r/science BSc | Neuroscience Oct 06 '22 All-Seeing Upvote 1

Mitochondrial DNA Is Working Its Way Into the Human Genome Biology

https://www.technologynetworks.com/genomics/news/mitochondrial-dna-is-working-its-way-into-the-human-genome-366341
1.0k Upvotes

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u/HollandJim Oct 06 '22

Okay, I’m no scientist - what does this actually mean?

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u/[deleted] Oct 06 '22

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u/[deleted] Oct 06 '22 edited Oct 11 '22

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u/HollandJim Oct 06 '22

I thought mitochondrial DNA was something we had already, passed down through our mothers. That’s (in theory) how the idea of “Mitochondrial Eve” came about.

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u/Antique-Painting-627 Oct 06 '22

We already have mitochondrial DNA... But it is confined to the mitochondria. This says that the mitochondrial DNA is moving into the nucleus

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u/Jaded_Prompt_15 Oct 06 '22

This says that the mitochondrial DNA is moving into the nucleus

It also says that might be causing cancer...

In some cases, the insertion of mtDNA contributes to the development of cancer. “Our nuclear genetic code is breaking and being repaired all the time,” said Chinnery. “Mitochondrial DNA appears to act almost like a band-aid, a sticking plaster to help the nuclear genetic code repair itself. And sometimes this works, but on rare occasions if might make things worse or even trigger the development of tumors.”

I feel like they buried the lede there

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u/DarbyBartholomew Oct 06 '22

Am I wrong to interpret that as "some of the time this reduces your chances of getting cancer but on rare occasions it increases it instead"? So might cause cancer, might prevent cancer?

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u/ScoobyDeezy Oct 06 '22

DNA editing is a crap shoot. Good mutations survive and get passed on, bad mutations die.

It’s a tale as old as time.

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u/verasev Oct 06 '22

Even then, some genes offer both benefits and negatives. It might be better to stop categorizing mutations as good or bad and just examine whether they're useful for a given context.

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u/Technic235 Oct 07 '22

The only questions that matters is can I survive and can I reproduce? If both are yes, then the mutation is an evolutionary win.

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u/verasev Oct 07 '22

By survive, you mean survive long enough to reproduce. Nature doesn't reward long life, it rewards reproduction. Life is just an entropic process. It's all the things that come as side effects that matter to humans. I read a book that argued destroying our consciousness would be an evolutionary boon. Made me think that at a certain point you have to choose between quality of life or evolutionary fitness.

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u/rephaim_ Oct 06 '22 edited Oct 06 '22

Bad mutations that aren't known, aren't cared about, or don't present until after children are reared get passed on. That's why we still have known bad mutations on top of the garden variety natural mutations.

[Edit: typos]

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u/Olorin_in_the_West Oct 07 '22

If our genetic codes are breaking, why don’t they just fill the gaps with frog dna?

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u/f_d Oct 06 '22

Anything that tampers with the genome has the potential to contribute to cancer. It's not that shocking.

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u/KnightCreed13 Oct 06 '22

Well why tf is it doing that?

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u/Darkhorseman81 Oct 06 '22

Some Viruses want to avengers assemble. Ask cytoskeletal ARC why. It's responsible for the efficiency of human long term memory, but started as an ancient aids like virus.

I'm sure there are many other examples.

You can reverse amnesia by stimulating arc protein expression. Chems like Withanolides stimulate it.

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u/catty_big Oct 06 '22

Amnesia, of course! I knew there was something I wanted to try to reverse. Now if only I could remember what that thing was I wanted to try to reverse.

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u/mrsmoose123 Oct 06 '22

This so cool! How plants work as medicine in our bodies seems to be getting a better evidence base.

How are we able to find things like this out? I'm aware genetic sequencing is involved, but it baffles me how we know which proteins do what.

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u/danielravennest Oct 06 '22

it baffles me how we know which proteins do what.

Mice have 85% of the same DNA as we do. So-called "knockout mice" have bits of DNA removed, then they see what problem removing it causes.

The other approach is finding an antigen that blocks the particular protein, then see what happens.

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u/BiggWigg92 Oct 06 '22

Can ypu elaborate on that or share a good source to read up on that please?

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u/[deleted] Oct 06 '22 edited Oct 06 '22

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u/adamtheskill Oct 06 '22

Probably just because it's possible, it's not like the dna has a goal. It's just pure chance and if any changes increase the chance of dna getting passed on they will persist. It's not like a higher chance of getting cancer in old age has any effect on how many children a person has on average.

