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Author Topic:   From Prokaryotes to Eukaryotes--Development of the Nucleus
Snikwad
Inactive Member


Message 1 of 16 (136462)
08-24-2004 2:57 AM


One of the factors used to differentiate between prokaryotic and eukaryotic cells is the existence of a nucleus surrounded by a membrane, containing individual chromosomes, in eukaryotes.
If I recall correctly, primitive eukaryotic cells obtained as symbionts other prokaryotes, which became organelles like mitochondria, chloroplasts, etc. As far as I know, the incorporation of a symbiont is not how the nucleus developed.
My question is whether there exist any theories that address the evolutionary development of the nucleus.

"Chance is a minor ingredient in the Darwinian recipe, but the most important ingredient is cumulative selection which is quintessentially nonrandom."
--Richard Dawkins, The Blind Watchmaker

Replies to this message:
 Message 3 by Wounded King, posted 08-24-2004 5:39 AM Snikwad has replied

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 2 of 16 (136473)
08-24-2004 4:35 AM


Thread moved here from the Proposed New Topics forum.

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 3 of 16 (136480)
08-24-2004 5:39 AM
Reply to: Message 1 by Snikwad
08-24-2004 2:57 AM


There are hypothetical models for the origin of the nucleus as the result of endosymbiosis. The following is a freely available full text review covering some work on a symbiotic origin.
And a more recent paper provides some genetic evidence for the integration of archaeal genes associated with nuclear function in the eukaryota.
TTFN,
WK

This message is a reply to:
 Message 1 by Snikwad, posted 08-24-2004 2:57 AM Snikwad has replied

Replies to this message:
 Message 4 by Snikwad, posted 02-04-2005 3:56 PM Wounded King has not replied
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Snikwad
Inactive Member


Message 4 of 16 (183132)
02-04-2005 3:56 PM
Reply to: Message 3 by Wounded King
08-24-2004 5:39 AM


Thanks for the sources Wounded King (a bit late, I knowsorryI went through another I lost my password phase but had intended to respond immediately). I have another [slightly tangential] question. Again it’s about the evolution of eukaryotic cells. An endosymbiotic origin for mitochondria and chloroplasts certainly makes sense, given that they contain their own DNA that replicates when the organelle divides, and that the genes that the organelles encode are actually transcribed inside of the organelle, and are subsequently translated on organelle ribosomes.
My question is: how does this incorporation work? I mean, on the surface it seems soLamarckian. How does the DNA within the nuclear membrane come to know how to encode for the development of chloroplasts, for example?
My original guess was that perhaps the chloroplast’s DNA made it into the nucleus of the cell and some sort of synthesis occurred. However, I’m almost certain that DNA can’t pass through the nuclear membrane, so now I’m thinking perhaps it was the RNA analogue of the chloroplast’s DNA that made it into the nucleus and then some synthesis occurred (perhaps via some sort of reverse transcription). I’m quite sure RNA can cross the nuclear membrane. I’m probably way off the mark, but none of the textbooks I have seem to address this issue.
My question, put simply, is what is the mechanism by which nuclear DNA comes to code for organelles incorporated by endosymbiosis?
This message has been edited by Snikwad, 02-04-2005 15:57 AM

"Chance is a minor ingredient in the Darwinian recipe, but the most important ingredient is cumulative selection which is quintessentially nonrandom."
--Richard Dawkins, The Blind Watchmaker

This message is a reply to:
 Message 3 by Wounded King, posted 08-24-2004 5:39 AM Wounded King has not replied

Replies to this message:
 Message 5 by Gary, posted 02-05-2005 7:30 PM Snikwad has replied
 Message 7 by RAZD, posted 02-05-2005 11:05 PM Snikwad has replied
 Message 11 by TheLiteralist, posted 02-06-2005 2:25 AM Snikwad has replied

  
Gary
Inactive Member


Message 5 of 16 (183331)
02-05-2005 7:30 PM
Reply to: Message 4 by Snikwad
02-04-2005 3:56 PM


I don't know how the nucleus came about, but I know that the chloroplasts and mitochondria contain their own genomes with a limited number of genes. Though dependent on the nucleus, they produce some of their own proteins. I believe it is sometimes possible for DNA to move from the chloroplast or mitochondrion to the nucleus.

