating herd of mitochondria in every cell, the evolved descendants of ancient symbiotic bacteria now well integrated into cellular mechanisms. They still bear a small remnant of the original bacterial DNA, however, and this is prone to mutational damage. Some forms of this damage cause mitochondria to both malfunction and become more resilient or more able to replicate than their peers. As a result, the cell is quickly overtaken by broken mitochondria and becomes broken itself, exporting damaging reactive molecules into surrounding tissues, the bloodstream, and the body at large.

This process is one of the root causes of aging, so it is a matter of considerable interest to the research community to understand exactly how it is that these damaged mitochondria can so quickly replicate to fill a cell with their descendants. That said, the beauty of the SENS rejuvenation research approach to the problem is that it really doesn't depend on how the damage occurs or spreads. It aims to place backup copies of mitochondrial genes into the cell nucleus, thus ensuring that there is always a supply of the proteins encoded in mitochondrial DNA. So if mitochondrial DNA does become damaged, then there are no further consequences, and mitochondria will nonetheless continue to function correctly.

An intriguing hallmark of aging in mammals is the appearance of cells carrying significant burdens of mitochondrial DNA (mtDNA) mutants. Unlike the mtDNA mutations which cause inherited diseases, those associated with aging appear to be somatically acquired. Within a given tissue, there is often considerable heterogeneity in the burden of mtDNA mutations, such that affected cells co-exist side by side with healthy cells that carry few, if any, mutations. Furthermore, the frequency of affected cells tends to increase with age and there is evidence that within individual cells, the mitochondrial population is commonly overtaken by a single mutant type, very often a deletion in which a part of the normal mtDNA genome has been lost. The precise mutations tend to differ from one affected cell to another, suggesting that individual mtDNA mutations arise at random. How these mtDNA mutations undergo clonal expansion is a question of longstanding interest.

The possibilities that they multiply either because of a so-called vicious cycle such that defective mitochondria simply generate more reactive oxygen species (ROS), which in turn cause more mutations, or because of random drift, have both been considered but found to be unsatisfactory. Instead, it seems most likely that new mtDNA mutations are acted upon by some form of intracellular selection, causing the expansion of a clone of mutant mitochondria that may come to dominate or entirely exclude the wild type population.

Among the various possibilities to account for a selective advantage favoring mtDNA deletions are that: (i) in a cell where wild type and deleted mtDNA molecules co-exist, there may be a selection advantage for deletion mutants since they have a smaller genome size, which might result in a shorter replication time; (ii) if mitochondria that are compromised by a high burden of mutations have a slower rate of metabolism, they may be less damaged by ROS and so relatively spared from deletion by mitophagy, thereby resulting in survival-based selection through a process that has been termed survival of the slowest; (iii) the selection advantage of mtDNA deletions might be based on features relating to some aspect of the machinery for mtDNA replication, of which several possibilities exist, at least hypothetically.

Possibility (i) has been closely examined but found to be implausible, chiefly because the time required for replication of an mtDNA molecule is only a tiny fraction (less than 1%) of the half-life of mtDNA, which drastically diminishes any scope for a size-based replication advantage to be important. Possibility (ii) has also been found to be unlikely, since not only is it incompatible with mitochondrial dynamics, but it also appears that dysfunctional mitochondria are degraded preferentially rather than more slowly than intact ones By a process of elimination, it appears probable, therefore, that the enigma of clonal expansion of mtDNA deletions requires explanation in terms of the machinery for DNA replication.

Recently, we noticed that when the locations of mtDNA deletions, which had been reported from rats, rhesus monkeys, and humans, were compared, there was a stretch of mtDNA that was overlapped in nearly every instance. Based on this observation and noting that the primer required for DNA replication is provided by processing an mRNA transcript, we suggested a novel mechanism based on this intimate connection of transcription and replication in mitochondria. If a product inhibition mechanism exists that downregulates the transcription rate if sufficient components for the respiration chain exist, then deletion events removing a region of the genome involved in this feedback-loop would confer to such deletion mutants a higher rate of replication priming, leading to a substantial selection advantage. In this article, we report additional data from mice that are strongly consistent with our previous analysis of rats, monkeys, and humans, and we further examine the implications of the hypothesis that a shared sequence, falling within the common overlap of these many individual deletions, might throw light on the underlying mechanism for clonal expansion.