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u/Lvl100Glurak Oct 06 '22

so mitochondria are weak creatures and they know. so instead of becoming strong themselves, they offered help to strong creatures. this seemed very kind, but in reality they're playing the long game and soon they overtake those strong creatures, as the strong creatures are 100% dependent on the ATP mitochondria produce. they're like the hidden elite in our bodies.

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u/rephaim_ Oct 06 '22

Getting into more genomes is an endgame. There are viruses fossilized in our genomes, it's good for the virus because it's dna gets passed on with no additional work, and it's good for the host because that virus won't trigger immune responses since it's now recognized as part of the host.

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u/[deleted] Oct 06 '22

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u/HollandJim Oct 06 '22

Ah, okay - my last science class was in the late 1970s, so at least I learned a new thing today!

Thanks!

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u/ctothel Oct 06 '22 Silver Helpful I'll Drink to That

To be clear, mitochondria were once separate organisms, which had evolved to process oxygen for their energy.

Our single-called ancestors probably got energy from hydrogen, or from fermentation, but one of them engulfed a mitochondria (actually, an ancestor of what we call mitochondria) and was then able to use the energy produced by it.

When that cell divided, the mitochondria divided too, going along for the ride. This line of symbiotic cells was very successful, and is the ancestor of all plants and animals.

The exact same thing happened on a sub branch of this line, but with the cell also incorporating a kind of photosynthetic bacteria we now call chloroplasts. This sub branch evolved into plants.

Both chloroplasts and mitochondria have their own separate DNA that has nothing to do with ours. They are literally separate organisms that make up part of our cells.

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u/Rheytos Oct 06 '22

Every time man. It gives me the thrills how wonderfully complicated nature is. Truly marvelous

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u/ctothel Oct 06 '22

Right?? So fascinating.

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u/[deleted] Oct 06 '22

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u/[deleted] Oct 06 '22

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u/ctothel Oct 07 '22

Hey do you know why your other reply to me was removed?

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u/Rheytos Oct 07 '22

I don’t. I don’t think we said anything wrong… Reddit mods gotta mod I guess

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u/peolorat Oct 06 '22

Didn't know this, my mind is currently blown. I though that somewhere in one of our chromosomes there was the genetic sequences for all the proteins that make up a mitochondria as well.

So what happens if we introduce chloroplasts into an animal? Did anyone try?

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u/ctothel Oct 06 '22

Mind blowing is the appropriate response!

I’m not sure if anybody has tried what you’re suggesting. It would probably just be broken down though, unless there was some technique nobody knows about.

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u/Guciguciguciguci Oct 06 '22

It will be the first animal that doesn’t have to eat!!

If humans could stand in the sun three times a day and then be like: ah, that was delicious. Now back to work.

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u/UmdieEcke2 Oct 08 '22

Sure, although you would probably have to sunbath around 300 hours per day to cover your energy needs.

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u/Darkhorseman81 Oct 06 '22

H2S hydrogen and sulphur. It's why H2S is still such an important epigenetic signalling molecule.

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u/Alternative-Flan2869 Oct 06 '22

Is the euglena the crossroad point of plant/animal separation/ evolution?

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u/ctothel Oct 06 '22 edited Oct 06 '22

It doesn’t really make sense to look at a species that’s alive today and think of it as the last common ancestor of two branches, because that species has been changing as well (even if not very much).

Plus, given we don’t have chloroplasts but the Euglena does, it might be safe to assume it split off the branch that would eventually form plants after we did. Unless we once had chloroplasts but got rid of them, but I haven’t heard that theory.

But it seems as though the Euglena split off quite early, yes.

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u/kongx8 Oct 07 '22

It is thought that euglena split off from the plant/green algae line before the development chloroplasts from captured Cyanobacteria. It likely that Euglena’s ancestors received their chloroplasts from engulfing an eukaryotic green algae. Over time, the engulfed algae was reduced to a chloroplast and a nucleus, thus serving a similar function to the original chloroplasts.

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u/travelling-through Oct 06 '22

so what does this change mean for us? do we have an idea?

by we I mean any human anywhere who is qualified to have an educated guess

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u/ctothel Oct 07 '22

If I understand your question, mitochondria are probably responsible for us existing at all. The partnership between our cells and theirs granted the energy required to become multi-cellular, and to start increasing the size of the genome.

It takes energy to copy a gene, and more genes require more energy. Oxygen is much more efficient energy source for cells than the alternatives.