This message is a reply to:
 Message 4 by Snikwad, posted 02-04-2005 3:56 PM Snikwad has replied

Replies to this message:
 Message 6 by Snikwad, posted 02-05-2005 10:20 PM Gary has not replied

  
Snikwad
Inactive Member


Message 6 of 16 (183370)
02-05-2005 10:20 PM
Reply to: Message 5 by Gary
02-05-2005 7:30 PM


Gary writes:
I believe it is sometimes possible for DNA to move from the chloroplast or mitochondrion to the nucleus.
Which I suppose is what I’m asking. How does it do this? mRNA has the potential to cross the nuclear membrane because before leaving the nucleus, it has added to it around 200 or so adenine nucleotides to the 3’ end of it. If I recall correctly this is called a poly-A tail, and it’s what controls how mRNA moves across the nuclear membrane. Note that as far as I know, this is just movement from the nucleus into the cytoplasm. If DNA is capable of moving from the mitochondria and/or chloroplasts into the nucleus, how does it do this?

"Chance is a minor ingredient in the Darwinian recipe, but the most important ingredient is cumulative selection which is quintessentially nonrandom."
--Richard Dawkins, The Blind Watchmaker

This message is a reply to:
 Message 5 by Gary, posted 02-05-2005 7:30 PM Gary has not replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 7 of 16 (183373)
02-05-2005 11:05 PM
Reply to: Message 4 by Snikwad
02-04-2005 3:56 PM


My question is: how does this incorporation work? I mean, on the surface it seems soLamarckian. How does the DNA within the nuclear membrane come to know how to encode for the development of chloroplasts, for example?
isn't your answer already contained in:
. An endosymbiotic origin for mitochondria and chloroplasts certainly makes sense, given that they contain their own DNA that replicates when the organelle divides, and that the genes that the organelles encode are actually transcribed inside of the organelle, and are subsequently translated on organelle ribosomes.
Remember that the nucleus is always inside a cell and that the whole cell divides to reproduce (whether sexually or asexually).

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

This message is a reply to:
 Message 4 by Snikwad, posted 02-04-2005 3:56 PM Snikwad has replied

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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 8 of 16 (183380)
02-05-2005 11:51 PM


Something half way to multicellular
This is a bit off to the side of this topic. But it is also related so I thought I would toss it in. I just found it fascinating.
It is from Dawkins' "The Ancestor's Tale" (about page 441)
He discusses the symbiotes that live in termites guts and digest cellulose for them.
Then he looks at (appropriately enough) Darwin's Termite(Mastotermes darwiniensis) and it's gut symbiote Mixotricha paradoxa. This is a "large protozoan about half a millimetre long or more".
Then this::
quote:
Mixotricha itself is a town. The full story was revealed by the work of L.R. Cleveland and A.V. Grimstone, but it especially the Amberican biolgist Lynn Margulis who has drawn our attention to Mixotrica's significance for evolution.
When J.L. Sutherland first examined Mixotricha in the early 1930's she saw two kinds of 'hairs' waving on its surface. It is almost completely carpeted by thousands of tiny hairs, beating to and fro. She also saw a few very long, thin, whip-like structures at the front end. Both seemed familair to her, the small ones as 'cilia', the large as 'flagella'. Cilia are common in animal cells, ....Another recognized group of protozoans, the flagellates, have much longer, whip like 'flagella' ...
Mixotricha, or so it seemed to Sutherland, has both cilia and flagella. It violates protozoological protocol. .... or so it seemed.
(note from Ned -- none of the protozoans have BOTH).
As it has turned out, Mixotricha's 'cilia' are even more unexpected than Sutherland realized, and they don't violate precident in the way she feared. ...
they demonstarted with the electron microscope that the 'cilia' are not cilia at all. They are bacteria. Each one of the hundreds of thousands of tiny hairs is a single spirochaete-- a bacterium whose entire body is a long, wiggling hair. ...
but Mixotricha's sirochaetes are stuck to its body wall, exactly as though they were cilia.
The don't move like cilia however, they move like spirochaetes. ...Amazingly, they seem to be co ordinated with each other, moving in waves that begin at the front of the body ...
It goes on to discuss the oher separate bacteria that make up part of Mixotricha. It is almost worth the cost of the book to read about this one critter.
I do btw recommend the book. Interesting read, clearly presented.