Link: http://dx.doi.org/10.3390/genes9030126

Comments

Wasn't the whole idea of clonal expansion of mutant mitochondria to a lack of surface damage Aubrey de Grey's big original idea (other than that aging could be brought under control via a divide and conquer strategy)?

Pretty odd that the authors of this paper don't cite his mitochondria paper.

Posted by: Jim at March 9th, 2018 4:09 AM

@Jim: I believe they cite one of Aubrey's papers for possible mechanism (ii).

Posted by: Reason at March 9th, 2018 5:03 AM

"Based on this observation and noting that the primer required for DNA replication
is provided by processing an mRNA transcript, we suggested a novel mechanism based on this intimate
connection of transcription and replication in mitochondria. If a product inhibition mechanism exists
that downregulates the transcription rate if sufficient components for the respiration chain exist, then
deletion events removing a region of the genome involved in this feedback-loop would confer to such
deletion mutants a higher rate of replication priming, leading to a substantial selection advantage
(Figure 1). In this article, we report additional data from mice that are strongly consistent with our
previous analysis of rats, monkeys, and humans, and we further examine the implications of the
hypothesis that a shared sequence, falling within the common overlap of these many individual
deletions, might throw light on the underlying mechanism for clonal expansion."

What imlications, if any, does this have for the SENS Foundation's approach of moving mtDNA genes to the mucleus?

Posted by: Jim at March 9th, 2018 6:16 AM

@Jim: I would imagine no effect. Allotopic expression can rescue mutant cells completely lacking a mitochondrial gene, so it should be agnostic on all mechanisms related to causation and propagation of mitochondrial mutations. It doesn't matter how the mutations happen or why or how they spread. Mitochondria will continue to function correctly.

Posted by: Reason at March 9th, 2018 6:25 AM

"Experimental data sets from mouse, rat, rhesus monkey, and human specimens all point to a
region of mtDNA that is shared between most of the deletions. The genes of this region, ND4 and
possibly ND5, are prime candidates for components of the proposed feedback mechanism."

If it is only DNA loss in the ND4/ND5 region, doesn't this make the job easier? You'd only have to allotopically express that region to prevent clonal expansion of mutant mitochondria? Deletions in other parts of the mitochondrial DNA would be taken care of by the higher rate of autophagy observed in mitochondria with deletions?

In fact you could test this (although not easily I imagine) by germline gene editing mice to allotopically express the ND4/ND5 region and seeing if they ever experience mitochondrial clonal mutant expansion and takeover of cells.

Posted by: Jim at March 9th, 2018 6:44 AM

All: a very intelligent question, Jim. Short answer: "maybe."

As background, let's fill in a couple of things. First, part of the reason why Dr. de Grey's proposed "Survival of the Slowest" (SOS) mechanism for why large deletions clonally expand in aging cells' mitochondrial populations is that such deletions (and particularly the "common deletion," mtDNACD4977) cover the genes encoding large numbers of transfer RNAs (tRNA), which transport the amino acids instructed in the memory RNA (mRNA) over to the ribosome to assemble the encoded protein. Without the ability to make so many tRNAs, it would be impossible for the mitochondria to translate any of their own protein-encoding genes into proteins, irrespective of the condition of the specific gene(s) for those protein(s). So on that basis, the common finding of deletion of the ND4 (and possibly ND5) region as part of such deletions would be of no particular significance, since no protein would be produced.

In the years since SOS was formulated, the probes for mtDNA have gotten a lot better, and there's now pretty good evidence that other, smaller deletions may also clonally expand in aging cells, and these do not necessarily cover as many tRNA genes. However, there are tRNA genes between ND4 ad ND5, so it's certainly possible that this is still the key reason why smaller deletions still encompassing this region clonally amplify.

Additionally, it's a bit odd and maybe even slightly perverse that they say that SOS has "been found to be unlikely, since ... it also appears that dysfunctional mitochondria are degraded preferentially rather than more slowly than intact ones." From the beginning, the SOS hypothesis was based on the idea that because the knockout of the tRNAs leads to the inability to assemble an electron transport chain (ETS) and therefore carry out oxidative phosphorylation (OXPHOS), it would necessarily produce very few or no free radicals, which would then cause less damage, not more, to the mitochondrial membrane. And as the authors correctly state - and as Dr. de Grey predicted, even before the mechanism was understood - subsequent results have validated that it is exactly the more damaged mitochondria, with highly depolarized membranes, that are selectively degraded by mitophagy.