There’s also a theory that having a separate set of genes that handled energy means the host cell didn’t need to worry about that bit, which allowed both us and our “powerhouse” to adapt more quickly and effectively to our environment.

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u/travelling-through Oct 07 '22

I was mislead by the title. I thought the mitochondria is now working its way in to nuclear DNA and it didn't do that before, so thats why I was asking about how this will affect us

Now I had time to read the full article and I get it.
Thanks for trying to answer though.

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u/ctothel Oct 07 '22

Oh I see! I thought you meant the change that came from the original incorporation of mitochondria. Makes sense now :-)

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u/ClarkFable PhD | Economics Oct 06 '22

but that mitochondrial DNA is printed from some subset of the 46 chromosomes as everything else, so what's the distinction? i.e., humans start as a zygote, not a zygote + some mitochondrial DNA, right?

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u/kanated Oct 07 '22

that mitochondrial DNA is printed from some subset of the 46 chromosomes

It's not.

Don't think of mitochondria as just another organelle. Think of them as something similar to a parasite that lives inside your cells, except it's beneficial.

They have their own DNA, they reproduce independently. They aren't formed in the zygote, they already come inside the egg. They spread from mother to child this way for billions of years. Each time a cell divides, some of them go along.

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u/ClarkFable PhD | Economics Oct 07 '22

Thanks! TIL.

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u/rintryp Oct 06 '22

Actually the mitochondria are a given from the mother, so the egg already has mitochondria whereas semen only brings in some nucleus DNA but no mitochondria.

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u/Arcal Oct 06 '22

Mitochondria have their own chromosomes, tens to thousands of copies per cell. Your mother's egg cell had its own mitochondria with its own DNA. That's what all your mitochondria have now. Somehow, the mitochondria from sperm are specifically targeted and eliminated. We're still working on that mechanism.

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u/TheGreat_War_Machine Oct 06 '22

Sperm don't have mitochondria in the first place, do they not?

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u/Arcal Oct 07 '22

They do, hard working ones too, for all that swimming.

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u/BigUptokes Oct 06 '22

Okay, I’m no scientist - what does this actually mean?

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u/Dragonmodus Oct 06 '22

This mitochondrial DNA is -in- the mitochondria, we have two sets of DNA. That DNA is being copied (moved?) to the nucleus for some reason.

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u/Sonic_Sugar Oct 06 '22

I am also not a scientist, but my understanding of the read was that mtDNA is being inserted to repair DNA. I don’t understand all the jargon and processes, though, and this week I don’t have the time to deep dive into it as I would like to.

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u/Arcal Oct 06 '22

The nucleus is a safer place for DNA, protected and with more advanced repair mechanisms, so its advantageous to have the genes drift over. The original pre-mitochondrial microbe didn't have a nucleus, and it doesn't matter so much with single celled organisms.

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u/DarthDannyBoy Oct 06 '22

We do. In the mitochondria.

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u/SpaceProphetDogon Oct 07 '22

It's also how the idea of "Parasite Eve" came out.

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u/Nicodolivet Oct 06 '22

And mRNA can be integrated to human DNA.

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u/TheGreat_War_Machine Oct 07 '22

mRNA is created using DNA, so it doesn't make sense for mRNA to be integrated into DNA. Not to mention the fact that it is impossible, because both use different nucleotides.

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u/Explicit_Tech Oct 07 '22

Only with reverse transcriptase.

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u/thenaterator Grad Student | Neuroscience Oct 06 '22 edited Oct 06 '22 Silver

Scientist here. As usual the press release (at least the headline) is misleading, and invokes a lot in the imagination of readers.

You have 2 places where DNA are stored, and they are for all practical purposes, completely different. (1) In the nucleus of all of your cells. This is, in a sense, YOUR DNA. It encodes all the stuff that makes you. (2) In the mitochondria of all of your cells (often called "the powerhouse of the cell). It encodes all the stuff the mitochondria needs to generate "power."

All organisms we call "Eukaryotes" have these 2 stores. That's because (we think), Eukaryotes came into being when two different types of organisms fused together into one symbiotic organism. Hence the 2 different stores of DNA. Each store is descended from those ancestral organisms.

We already know that DNA can be transferred from the mitochondria to the nuclear store. In principle it's similar to how DNA can be shared across species (called "Horizontal Gene Transfer").

This paper? It describes these DNA transfer events in 66,083 human genomes, and speculates on the downstream effects of those transfers.

It isn't something just happening to humans.