  
Snikwad
Inactive Member


Message 9 of 16 (183383)
02-06-2005 12:14 AM
Reply to: Message 7 by RAZD
02-05-2005 11:05 PM


RAZD writes:
isn't your answer already contained in:
Yes and no.
It’s my understanding that as time went on, a whole lot of the genes that were present in the original bacteria that would ultimately become the chloroplasts and mitochondria came to be incorporated into the nuclear genome of the cell, and so fewer and fewer parts of the mitochondria and chloroplasts were encoded by the organelle genomes themselves. The question I’m asking (which I may not have expressed clearly enough) is how does this incorporation work? How does organelle DNA become incorporated into the nuclear DNA? Can organelle DNA cross through the nuclear membrane? If so, how does organelle DNA cross through the nuclear membrane?
I think I see what you’re saying. Since the whole cell divides it is not necessary for the nuclear genome to end up coding for the organelles, and the organelles could just divide independently in the cytoplasm, and when the cell splits, each cell ends up with half of the organelles, which can then independently produce (by which I mean, the organelles’ genomes could produce) more of the organelles. This would preserve the existence of organelles within the cells throughout all subsequent generations. The issue here is that the nuclear DNA came to incorporate the genes present in the mitochondria and chloroplasts. How does this happen?
Note that I am not challenging a symbiotic origin for mitochondria and chloroplaststhere’s no other plausible scenario that I know of. I’m just interested in the mechanism by which organelle genes are incorporated into nuclear DNA.
Did that help clarify what I’m asking?

"Chance is a minor ingredient in the Darwinian recipe, but the most important ingredient is cumulative selection which is quintessentially nonrandom."
--Richard Dawkins, The Blind Watchmaker

This message is a reply to:
 Message 7 by RAZD, posted 02-05-2005 11:05 PM RAZD has not replied

  
TheLiteralist
Inactive Member


Message 10 of 16 (183398)
02-06-2005 2:11 AM
Reply to: Message 3 by Wounded King
08-24-2004 5:39 AM


observed or inferred?
Hi WK,
The first article you quote says:
This does not seem to raise much difficulty, however, given the numberous, well-documented examples in which chloroplast and mitochondrial DNA has been acquired by the nucleus.
Do they mean that this is an often-observed process or do they mean it is an often inferred process? IOW, have they often observed organelle DNA being incorporated in the nuclear DNA? Or, have they often discovered the organelle DNA in the nuclear DNA, and, since they have this theory of endosymbiosis, they conclude, therefore, that it was thus incorporated?
And, by "acquired by the nucleus" do they mean it became incorporated into the nuclear DNA, or do they mean simply that it successfully migrated into the nuclear area?
This message has been edited by TheLiteralist, 02-06-2005 02:14 AM

This message is a reply to:
 Message 3 by Wounded King, posted 08-24-2004 5:39 AM Wounded King has replied

Replies to this message:
 Message 16 by Wounded King, posted 02-10-2005 8:52 AM TheLiteralist has not replied

  
TheLiteralist
Inactive Member


Message 11 of 16 (183399)
02-06-2005 2:25 AM
Reply to: Message 4 by Snikwad
02-04-2005 3:56 PM


Cool Coincidence!
Snikwad,
I'm on the other side of the fence--that is, I'm a YEC. I had wanted to raise this very idea of nuclear DNA coordinated reproduction of cell organelles as an argument AGAINST endosymbiosis. But I wasn't even sure that cell organelle replication WAS coordinated by nuclear DNA.
Of course, my thought is the seemingly hyper-parsimonious idea that "God made it that way."
I shall watch this thread with interest.

