Absorbing DNA

Loudmouth · Feb 8, 2017

Resha Caner said:
Yeah, OK. As I thought, the number of DNA changes involved is probably much greater than 5E4, yet at the same time it's still basically unknown how many of those are propagated and further how many lead to an emergent functional change.

They have sequenced the genome of many of those saved generations, so they do have an idea of both variation within the population and what mutations have been propagated.

As to the number of mutations compared to generations, that's a bit tougher to get a handle on, although population genetics isn't my strength. The mutation rate is about 1 mutation in every 2-3 generations which means about 250 mutations in 500 generations. But that is in just a single lineage. You have a lot of bacteria growing in parallel, so a population of 1 million bacteria will produce about 500,000 mutations in a single generation. Every 5-6 generations 99% of the population is wiped out, and a new population is started with just 1% of the population. How all of this balances out in the end I'm not sure, but someone with more knowledge of pop genetics could definitely add more.

Loudmouth · Feb 8, 2017

Resha Caner said:
I'm getting that euphoric feeling that I'm about to learn something very interesting. So there are multiple and distinct "sets" of DNA in a eukarytotic cell? As I asked earlier, how is this fixed? In other words, how does the organism then reproduce such that its descendants also have the organelles?

When a cell divides the cytoplasm is split between the two new cells. That cytoplasm contains mitochondria so that the mitochondria are split between the two new cells. The mitochondria start dividing to repopulate the new cells.

Resha Caner · Feb 8, 2017

Loudmouth said:
They have sequenced the genome of many of those saved generations, so they do have an idea of both variation within the population and what mutations have been propagated.

As to the number of mutations compared to generations, that's a bit tougher to get a handle on, although population genetics isn't my strength. The mutation rate is about 1 mutation in every 2-3 generations which means about 250 mutations in 500 generations. But that is in just a single lineage. You have a lot of bacteria growing in parallel, so a population of 1 million bacteria will produce about 500,000 mutations in a single generation. Every 5-6 generations 99% of the population is wiped out, and a new population is started with just 1% of the population. How all of this balances out in the end I'm not sure, but someone with more knowledge of pop genetics could definitely add more.

That would be cool to know. One could say the employed process is very inefficient. Were it to be made more efficient it seems the time scale could be considerably reduced.

Resha Caner · Feb 8, 2017

Loudmouth said:
When a cell divides the cytoplasm is split between the two new cells. That cytoplasm contains mitochondria so that the mitochondria are split between the two new cells. The mitochondria start dividing to repopulate the new cells.

OK. So ... 1) In sexual reproduction, does the zygote contain organelles with DNA from both parents? 2) Is it determined that will be the result, or could it end up with organelles from just one parent? 3) Do any organelles every affect morphology?

Loudmouth · Feb 8, 2017

Resha Caner said:
That would be cool to know. One could say the employed process is very inefficient. Were it to be made more efficient it seems the time scale could be considerably reduced.

Well, we already know the results for earlier generations. They have published some of their results over the years.

Tempo and mode of genome evolution in a 50,000-generation experiment : Nature

It appears that one of the lineages increased its mutation rate. Nonetheless, those graphs should give you an idea of how mutations accumulated over that time.

Loudmouth · Feb 8, 2017

Resha Caner said:
OK. So ... 1) In sexual reproduction, does the zygote contain organelles with DNA from both parents?

No. As it turns out, the mitochondria in the sperm is concentrated in the tail section. That tail is shed outside of the egg upon fertilization. This means that children only inherit their mother's mitochondria. This is why maternal bloodlines can be traced though an uninterrupted lineage of women.

3) Do any organelles every affect morphology?

Mutations in mitochondria can probably cause disease which would result in a diseased morphology. I would tend to think that changes in mitochondrial efficiency, number, or output would be tied closer to muscle mass and then the compensatory changes in skeletal structure to accommodate those changes in muscle mass.