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u/GypsyV3nom Oct 06 '22

It also happens more in obligate aerobes who need those mitochondria for respiration. Facultative anerobes (like most yeasts) have some pretty chunky mitochondrial DNA, especially compared to the highly slimmed-down versions found in mammals.

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u/thenaterator Grad Student | Neuroscience Oct 07 '22

Neat!

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u/rosellem Oct 06 '22

How is the headline misleading?

I mean, it's not the full story, but you can never get the full story from a headline. If you just read the headline, yeah a lot will be left to the imagination, but then, your ignorance is no ones fault but your own.

A headline that leaves out important details is not misleading, it's just a normal headline. The details are in the article.

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u/LordAlveric Oct 07 '22

I like my headlines to be accurate and factual. The headline for this article is click bait, clearly aimed at the uninformed. I almost ignored it myself, because cross transfer of this nature is hardly anything new. But the headline makes it seem as though this is something novel, which is intellectually dishonest.

Of course, only a fool would expect honesty in a headline, and in today's cyberworld that is driven by clicks and eyeballs, it is tough for the publishers to resist the temptation.

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u/rosellem Oct 07 '22

I like my headlines to be accurate and factual.

What part of this headline is inaccurate or untruthful?

But the headline makes it seem as though this is something novel, which is intellectually dishonest.

Where? how? The headline is a simple, factual statement.

The only thing that implies it is "new", is that they are writing a story about it. The headline is very simple and implies nothing. If you read this headline and make the assumption it is "novel", that is your fault. You should not make that assumption. You can't make assumption's when reading headlines.

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u/HollandJim Oct 06 '22

Only goes to show what passes for a “normal” headline these days. I’d say the headline misdirects the reader with an vague inference, and it’s up to them to run through the article to straighten themselves out (if they can understand the details). The tone of the headline itself is almost worrying if you have no idea what they’re suggesting.

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u/rosellem Oct 06 '22

it’s up to them to run through the article to straighten themselves out

Yes! You need to read articles to not be ignorant. That's the way it has always worked. That's not something that happens "these days".

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u/HollandJim Oct 07 '22

I would rather not panic people into reading an article - I’d prefer to encourage them instead of generating a fight-or-flight response. That’s my point.

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u/HollandJim Oct 07 '22

I neglected to say thank you for that detailed response. Looking back now, I think I learned more about “Eve” from Time magazine and Battlestar Galactica than in university in the day.

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u/thenaterator Grad Student | Neuroscience Oct 07 '22

Glad it was helpful!

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u/[deleted] Oct 06 '22

So we might have some feature of bacteria in the future

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u/ClarkFable PhD | Economics Oct 06 '22

How is mitochondrial DNA stored separately if all humans start as a zygote? It's not a zygote + some mitochondrion, is it?

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u/Arcal Oct 06 '22

Yes, it is. All the zygote mitochondria are maternally derived an have their own DNA. The fathers are selectively degraded.

Over millennia, genes have been moving from the mitochondria to the nuclear DNA, there are only 13 protein coding genes left in the mitochondrial genome now vs 30,000 ish in the nucleus.

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u/ClarkFable PhD | Economics Oct 07 '22

TIL. Thanks

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u/DanielNoWrite Oct 06 '22

It's passed along with the human dna, primarily in the egg, meaning it's inherited maternally (though I believe there are some exceptions to this).

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u/Arcal Oct 06 '22

Mitochondria likely started as free-living bacteria with thousands of genes on its own chromosomal DNA. This was engulfed by an early proto-eukaryote. This was a long time ago, but the arrangement was advantageous. Over time, genes have moved from the bacterial genome to the host nuclear genome. Now, the mitochondria only have 13 protein-coding genes left out of thousands.

Why? is the interesting question. One answer is that storing DNA in a specialized nucleus with much more sophisticated repair machinery keeps those genes in good order. A bit like keeping the plans in an office and not down on the shop floor with all the dangerous machinery.

There are organisms which have already transferred the whole mitochondrial DNA to the nucleus.

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u/[deleted] Oct 06 '22

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u/Seeker0fTruth Oct 06 '22

I do have a biology degree, but it's been ten years since I've used it, but some of you want a tl;Dr, so here goes.

A long time ago, the ancestors of Multicellular organisms ate a small bacteria-like thing. For whatever reason, this bacteria like thing didn't die, and instead survived and reproduced. Multicellular organisms got a pretty sweet deal out of this; if we provided these little guys with sugar, they would do the hard work of turning the sugar in the energy. They'd keep a little for themselves to keep the lights on, and give the rest of the energy to us.

