Where the heck did all those structures inside complex cells come from?

There are competing theories about the origin of the nucleus and endoplasmic reticulum.

See full article...

 

[AdrianS]

Interesting article, thanks.
I'm enjoying these knowable articles.

 

[ZenBeam]

OK, this is just stupid. I'm reading this interesting article, but I'm thinking it really could do with some pictures or diagrams to explain what they are talking about. And then the original article in Knowable Magazine has them! Why aren't they included here? Someone brought that article here, why can't they take a little more time and bring all of it?

I'd insert them inline here myself, but when I try it doesn't work.

 

[Uncivil Servant]

One thing that does seem certain is that eukaryogenesis happened relatively rapidly. All eukaryotic cells have a basic "eukaryote package": mitochondria, internal membranes, nucleus, multiple straight chromosomes, meiosis, and at least the genetic machinery for sexual reproduction, even in the few non-sexual species.

That implies strongly that once the process started, a sexually reproducing gene pool was created. Asexual reproduction would have resulted in a lot more branches of the eukaryote tree.

 

[Cloudgazer]

This is a way better weekend syndication article than the usual fare from Wired or the FT, but since this is Ars, former home of John Siracusa, we must remain hypercritical.


The power of the inside-out model, Buzz Baum says, is that it gives the cell eons of time, before the alphaproteobacterium becomes fully enclosed, to evolve ways to regulate the number and size of the mitochondrion and other membrane compartments that would eventually become fully internal. “Until you can regulate them, you’re dead,” Buzz Baum says.


/pedant-hat-on

Surely that should read 'the number and size of the mitochondria' - you can't have 'the number of' and then a singular. 'the number and size of the [singular-thing]' makes no sense unless we're talking about some sort of unique serial number. If number is only supposed to apply to the 'other membrane compartments' and not to the mitochondria then the sentence probably needs to be significantly re-arranged because that's not how it reads at present, at least not to me.

 

[I-ku-u]

If I understand this article correctly, the "mitochondria-early" hypothesis suggests/assumes that all the protective vesicles evolved after the endosymbiont was absorbed, to protect the full cell. But the experiments described at the end suggest that the protective vesicles were a function of the eventual endosymbiont, before it was absorbed (to protect itself?)

That would solve the problem of '“Until you can regulate them, you’re dead,” Buzz Baum says.' while also providing a means for selective pressure that's absent from the inside-out model.

 

[Smithy6482]

+1 to the knowable articles, and another +1 to ZenBeam's complaint about bringing in the original article's diagrams!

 

[justageezer]

The protobacteria are to blame - their alpha committed the sin.
Wanna know why we're all the same, the answer eukarywithin.

 

[Chuckstar]

So we’re assuming that because the modern mitochondria do X that it means the original mitochondria did, also? And the argument for that is that modern mitochondria from different eukaryotes do it?

Aren’t we missing a few steps in that argument? At best, they’ve shown mitochondria had that ability early, not necessarily immediately. At worst they’ve rediscovered parallel evolution.

 

[Chuckstar]

Another problem is the assumption that vessicles started out as offshoots from mitochondria. Are they all still offshoots of mitochondria? If not how/why did nuclear DNA take over construction of those vessicles?

 

[ej24]

This is a way better weekend syndication article than the usual fare from Wired or the FT, but since this is Ars, former home of John Siracusa, we must remain hypercritical.


The power of the inside-out model, Buzz Baum says, is that it gives the cell eons of time, before the alphaproteobacterium becomes fully enclosed, to evolve ways to regulate the number and size of the mitochondrion and other membrane compartments that would eventually become fully internal. “Until you can regulate them, you’re dead,” Buzz Baum says.


/pedant-hat-on

Surely that should read 'the number and size of the mitochondria' - you can't have 'the number of' and then a singular. 'the number and size of the [singular-thing]' makes no sense unless we're talking about some sort of unique serial number. If number is only supposed to apply to the 'other membrane compartments' and not to the mitochondria then the sentence probably needs to be significantly re-arranged because that's not how it reads at present, at least not to me.

You're right. Mitochondria is plural. Mitochondrion is singular.
Your cells don't have a single Mitochondrion, they have thousands. It's hardly the most egregious thing thing though. The jelly bean stylized depiction is terrible and needs to die. It's much more like the endoplasmic reticulum, a web of mitochondrion.