PsychoSarah · Feb 8, 2017

Resha Caner said:
I'm getting that euphoric feeling that I'm about to learn something very interesting. So there are multiple and distinct "sets" of DNA in a eukarytotic cell? As I asked earlier, how is this fixed? In other words, how does the organism then reproduce such that its descendants also have the organelles?

The organelles reproduce independently of the entire cell over the course of its life. When a cell splits to reproduce, the cell contents of the parent cell are divided roughly evenly between the two daughter cells.

The organelles that have their own DNA in eukaryotic cells are mitochondria, which are in all eukaryotic cells, and chloroplasts, which are only found in cells which carry out photosynthesis. Both of these organelles also have circular DNA, like bacteria do. They replicate themselves. The rest of the organelles replicate with direction from proteins produced by ribosomes, which are made in the nucleolus, part of the nucleus, which contains the DNA.

Something worth noting is the fact that chloroplasts and mitochondria are the organelles responsible for energy production.

Resha Caner · Feb 8, 2017

Am I interpreting this correctly that it is possible to exchange DNA between the mitochondria and the nucleus?

DNA Transfer

Loudmouth · Feb 8, 2017

Resha Caner said:
Am I interpreting this correctly that it is possible to exchange DNA between the mitochondria and the nucleus?

DNA Transfer

That is correct. NUMTs have been known about for a while now. In fact, they have been used as phylogenetic markers for determining evolutionary histories.

Resha Caner · Feb 8, 2017

Loudmouth said:
That is correct. NUMTs have been known about for a while now. In fact, they have been used as phylogenetic markers for determining evolutionary histories.

Given that, this article seems interesting: Intercellular Organelle Traffic

Loudmouth · Feb 8, 2017

Resha Caner said:
Given that, this article seems interesting: Intercellular Organelle Traffic

The mitochondria is an organelle, but not all organelles are mitochondria. That article appears to be talking about Golgi complexes which do not have their own genome. Perhaps there is something else that you find interesting in that article?

Resha Caner · Feb 8, 2017

Loudmouth said:
The mitochondria is an organelle, but not all organelles are mitochondria. That article appears to be talking about Golgi complexes which do not have their own genome. Perhaps there is something else that you find interesting in that article?

I missed that. Thanks for pointing it out. My interest was in the idea of intercellular movement by mitochondria.

Loudmouth · Feb 8, 2017

Resha Caner said:
I missed that. Thanks for pointing it out. My interest was in the idea of intercellular movement by mitochondria.

I think they are pretty passive and just kind of go with the flow. They don't have any flagella or other means of propulsion, so they are reliant on other features in the cell such as the actin bioskeleton.

PsychoSarah · Feb 8, 2017

Loudmouth said:
They have sequenced the genome of many of those saved generations, so they do have an idea of both variation within the population and what mutations have been propagated.

As to the number of mutations compared to generations, that's a bit tougher to get a handle on, although population genetics isn't my strength. The mutation rate is about 1 mutation in every 2-3 generations which means about 250 mutations in 500 generations. But that is in just a single lineage. You have a lot of bacteria growing in parallel, so a population of 1 million bacteria will produce about 500,000 mutations in a single generation. Every 5-6 generations 99% of the population is wiped out, and a new population is started with just 1% of the population. How all of this balances out in the end I'm not sure, but someone with more knowledge of pop genetics could definitely add more.

It actually gets more complicated, because some species have more frequent mutation than others. For example, each human is born with 40-60 mutations not present in either of their parents. The number is significantly less for all bacteria compared to that, and it's not as if it is precisely the same for every species of bacteria either. Not to mention environmental impact... thank goodness viruses are really simple and predictable about it, otherwise making a yearly flu vaccine would be a nightmare.

Resha Caner · Feb 9, 2017

Loudmouth said:
I think they are pretty passive and just kind of go with the flow. They don't have any flagella or other means of propulsion, so they are reliant on other features in the cell such as the actin bioskeleton.

It appears the idea is being studied, though this link states it is uncertain whether this is an in vivo phenomena.