This message is a reply to:
 Message 4 by Snikwad, posted 02-04-2005 3:56 PM Snikwad has replied

Replies to this message:
 Message 12 by Snikwad, posted 02-06-2005 3:07 AM TheLiteralist has not replied

  
Snikwad
Inactive Member


Message 12 of 16 (183402)
02-06-2005 3:07 AM
Reply to: Message 11 by TheLiteralist
02-06-2005 2:25 AM


Re: Cool Coincidence!
From Mitochondrial genomes: anything goes by Burger et al.,
Another issue that can now be investigated is whether the propensity to insert foreign DNA is the same for the mitochondrial genome and nuclear genome of a given organism. In flowering plants, acquisition of foreign DNA is rampant both in the nucleus and in mitochondria (but not in chloroplasts), whereas in yeast, DNA escapes from mitochondria to the nucleus (but not in the opposite direction) at a notably high frequency. Moreover, in primates, nuclear genomes contain substantial numbers of mtDNA insertions, but the mitochondrial genome in these cases is free of foreign DNA. These contrasting examples illustrate the concept that evolution of the nuclear and organellar genomes of a given eukaryote can proceed in very different directions.
The question is not whether the incorporation happens. I’m asking about the chemistry that is involved in incorporating mitochondrial DNA, for example, into the nuclear DNA. How does mtDNA make its way into the nuclear genome? More specifically, what allows it to cross the nuclear membrane? As I said above:
mRNA has the potential to cross the nuclear membrane because before leaving the nucleus, it has added to it around 200 or so adenine nucleotides to the 3’ end of it. If I recall correctly this is called a poly-A tail, and it’s what controls how mRNA moves across the nuclear membrane. Note that as far as I know, this is just movement from the nucleus into the cytoplasm.
I’m wondering if something similar happens to DNA so it can cross the nuclear membrane. That’s my basic question. What allows mtDNA to cross the nuclear membrane?
My second question is, once mtDNA is inside of the nucleus, how is it incorporated into the nuclear DNA? What is the chemical process that occurs? This is assuming that this is how it happensI’m still wondering whether it is the RNA analogue of the mtDNA sequence that crosses the nuclear membrane, and then is subsequently reverse-transcribed back into DNA, and then incorporated into the nuclear genome. Yes, yes, it seems ridiculously roundabout, but I still would not be surprised if this is what went on.
TheLiteralist writes:
I'm on the other side of the fence--that is, I'm a YEC.
Depends on what you mean by the fence.
Yes, it is evident that evolution is currently the only theory capable of explaining the observed biodiversity on earth. Unless you’ve got a better one that explains all the evidence in a scientific manner, I’m sticking to evolutionary theory.
However, don’t let the fact that I quote Dawkins fool youI’m a Christian myself. So I suppose we’re on the same side of the fence in that respect.
Of course, my thought is the seemingly hyper-parsimonious idea that "God made it that way."
Hyper-parsimonious indeed. Just remember that the theory that explains everything, explains nothing. God did it, won’t get you very far in understanding the universe we inhabit.

"Chance is a minor ingredient in the Darwinian recipe, but the most important ingredient is cumulative selection which is quintessentially nonrandom."
--Richard Dawkins, The Blind Watchmaker

This message is a reply to:
 Message 11 by TheLiteralist, posted 02-06-2005 2:25 AM TheLiteralist has not replied

Replies to this message:
 Message 13 by pink sasquatch, posted 02-06-2005 4:48 PM Snikwad has replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 13 of 16 (183564)
02-06-2005 4:48 PM
Reply to: Message 12 by Snikwad
02-06-2005 3:07 AM


No need to cross the nuclear membrane...
That’s my basic question. What allows mtDNA to cross the nuclear membrane?
The nuclear membrane breaks down during mitosis.
Thus there is no need to actively cross it while intact, since the nuclear DNA is exposed (and at its most vulnerable for insertion events) during mitosis.
My second question is, once mtDNA is inside of the nucleus, how is it incorporated into the nuclear DNA? What is the chemical process that occurs?
I'm not sure what the prevailing theory is here, but it is likely incorporated during DNA replication, essentially as a mistake in a recombination or DNA repair process. (I'll poke around on the net and see if I come up with anything more specific to mtDNA).
Keep in mind, this isn't something that happens "regularly", so it may not have a standard way of occurring; rather it is the result of occasional genetic accidents.