 

[Chuckstar]

Final question: Why would it be a problem for the inside-out model that the mitochondria ended up in the cytoplasm? We believe that the mitochondria had to move through the outer membrane into the cell, but moving from the endoplasmic-reticulum into the cytoplasm becomes a “problem”? For other models, we have this whole ballet of membrane creation within the cell that has to play out after the mitochondria takes up residence, yet that’s more likely that the mitochondria moving out of the endoplasmic-reticulum into the cytoplasm?

 

[Zoc]

... the number and size of the mitochondrion and other membrane compartments ...


/pedant-hat-on

Surely that should read 'the number and size of the mitochondria' - you can't have 'the number of' and then a singular. 'the number and size of the [singular-thing]' makes no sense unless we're talking about some sort of unique serial number. If number is only supposed to apply to the 'other membrane compartments' and not to the mitochondria then the sentence probably needs to be significantly re-arranged because that's not how it reads at present, at least not to me.

I read that as "the number and size of the mitochondrion [compartments] and other membrane compartments," that is, "mitochondrion" is acting as an adjectival noun modifying "compartment." It might have been clearer as "the number and size of the mitochondrial and other membrane compartments," but perhaps the author thought that would imply compartments within the mitochondria rather than compartments enclosing the mitochondria.

 

[train_wreck]

Interesting article, thanks.
I'm enjoying these knowable articles.

I’ll take them over the FT reposts any day.

 

[CrystalCowboy]

Interesting and very speculative.

So let's layer on some more speculation. The origin of the nucleus was a defense against viruses as cells emerged from the RNA World.

 

[Uncivil Servant]

Another problem is the assumption that vessicles started out as offshoots from mitochondria. Are they all still offshoots of mitochondria? If not how/why did nuclear DNA take over construction of those vessicles?

That's not as huge a problem as it sounds (although I doubt the vesicles came directly from mitochondria):

Mitochondrial DNA is very short, encoding a small number of proteins that are likely necessary for responding to rapidly changing internal environments. Most of the original mitochondrial DNA appears to have migrated to the nucleus, and proteins are produced and transported to the mitochondria. Much of this may have occurred early, before the development of the nucleus, as mitochondria died and their DNA mixed with that of the host.

As an aside, some biologists have suggested that this is also the origin of straight chromosomes and the spliceosome. Some bacteria are known to have self-splicing "jumping" introns, remnants of retroviruses, that cut themselves out of the DNA and re-insert themselves elsewhere. These self-splicing introns would have played merry hell with the host's DNA, cutting it up into smaller pieces. The fact that self-splicing introns closely resemble the spliceosome could be convergent evolution, of course, but it's rather uncanny.

But you can see how this would have to happen before the nucleus evolved. Once it occurred, though, the doubling of chromosomes and massive increase in genetic material allowed each cell to have a massive gene library, as compared to bacteria.

 

[Uncivil Servant]

So we’re assuming that because the modern mitochondria do X that it means the original mitochondria did, also? And the argument for that is that modern mitochondria from different eukaryotes do it?

Aren’t we missing a few steps in that argument? At best, they’ve shown mitochondria had that ability early, not necessarily immediately. At worst they’ve rediscovered parallel evolution.

Well no, there's evidence that the original mitochondria probably didn't directly give ATP to the cell. They likely scavenged oxygen and pooped out hydrogen, similar to the much-reduced hydrogenosomes in the archeozooans. At some point, probably early on since I think all eukaryotes possess the gene, the ATP-ADP transporter had to evolve to transport ATP out of the mitochondria and refill it with ADP to process.

The effect would have been profound, opening up vast energy supplies beyond what any single cell could have accomplished at any prior point in Earth's history.

 

[lobabobloblaw]

It is a tune, sweet as it is complex; I’m fascinated by the granularity of it all.

 

[belrick]

I wish all the prose in this article could be the voice-over to animations of what it is describing, occasionally zooming in and out to different scales to show both the wide picture of what is being described (like showing the large structural differences between the inside-out (late?) model and the early model but then also the small differences envisioned between them (like the detailed differences in the filtering/separation function of structure walls at different times), each showing the short and long-term story they are trying to tell.

I'm sure biologists and biochemists can picture it all but for everyone else, there are tons of things for which we don't have pictures in our heads.

 

[Veritas super omens]

Nice write up. Plus 1 on Knowable and The Conversation articles. Better selection criteria for Wired and FT articles por favor.

 

[odikweos]

The nice version of Fermi's paradox is we go out and find a lot of bacteria and viruses, and it turns out a lot of stuff just has to go right to get intelligent beings. Not anything to bet the farm on, but it'll be super handy if that terms out to be true.

