Absorbing DNA

[FrumiousBandersnatch]

Sorry. That was a typo. It should have read, "Could the bacteria pick up enough DNA from the mammoth to become a eukaryote?"

Ah, OK; that makes more sense. It's not going to happen, there's too many differences between them. I doubt even that inserting a complete eukaryotic nucleus into a bacterium would be viable.

 

[Resha Caner]

Ah, OK; that makes more sense. It's not going to happen, there's too many differences between them. I doubt even that inserting a complete eukaryotic nucleus into a bacterium would be viable.

Well, the hypothesis is that eventually it happened somehow. Yes? If not, UCA is in danger.

 

[Loudmouth]

Well, the hypothesis is that eventually it happened somehow. Yes? If not, UCA is in danger.

Yes, it occurred eventually over millions and millions of years, not all at once from one giant HGT event.

 

[Resha Caner]

Yes, it occurred eventually over millions and millions of years, not all at once from one giant HGT event.

And not necessarily all HGT events, yes? The conditions just had to be right to promote whatever series of events were necessary. So what might the minimum number of events be?

 

[Loudmouth]

And not necessarily all HGT events, yes?

Correct. However, HGT events are thought to have been much more common at the root of the eukaryote/prokaryote/archae tree. Today, HGT in eukaryotes is exceedingly rare.

The conditions just had to be right to promote whatever series of events were necessary. So what might the minimum number of events be?

I don't think that number is even calculable. The first problem you run into is the minimum number of events vs. the number of events that actually occurred.

As an example, humans have created a bacterial genome from scratch, which is kind of cool. They created a streamlined genome contains 500k base pairs and about 450 genes.
Design and synthesis of a minimal bacterial genome | Science

While streamlined, this is probably not the absolute minimal genome that could support life. Even then, this artificial genome is much smaller and more streamlined than many naturally occurring genomes. The moral of the story is that evolution really doesn't optimize for genome size, so it makes it difficult to figure out what the smallest genome possible is.

 

[Resha Caner]

I don't think that number is even calculable. The first problem you run into is the minimum number of events vs. the number of events that actually occurred.

I realize that in a non-deterministic system the chances of the actual number of events equaling the minimum is extremely small. I also half expected you to say it might not be possible to know the minimum. Further, isn't it possible that something useful may not emerge until the end of the event chain? All of the changes may lie dormant until the end, and then suddenly express the change.

But has anyone tried to make some ballpark estimates? Has a series of DNA change events been observed with an emergent characteristic recorded at the end? I'm just curious if it would mean ten, a thousand, a million events?

 

[Loudmouth]

I realize that in a non-deterministic system the chances of the actual number of events equaling the minimum is extremely small.

I would think that the same would be true of a deterministic system.

Further, isn't it possible that something useful may not emerge until the end of the event chain?

That would apply more to abiogenesis. Once you have a simple replicator that successfully survives and reproduces you have something useful in a biological sense. If we are talking about the split between prokaryotes and eukaryotes you are starting with something useful.

Has a series of DNA change events been observed with an emergent characteristic recorded at the end?

Sure. There are many known single nucleotide substitution mutations that produce a phenotypic change. Single mutations can confer antibiotic resistance in many bacterial species, just as an example off the top of my head.

 

[FrumiousBandersnatch]

Well, the hypothesis is that eventually it happened somehow. Yes? If not, UCA is in danger.

I was referring to contemporary bacteria and eukaryotic cells, which have had 3 billion-odd years of evolutionary divergence and increasing sophistication. Back in the day, organisms were very much simpler and more alike than they are now.

 

[Resha Caner]

Sure. There are many known single nucleotide substitution mutations that produce a phenotypic change. Single mutations can confer antibiotic resistance in many bacterial species, just as an example off the top of my head.

OK ... maybe there's nowhere else for the conversation to go. We have an example of a single event (single nucleotide change) that causes a functional change in an organism. What would be the largest change (longest chain of observed events) you know of?

 

[Loudmouth]

OK ... maybe there's nowhere else for the conversation to go. We have an example of a single event (single nucleotide change) that causes a functional change in an organism. What would be the largest change (longest chain of events) you know of?

Whole genome duplications would probably fit the bill. This is where the genome doubles in a single generation. It is thought to have happened in the vertebrate lineage at least once. There are also polyploidy plants used in agriculture that have 2x or 4x the normal chromosome count (e.g. strawberries).

 

[Resha Caner]

Whole genome duplications would probably fit the bill. This is where the genome doubles in a single generation. It is thought to have happened in the vertebrate lineage at least once. There are also polyploidy plants used in agriculture that have 2x or 4x the normal chromosome count (e.g. strawberries).