This message is a reply to:
 Message 12 by Snikwad, posted 02-06-2005 3:07 AM Snikwad has replied

Replies to this message:
 Message 14 by Snikwad, posted 02-06-2005 7:17 PM pink sasquatch has replied

  
Snikwad
Inactive Member


Message 14 of 16 (183585)
02-06-2005 7:17 PM
Reply to: Message 13 by pink sasquatch
02-06-2005 4:48 PM


Re: No need to cross the nuclear membrane...
The nuclear membrane breaks down during mitosis.
Thanks pink sasquatch! This is precisely the kind of answer I was looking for. It’s so blatantly obvious I don’t understand how I could have overlooked it.
I'm not sure what the prevailing theory is here, but it is likely incorporated during DNA replication, essentially as a mistake in a recombination or DNA repair process.
So I take it’s an insertion mutation that gets overlooked in the DNA proofreading process. Where is it likely that this insertion occurs? When DNA replicates you end up with two double-stranded molecules of DNA, each one with one strand of old DNA. Would the mtDNA have a tendency to be inserted into the old DNA strand? If so, how (by which I mean by what chemical process) is the old DNA strand broken up so as to permit the insertion of the mtDNA sequence? If, on the other hand, the insertion occurs on the new complement segment, how does it manage to combine with the base pairs on the old DNA strand? Let’s say we start off with the following DNA molecule:
AATTCGATTCCG
TTAAGCTAAGGC
And when the double-stranded DNA splits, you get:
AATTCGATTCCG
And
TTAAGCTAAGGC
Now, let’s say we want to insert the following sequence from mtDNA:
GACTTA
The first strand copies perfectly, so we end up with a double-stranded DNA molecule that looks like
AATTCGATTCCG
TTAAGCTAAGGC
But the mtDNA sequence is inserted into the second complementary strand that is being constructed:
TTAAGCTAAGGC
AATTCGGACTTAATTCCG
How would the DNA molecule come together to form a double helix if the base pairs don’t match up?
Edited to add:
Ok, I’ve been doing some reading, and perhaps the way in which the double helix forms is through something similar to excision repair. Carrying on with the example I used:
TTAAGCTAAGGC
AATTCGGACTTAATTCCG
Maybe the error is recognized and, using 3’ and 5’ nucleases, either side of the error in the original [red] DNA strand is cleaved, and the gap is filled using the complementary [yellow and orange] DNA strand as a template.
So you end up with
TTAAGC
AATTCGGACTTA
And then, using the complementary [yellow and orange] DNA strand as a template:
TTAAGCCTGAAT
AATTCGGACTTA
And you end up with a DNA molecule capable of forming a double-helix. And with the crazy mtDNA mutation to boot.
Is this anywhere in the ballpark?
This message has been edited by Snikwad, 02-07-2005 01:28 AM

"Chance is a minor ingredient in the Darwinian recipe, but the most important ingredient is cumulative selection which is quintessentially nonrandom."
--Richard Dawkins, The Blind Watchmaker

This message is a reply to:
 Message 13 by pink sasquatch, posted 02-06-2005 4:48 PM pink sasquatch has replied

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 Message 15 by pink sasquatch, posted 02-10-2005 1:01 AM Snikwad has not replied

  
pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 15 of 16 (184317)
02-10-2005 1:01 AM
Reply to: Message 14 by Snikwad
02-06-2005 7:17 PM


bizarro DNA?
Is this anywhere in the ballpark?
You seem to be on the right track, that an error during replication (false recombination or strand break, perhaps) opens up the opportunity for an insertion to take place.
Also think about secondary and tertiary DNA structure (like "hairpin loops") - DNA isn't always a nice double-stranded helix, especially when bizarre things are going on. During an insertion event, DNA at the site may give up its simple double-strand pairing for a more complex folded structure to compensate for basepair mismatches. The folded structure only needs to persist until the next round of DNA replication, when each half of the strand serves as a template to produce a complementary strand.
If you are still interested in more details, you might try searching about for information on "transposons" or "mobile genetic elements", which are genetic sequences that are especially good at inserting themselves in the genome, and sometimes multiplying once they are there. A decent amount of research has been done trying to characterize the mechanisms these elements use during insertion - I believe use of secondary structures may be involved.

This message is a reply to:
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