 

[Chuckstar]

Well no, there's evidence that the original mitochondria probably didn't directly give ATP to the cell. They likely scavenged oxygen and pooped out hydrogen, similar to the much-reduced hydrogenosomes in the archeozooans. At some point, probably early on since I think all eukaryotes possess the gene, the ATP-ADP transporter had to evolve to transport ATP out of the mitochondria and refill it with ADP to process.

The effect would have been profound, opening up vast energy supplies beyond what any single cell could have accomplished at any prior point in Earth's history.

Doesn’t that support my point? That all you learn from commonality among mitochondria is what the mitochondria in the last common ancestor could do, and not what the basal mitochondrion could do?

 

[keltor]

OK, this is just stupid. I'm reading this interesting article, but I'm thinking it really could do with some pictures or diagrams to explain what they are talking about. And then the original article in Knowable Magazine has them! Why aren't they included here? Someone brought that article here, why can't they take a little more time and bring all of it?

I'd insert them inline here myself, but when I try it doesn't work.

Per Knowable's resharing guidelines - "Photographs and illustrations are not included in this license."

I assume the editor who reposts them on Ars checks if any of the images themselves have permissive licenses (they do sometimes).

 

[ZenBeam]

Per Knowable's resharing guidelines - "Photographs and illustrations are not included in this license."

I assume the editor who reposts them on Ars checks if any of the images themselves have permissive licenses (they do sometimes).

Then they need to replace them with similar figures, not just leave them out.

 

[Martin123]

Then they need to replace them with similar figures, not just leave them out.

I guess that would defeat the purpose, which is to give the Ars staff a break over the weekend... (Also, simply creating an equivalent figure may well be problematic with respect to their license.)

 

[Fatesrider]

So we’re assuming that because the modern mitochondria do X that it means the original mitochondria did, also? And the argument for that is that modern mitochondria from different eukaryotes do it?

Aren’t we missing a few steps in that argument? At best, they’ve shown mitochondria had that ability early, not necessarily immediately. At worst they’ve rediscovered parallel evolution.

I think you're forgetting a few things.

First of all, this happened extremely early in "life" on Earth. The populations of cells would have been fairly low compared to modern times, and they were probably easily killed due to starvation, etc. Originally, there was NO mitochondria. That structure apparently arose from two cells merging into a symbiotic one. Given that it has clear advantages in energy management, I'd expect such cells to easily out-compete other cells lacking such a feature.

I think you may be tripped up by this:

The archaeal cell would have had long protrusions, as seen on some modern-day archaea that live in close association with other microbes. The alphaproteobacterium would have nestled up against these slender extensions.

Describing ancient cell characteristics is based on the same kind of cell today. Not all fish look alike, but they share a lot of characteristics due to their environment and other factors.

So if the BASIC characteristics of a "modern" cell sans mitochondria existed back then, and it likely did, then there's little mystery about how this happened.

Going back to the fish analogy, the cells back then may not have looked exactly like modern cells, but they probably had similar ENOUGH structures and characteristics to allow for the evolutionary results of absorbing a "mitochondria cell" to happen. Much of that is simply chemistry and how similar proteins and such will fold in similar ways.

The thing you might be missing is that, from a biological point of view, given the environment and competition, ONE cell equipped with a mitochondria in a sea of other cells that didn't have a mitochondria could, over time, displace ALL OTHER LIFE.

While it's unlikely to have been a single event, there's no biological barrier to a one-off, chance merging of a cell without a mitochondria and a mitochondria cell getting together and dividing and becoming the basis for all modern life.

Proving THAT would be problematic, especially after billions of years, but there's really nothing discovered here that conflicts with life as we know it today. After all, if all life arose from ONE chance encounter between two cells who, instead of one having the other for lunch, managed to create a beneficial detente and took over the world, we'd not have much evidence of what came before then other than the genetic heritage of that first cell (and whatever evolution did to it over billions of years).

No parallel evolution needed in that case. Sufficient competitive advantage can do it all by itself. And the acquisition of a mitochondria WAS sufficient competitive advantage back then for one cell to dominate the world.

At least in theory.

 

[DovePig]

Per Knowable's resharing guidelines - "Photographs and illustrations are not included in this license."

I assume the editor who reposts them on Ars checks if any of the images themselves have permissive licenses (they do sometimes).

The graphics created by Knowable are under CC BY‑ND (which probably includes at least the most important ones here, the two models [img links], at least according to their credit).