Loudmouth · Feb 9, 2017

PsychoSarah said:
It actually gets more complicated, because some species have more frequent mutation than others. For example, each human is born with 40-60 mutations not present in either of their parents. The number is significantly less for all bacteria compared to that, and it's not as if it is precisely the same for every species of bacteria either. Not to mention environmental impact... thank goodness viruses are really simple and predictable about it, otherwise making a yearly flu vaccine would be a nightmare.

It would appear that the mutation rate isn't even the same for all populations of E. coli. One of the E. coli populations in Lenski's study had a much higher mutation rate. I think we can all agree that population genetics is a complicated subject.

As to viruses, it would be problematic if viruses mutated more quickly than they do. If a new strain appeared every 2 weeks it would be quite difficult to keep up.

Loudmouth · Feb 9, 2017

Resha Caner said:
It appears the idea is being studied, though this link states it is uncertain whether this is an in vivo phenomena.

I didn't look into it much, but you might want to look into autophagy. I believe the process involves the capture and breakdown of mitochondria in intracellular vesicles.

Resha Caner · Feb 9, 2017

Thanks. I'm not wedded to any particular mechanism, so I'll keep that in mind if I hit a dead end. I'm more interested in finding if there are known mechanism(s) for prokaryote mediated transfer of DNA between eukaryotes. The original links I posted seemed to indicate there is ... These do as well:
Intercellular Nanotubes Mediate Bacterial Communication
Bacteria-mediated transfer of eukaryotic expression plasmids into mammalian host cells

The only aspect that seems to draw skepticism is the speed/extent of what would be transferred ... more digging.

Loudmouth · Feb 9, 2017

Resha Caner said:
Thanks. I'm not wedded to any particular mechanism, so I'll keep that in mind if I hit a dead end. I'm more interested in finding if there are known mechanism(s) for prokaryote mediated transfer of DNA between eukaryotes.

Not that I am aware of. HGT is exceedingly rare in eukaryotes to begin with, so this makes it doubtful that there is a common mechanism of HGT that is continuously moving DNA between species.

Here is a chart with numbers showing the number of genes from HGT in various lineages:

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

If we look at the primate tree we can see that in the H. sapiens lineage there has only been one gene acquired by HGT since the first branch in the entire primate tree. That's tens of millions of years, and only one gene shows evidence of being acquired by HGT.

The original links I posted seemed to indicate there is ... These do as well:
Intercellular Nanotubes Mediate Bacterial Communication
Bacteria-mediated transfer of eukaryotic expression plasmids into mammalian host cells

Not sure how this relates to situations in nature, if that is what you are interested in. In the second paper they are using an engineered bacteria to release a plasmid of DNA that already has eukaryotic genes and eukaryotic promoters. Bacteria in the wild would not be carrying these plasmids. On top of that, I am not sure the introduced plasmid would be replicated if during cell division since it is not being incorporated into the genome.

The only aspect that seems to draw skepticism is the speed/extent of what would be transferred ... more digging.

The reason for that skepticism is that we don't see much evidence for HGT in eukaryotes. If genes were moving willy nilly between species then it would be rather easy to detect. Any phylogenetic analysis would find these HGT events with ease.

Resha Caner · Feb 9, 2017

Loudmouth said:
Here is a chart with numbers showing the number of genes from HGT in various lineages:

How is it known to be HGT? Is it that the same sequences were found in different species or is there some other indicator?

Loudmouth said:
Not sure how this relates to situations in nature, if that is what you are interested in.

Finding an example in nature would be preferable, but I don't think it's absolutely necessary. One could argue that engineered solutions are natural - that we and what we do are part of nature. However, if the engineering is too extreme, that could be a problem.

Loudmouth said:
The reason for that skepticism is that we don't see much evidence for HGT in eukaryotes.

That's what I would expect. I wasn't looking for "willy nilly" HGT. I would expect that most of the time HGT events are low, but conditions may arise occasionally (such as during adaptive radiation time periods) that increase the frequency of HGT events.

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