In accordance with this, ρ0 cells (which are the closest in vitro model of mitos with large deletions), have more than half the proton gradient of normal ones (see PMID 10231371), while mitos with membranes damaged by free radical bombardment would be expected to have far less. Youle, who first mapped out how Parkin selectively marks damaged mitos for mitophagy, also specifically tested its effects in ρ0 cells, and found that its effect on them is quite low compared to that on normal mitos (PMID 20547844).

This means that the mitochondria with either genetic damage other than the large deletions typical of clonal expansion (which would still carry on OXPHOS, but in an error-prone way, and tend to throw out more free radicals), or that have just been around for a long time and have a lot of membrane damage from normal OXPHOS, are exactly the ones that get cleared out, leaving those with large deletions (or smaller deletions covering enough tRNAs) that are left behind and clonally expand.

All that said, it is still possible that the authors' hypothesis is correct, if the smaller deletions over the ND4-ND5 region that clonally expand don't hit enough tRNAs to prevent ETS assembly. It's also at least possible that both mechanisms are operative.

And to finally drill down to your specific question, Jim: if the authors' hypothesis is exclusively correct, it's quite possible that allotopic expression of just ND4 and maybe ND5 would do the trick. Happily ND4 is GenSight's lead candidate, although it might not yet have a strong enough system to deal with the problem of mosaic, clonally-expanded deletions (their LHON patients typically have defective rather than deleted ND4, and mitochondria bearing the mutations often exist in a mixed state with other mitochondria with normal genes).

One remaining uncertainty would be that they have no specific data showing that the mechanism linking expression of the genes into protein to negative feedback on replication: it could be on a gene product that is not a protein (some kind of RNA, for instance), which would still then need to be imported - and in a different way than allotopic expression. And there's always the possibility that the thing that matters is the DNA itself: for instance, that there is some nuclear-coded factor that binds to the critical region and stops replication, which is then bypassed when the gene region is deleted, allowing the mutant genome to clonally amplify. In this latter case, replacing proteins won't prevent expansion, but allotopic expression would still keep the mutant mitochondria functional: whether you'd need just ND4 and maybe -5 or comprehensive allotopic expression would depend on whether they just lack those specific genes, or whether (again) the missing tRNAs prevent all mito-encoded protein production despite (in this scenario) having nothing to do with the mechanism of clonal expansion itself.

Bottom line: SOS is still entirely consistent with the data, but this negative feedback mechanism seems viable as well; and in almost any scenario, comprehensive AE solves the problem, whereas in some scenarios, ND4 and -5 alone might do it.

Posted by: Michael at March 11th, 2018 6:17 PM

Thanks Michael for your detailed reply. So, given the above possibilities, would SRF give precedence to ND5 research above other genes? Would it be your next target after ATP6 and ATP8?

Posted by: Antonio at March 12th, 2018 4:04 AM

... people are explaining why sens's ideas are not so great after all. it would not hurt to take note:

http://www.longecity.org/forum/topic/100028-why-do-some-mitochondrial-mutations-expand-to-overtake-all-mitochondria-in-a-cell/

it is just the sens group that truly believe that their approach "solves everything". no wonder why mitosens went nowhere. the much trumpeted published paper is pretty much nothing.

if you want to learn a bit, learn from groups that are doing real research not white papers like sens:

https://www.cohbar.com/news-media/publications

once sens' ideas get into clinic things do not work as planned ... (another hint: look at the recent study with naked mole rats and senescent cells)

the "wonderful" explanations that michael is posting every time, calm the bases (= the group here), but (again) once the ideas move into the real world ... there is trouble ahead ...

Posted by: cba at March 12th, 2018 11:00 PM

Obvious troll is obvious...

If you have anything meaningful to say, say it by yourself.

Posted by: Antonio at March 13th, 2018 1:05 AM

Yep, cba, you're another idiot. When I told my son and wife 10 years ago that wr will soon have self driving cars, they laughed at me.

So, dumb ass, scoff all you want, but please do it elsewhere. This is a forward thinking group, which you're not capable of.

Posted by: Robert at March 13th, 2018 1:20 AM

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