Article text and graphics created by Knowable Magazine are published under a Creative Commons Attribution-NoDerivatives 4.0 license (CC BY-ND). Photographs, illustrations and other art used within articles are not covered by this license, and it is the responsibility of the republisher to arrange permission to use these images.

It's the other illustrations that would have to be negotiated for with respective rights holders or checked for CC permissions separately.

And Knowable's HTML republish tool simply doesn't include the graphics, so it would indeed take more work. A pity, I certainly agree, but I can feel for the editor intern or whoever doing it on weekends. Original and detailed news publishing got hit hard, and even as part of Conde Nast and with voluntary subscribers, Ars support crew is probably quite small. I remember how even copyeditors got seriously downsized in some national newspapers of record, and copyeditors were often the smartest people in the building (huge respect to them!). And even if your CMS allows you to prepare articles for deferred publishing on weekend during the work days, it still needs somebody to check if it went correctly and somebody to prepare it during the work days, when they might have to work on other Ars original content instead. Yes, it can be a bit sad and not ideal, but that's how it often is.

 

[Mongo McMongo]

It may never be possible to know for sure what happened such a very long time ago.

I appreciate the cautious tone, but (absent the invention of a time machine) in practice it is simply "it will never be known for certain..."

 

[Cathbadhian]

I think the article is fascinating in that I imagine many of us struggle a little with just how revolutionary multicellular life was on Earth, and would appreciate this dive into the topic. The usual summation in popular science rarely does it justice preferring to leave the incredible complexity it involved unmentioned, which can then be mistaken as it being simple. It's anything but.

I still don't know what to believe though, but can take comfort that most of my hosted population isn't too worried about the details so long as their cooperative efforts result in reproduction.

 

[gottathink]

I guess that would defeat the purpose, which is to give the Ars staff a break over the weekend... (Also, simply creating an equivalent figure may well be problematic with respect to their license.)

I’ve been wondering what solution to suggest for my time zone’s dearth of content on Mondays. It hadn’t occurred to me the republished articles might be it. Keep them coming!

 

[md5crypto]

All I know from watching ChubbyEmu videos is that the mitochondria is the 'powerhouse of the cell'.

 

[llanitedave]

The thing you might be missing is that, from a biological point of view, given the environment and competition, ONE cell equipped with a mitochondria in a sea of other cells that didn't have a mitochondria could, over time, displace ALL OTHER LIFE.

Well, "ALL OTHER LIFE", at least, is a little overstated, seeing as how a single mitochondria-less cyanobacterium, prochlorococcus, forms the base of the ocean food chain and contributes a significant portion of the atmosphere's oxygen.

 

[Veritas super omens]

Well, "ALL OTHER LIFE", at least, is a little overstated, seeing as how a single mitochondria-less cyanobacterium, prochlorococcus, forms the base of the ocean food chain and contributes a significant portion of the atmosphere's oxygen.

Polluters. Prime suspect in the first mass extinction...

 

[Uncivil Servant]

So if the BASIC characteristics of a "modern" cell sans mitochondria existed back then, and it likely did, then there's little mystery about how this happened.

No, it almost certainly did not. There's absolutely no evidence for eukaryotic cells lacking mitochondria. The archaeozooans were once viewed as such a "missing link", but further investigation showed that their hydrogenosome organelles were actually atrophied mitochondria that had lost most of their functions.

The implications are important: the only way to get to a "halfway" niche between prokaryotes and eukaryotes requires an atrophied eukaryote. Prokaryotes simply cannot get to that point due to energy constraints, and those constraints have downstream effects on things like genome size and overall cell volume.

The thing you might be missing is that, from a biological point of view, given the environment and competition, ONE cell equipped with a mitochondria in a sea of other cells that didn't have a mitochondria could, over time, displace ALL OTHER LIFE.

No. In fact there are a number of niches that prokaryotes inhabit alongside eukaryotes. There are even more that can only be inhabited by prokaryotes, but the evolution of plants and algal seaweed did not drive out cyanobacteria.

What a cell can do with mitochondria is exploit a whole new horizon of niches due to its extra energy. But equally important are all of the other aspecrs of the eukaryote package, like the massive genome stored in multiple duplicated parts. That allows for all sorts of new exaptations from existing genes. Or the use of cell compartments and intracellular transportation networks. And of course, multicellular organisms with differentiated tissue can only occur in organisms with large multipart genomes and the ability to switch genes on and off.

While it's unlikely to have been a single event, there's no biological barrier to a one-off, chance merging of a cell without a mitochondria and a mitochondria cell getting together and dividing and becoming the basis for all modern life.