This relationship has continued for a long time. And while our mitochondria have their own DNA (you often find people talking about 'mDNA' - that's the mitochondria's DNA), our DNA has been slowly taking over mitochondrial functions probably since our ancestors first ate them - that's what this paper is telling us.

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u/[deleted] Oct 06 '22

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u/[deleted] Oct 06 '22

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u/c0224v2609 Oct 07 '22

Thanks for clarifying!

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u/molrose96 BSc | Neuroscience Oct 06 '22

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u/Jaded_Prompt_15 Oct 06 '22

Something more important they barely touch on:

In some cases, the insertion of mtDNA contributes to the development of cancer. “Our nuclear genetic code is breaking and being repaired all the time,” said Chinnery. “Mitochondrial DNA appears to act almost like a band-aid, a sticking plaster to help the nuclear genetic code repair itself. And sometimes this works, but on rare occasions if might make things worse or even trigger the development of tumors.”

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u/alex20_202020 Oct 06 '22

a sticking plaster to help the nuclear genetic code repair itself.

That is indeed important. When it's working its way info nucleus?

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u/the1ine Oct 06 '22

I think they barely touch on it because it's not important. You don't work in cell biology without 'sometimes... cancer!' being the norm.

This does not change the findings, or their importance. We already knew cancer happens.

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u/shindleria Oct 06 '22

Mt genes have been doing this for billions of years to become fully integrated into cellular signalling processes. Many of the mRNAs have 5’UTR sequences which confer unique trafficking and translation pathways, essentially a privileged form of molecular communication between the cell and mitochondria to control energy expenditure within the cell under a vast array of conditions. Some viruses have evolved to mimic these genetic properties to continue protein synthesis when the cell attempts to arrest translation. Truly fascinating.

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u/knockonclouds Oct 07 '22

Came here to say exactly this. Mitochondrial genes present in nuclear DNA is not new - it’s been there for a very long time people.

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u/[deleted] Oct 06 '22

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u/JohnFByers Oct 06 '22

This has been going on for 2 billion years and the existence of gene transfer from mt to nucleus isn’t the point of the article.

Since we’re talking about a process that has lasted billions of years, there’s no particular worry at this point.

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u/Parazeit Oct 06 '22

In some organisms the mitochondria has shifted the entirety of its genome into "host" DNA. Mitosomes and hydrogensomes are the result.

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u/EquivalentAd2906 Oct 07 '22

They performed surgery on a grape.

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u/Storyteller-Hero Oct 07 '22

This article makes me hungry for a Parasite Eve remake.

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u/peolorat Oct 06 '22

Wait, I thought our chromosomes contained the DNA to build everything in a cell, including mitochondria. Are you telling me that mitochondria is actually a separate system on the side? So how are new mitochondria produced when a cell divides?

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u/Parazeit Oct 06 '22

Mitochondria divide and multiply independently within a cell. When the cell undergoes mitosis, some mitochondria stay in the mother cell and some go with the daughter cell.

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u/Arcal Oct 06 '22

It's a whole separate life cycle linked, but independent. They're constantly dividing like bacteria (but in a way that's initiated by the parent cell) and fusing together. Over time, damaged mitochondria accumulate and are selectively degraded.

They (still) have their own DNA, their own DNA replication, repair, transcription and translational machinery to make proteins. Interestingly, the proteins they make start with the same amino acid that bacterial ones do, so, if you get an injury that releases a lot of mitochondria into your circulation, your immune system recognises it as an infection. This can kill you.

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u/TheGreat_War_Machine Oct 07 '22

Mitochondria used to be separate organisms, but were integrated into other single celled organisms to make eukaryotes. The mitochondria still have their own DNA, and that DNA is passed down during cell division.

Babies inherit the same mitochondria that their mothers have, which can be detrimental if the mother has a preexisting mitochondrial disorder.

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u/undeterred_turtle Oct 06 '22

The article says that nuclear DNA cannot mix with mtDNA in the mitochondria, citing the non porous double membrane. My question is then, how does the mtDNA get out? What makes it's process of escaping the mitochondria and then getting into the nucleus easier than the opposite?

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u/[deleted] Oct 07 '22

Isn’t this translocation?

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u/koreanfertilityrate Oct 07 '22

There was already a PlayStation game about this decades ago called Parasite Eve.

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u/wazabee Oct 17 '22

I thought this was already well known? I don't understand what's new about it?

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