You're quick. You answered before I added a clarifying word. I meant to ask for the longest chain of observed events. And, again, is that 10, 1000, 1000000?

 

[Loudmouth]

You're quick. You answered before I added a clarifying word. I meant to ask for the longest chain of observed events. And, again, is that 10, 1000, 1000000?

The closest would probably be Lenski's evolution experiments where he mapped genetic changes in E. coli over decades and tens of thousands of generations. According to their website, they are up to 50,000 generations:

E. coli Long-term Experimental Evolution Project Site

This is the experiment where they observed the evolution of aerobic citrate metabolism which came about through a recombination event that moved a new promoter in front of the gene for the citrate enzyme (if memory serves).

 

[Resha Caner]

The closest would probably be Lenski's evolution experiments where he mapped genetic changes in E. coli over decades and tens of thousands of generations. According to their website, they are up to 50,000 generations.

OK, 5E4 generations over 30 years (The site says since Feb 1988, but I'm rounding). But what constitutes a "generation"? I assume it's not just one DNA change event, but multiple events amongst a population.

[edit] P.S. Your ability to recall these things continues to impress me.

 

[PsychoSarah]

Sorry. That was a typo. It should have read, "Could the bacteria pick up enough DNA from the mammoth to become a eukaryote?"

@PsychoSarah FYI, I'm male.

Sorry, the answer is still no, however, as a bacteria would never get enough eukaryotic DNA to do that, would still be lacking the various organelles of a eukaryote such as mitochondria, and the amount of DNA that would even come close to doing something comparable to that would be far more liable to cause total cell failure of the bacterium and kill it.

 

[Loudmouth]

OK, 5E4 generations over 30 years (The site says since Feb 1988, but I'm rounding). But what constitutes a "generation"? I assume it's not just one DNA change event, but multiple events amongst a population.

You can peruse their protocol here:

Overview of the E. coli long-term evolution experiment

They start each new 10 ml culture with 0.1 ml of the previous days culture. The bacteria need to divide 5 to 6 times (i.e. double their numbers 5 to 6 times) to reach 100% confluency with a 1% inoculum, so each day they start a new culture they produce 5 to 6 generations of bacteria. Every 75 days they freeze back a portion of the culture which represents 500 generations of accumulated mutations in many different lineages.

[edit] P.S. Your ability to recall these things continues to impress me.

Thank you.

 

[Resha Caner]

Sorry, the answer is still no, however, as a bacteria would never get enough eukaryotic DNA to do that, would still be lacking the various organelles of a eukaryote such as mitochondria, and the amount of DNA that would even come close to doing something comparable to that would be far more liable to cause total cell failure of the bacterium and kill it.

Yes, I understand that the current hypothesis is that the mitochondria originated by absorbing another organism into the cell. However, in order to fix that, didn't it require a concurrent change in DNA?

 

[PsychoSarah]

Yes, I understand that the current hypothesis is that the mitochondria originated by absorbing another organism into the cell. However, in order to fix that, didn't it require a concurrent change in DNA?

Mitochondria have their own DNA. There was certainly evolutionary changes over time that improved the symbiotic relationship, but just having the mitochondria there wouldn't have required concurrent changes in DNA, unless the organism that swallowed it would have typically been able to digest the organism, and had a mutation that made its digestion less effective.

 

[Loudmouth]

Yes, I understand that the current hypothesis is that the mitochondria originated by absorbing another organism into the cell. However, in order to fix that, didn't it require a concurrent change in DNA?

No. Many humans are carrying obligate intracellular parasites right now, such as chlamydia species. In fact, chlamydia can't survive outside of a host cell, hence the "obligate" moniker. Chlamydia also have greatly reduced genomes. Sound familiar? They are acting a lot like mitochondria.

 

[Resha Caner]

They start each new 10 ml culture with 0.1 ml of the previous days culture. The bacteria need to divide 5 to 6 times (i.e. double their numbers 5 to 6 times) to reach 100% confluency with a 1% inoculum, so each day they start a new culture they produce 5 to 6 generations of bacteria. Every 75 days they freeze back a portion of the culture which represents 500 generations of accumulated mutations in many different lineages.

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.

 

[Resha Caner]

Mitochondria have their own DNA. There was certainly evolutionary changes over time that improved the symbiotic relationship, but just having the mitochondria there wouldn't have required concurrent changes in DNA, unless the organism that swallowed it would have typically been able to digest the organism, and had a mutation that made its digestion less effective.

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?