Proving THAT would be problematic, especially after billions of years, but there's really nothing discovered here that conflicts with life as we know it today. After all, if all life arose from ONE chance encounter between two cells who, instead of one having the other for lunch, managed to create a beneficial detente and took over the world, we'd not have much evidence of what came before then other than the genetic heritage of that first cell (and whatever evolution did to it over billions of years).

I don't even know what you're trying to say here. The vast majority of life on Earth is prokaryotic, with no mitochondria, and eukaryogenesis occurred at least 1.5 billion years after abiogenesis.

As for the genetic heritage of what came before, yes we can reconstruct some of that. This is why scientists are so certain that mitochondria originated within the alphaproteobacteria, why they absolutely had to have been bacteria at least, why the host was almost certainly archaean, etc.

Every cell in our bodies tells this history. Your mitochondria have their own bacterial-style DNA and bacterial-style ribosomes. Your nucleus has DNA arranged differently from any prokaryote, but it produces ribosomes similar to those in archaeans.

 

[Rombobjörn]

Why would it be a problem for the inside-out model that the mitochondria ended up in the cytoplasm? We believe that the mitochondria had to move through the outer membrane into the cell, but moving from the endoplasmic-reticulum into the cytoplasm becomes a “problem”?

The number of membranes seems to be unexplained. The endoplasmatic reticulum spawns vesicles all the time. It could easily bud off a vesicle with a bacterium inside it to form a mitochondrion, but that would leave an additional membrane around the bacterium.

Wikipedia tells me that alphaproteobacteria are gram-negative. That means that they have an outer membrane surrounding their cell membrane. Mitochondria also have an outer and an inner membrane. The inside-out hypothesis should produce mitochondria with a third membrane around the alphaproteobacterium's original two. One of the three membranes would have to have been lost somehow.

The "mitochondria late" hypothesis has the same problem. Cells engulf things by wrapping their cell membrane around them and budding off a vesicle. White blood cells eat infectious bacteria that way. If that was how mitochondria originated, it should again add a third membrane, and one membrane must have been lost somehow.

If it had been a gram-positive bacterium instead, then the number of membranes would fit. Gram-positive bacteria have only one membrane, and either method of engulfing one would add a second membrane, forming a mitochondrion with two membranes. But everybody seem to agree that the ancestor was an alphaproteobacterium.

The "mitochondria early" hypothesis doesn't offer a better explanation. It just skips the problem by starting with the alphaproteobacterium already inside the archaeal cell.

 

[Router66]

The number of membranes seems to be unexplained. The endoplasmatic reticulum spawns vesicles all the time. It could easily bud off a vesicle with a bacterium inside it to form a mitochondrion, but that would leave an additional membrane around the bacterium.

Wikipedia tells me that alphaproteobacteria are gram-negative. That means that they have an outer membrane surrounding their cell membrane. Mitochondria also have an outer and an inner membrane. The inside-out hypothesis should produce mitochondria with a third membrane around the alphaproteobacterium's original two. One of the three membranes would have to have been lost somehow.

The "mitochondria late" hypothesis has the same problem. Cells engulf things by wrapping their cell membrane around them and budding off a vesicle. White blood cells eat infectious bacteria that way. If that was how mitochondria originated, it should again add a third membrane, and one membrane must have been lost somehow.

If it had been a gram-positive bacterium instead, then the number of membranes would fit. Gram-positive bacteria have only one membrane, and either method of engulfing one would add a second membrane, forming a mitochondrion with two membranes. But everybody seem to agree that the ancestor was an alphaproteobacterium.

The "mitochondria early" hypothesis doesn't offer a better explanation. It just skips the problem by starting with the alphaproteobacterium already inside the archaeal cell.

Two possible answers, or maybe parts of the answer.

1. Proto-mitochondria (the particular but theoretical alphaproteobacteria that became mitochondria) may have been quite different to any of the extant alphaproteobacteria.
Subsequent phylogenomic analyses that specifically address long branch attraction and compositional bias artefacts suggest that mitochondria did not evolve from Rickettsiales or any other currently recognized alphaproteobacterial lineage. Rather, our analyses indicate that mitochondria evolved from a proteobacterial lineage that branched off before the divergence of all sampled alphaproteobacteria.

2. Shedding organelles is trivial among cells. Red blood cells expel the nucleus, onion fruit cells shed their chloroplasts, etc. Losing or transforming a bacterial membrane is, maybe, fairly "easy" along such an evolutionary history.

Great article btw.

 

[AbboFun]

I'm still confused but now at a much higher level.