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Author Topic:   Problems with Chromosomal Evolution - From Circular to Linear
jt
Member (Idle past 5596 days)
Posts: 239
From: Upper Portion, Left Coast, United States
Joined: 04-26-2004


Message 16 of 58 (136325)
08-23-2004 12:53 PM
Reply to: Message 14 by AdminNosy
08-23-2004 11:46 AM


Re: Correction to opening post
If you make content changes to a post then following posts may become incomprehensible.
That makes sense. I restored the deleted portion and added a bracketed statement explaining the error.

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jt
Member (Idle past 5596 days)
Posts: 239
From: Upper Portion, Left Coast, United States
Joined: 04-26-2004


Message 17 of 58 (136326)
08-23-2004 12:57 PM
Reply to: Message 15 by crashfrog
08-23-2004 11:51 AM


Re: Correction to opening post
Just to clarify for Nosy, we used to have this guy here who would exessively and dishonestly redact his posts after people had responded to the things he had deleted.
Yeah, that would be annoying in an infuriating way. Nosy's post was slightly terse, but I completely understand why now. No hammer felt...

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 18 of 58 (136330)
08-23-2004 1:18 PM
Reply to: Message 8 by jt
08-22-2004 8:55 PM


waiting ...
JT writes:
Streptomyces (with linear chromosomes) have two types of telomeres - one has a protein cap, the other is a hairpin. They thus need telomerase and telomere resolvase. When they become circular, they retain those enzymes, and the regulatory systems for them. Returning to a linear state doesn't need anything new, it is simply a different shape.
RAZD - I'm working on your post, I'll get my reply to you probably tommorrow.
The above looks similar to my argument (2) ... but I'll wait for you to get to it.
(reference http://EvC Forum: Problems with Chromosomal Evolution - From Circular to Linear)

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 8 by jt, posted 08-22-2004 8:55 PM jt has replied

Replies to this message:
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jt
Member (Idle past 5596 days)
Posts: 239
From: Upper Portion, Left Coast, United States
Joined: 04-26-2004


Message 19 of 58 (136334)
08-23-2004 1:33 PM
Reply to: Message 7 by RAZD
08-21-2004 1:08 AM


[deleted repeat post]
This message has been edited by JT, 08-23-2004 12:35 PM

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jt
Member (Idle past 5596 days)
Posts: 239
From: Upper Portion, Left Coast, United States
Joined: 04-26-2004


Message 20 of 58 (136335)
08-23-2004 1:34 PM
Reply to: Message 7 by RAZD
08-21-2004 1:08 AM


Nice topic. The only comments I have to add are:
Thanks.
(1) That breaks in the circular chromosome would occur leading to repeated attempts at linear chromosome arrangements. These could just keep happening until a process co-evolves that allows it to survive...Remember that you are dealing with differential survival rates and those that do it better faster have more replicating survivors.
If a circular chromosome broke, one of two things would happen to the cell: either it would survive, or it would die. There is no better/worse, faster/slower, it is pass/fail. If an enzyme was present which was not functional, even if it was extremely close, the cell would still die. There would be no co-evolution - since the cell would die if the enzyme was not working all the way, there would be no selective pressures able to keep around almost functional proteins.
Also, if a line of cells (without the mechanisms necessary to maintain a linear chromosome) had the tendency to convert to linear chromosomes and die, they would soon lose that trait via natural slection. NS would simply kill any cells which had the trait, and soon there would be a purebred strain of firmly circular cells.
2) It could be argued that the original replication system would have used a linear system (see discussion of RNA replication), and thus have developed a primitive solution to the end problem before finding the more stable circular system, and that this would have continued to be available when such breaks occured as in (1) above.
There is no evidence for this type of system - it is purely speculative (to the best of my knowledge). That could have happened, hypothetically, but there are still a couple problems. That still doesn't solve the problem of how a chromosomal protection system was created, it just pushes it back further on the timeline.
Second, once the cells had developed circular chromosomes, natural selection would favor cells which cut the production of the useless enzymes, freeing up valuable resources for other needs. By the time linear chromosomes came again, the system for maintaining them would have degraded substantially or disappeared, and would likely not work.
I look forward to the next post
And I look forward to your response.

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jt
Member (Idle past 5596 days)
Posts: 239
From: Upper Portion, Left Coast, United States
Joined: 04-26-2004


Message 21 of 58 (136337)
08-23-2004 1:42 PM
Reply to: Message 18 by RAZD
08-23-2004 1:18 PM


Re: waiting ...
Looks like we cross posted. Does my post cover your argument enough? If not, I can be more thorough.

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pink sasquatch
Member (Idle past 6022 days)
Posts: 1567
Joined: 06-10-2004


Message 22 of 58 (136339)
08-23-2004 2:10 PM
Reply to: Message 8 by jt
08-22-2004 8:55 PM


Re: linear plasmids
hey JT-
This is a good discussion and I want to continue it, but unfortunately I'm in the process of moving my household, and so won't be able to contribute in the next two weeks. I haven't had a chance to check out the sources you linked yet to give a proper rebuttal...
Though a word of advice: Throughout this discussion and others like it, try to come up with the simplest form of the process rather than looking to add complexity. Unfortunately this often takes us into the realm of speculation, but often you can take that speculation and find evidence supporting it in the literature.
As a simple (speculative) example, a transient increase in temperature should be sufficient to unravel hairpin loops - perhaps an unstable environment aided in replication of some structures.
When I get back to the forum I'll check out the progress on this thread.

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


Message 23 of 58 (136343)
08-23-2004 3:06 PM
Reply to: Message 17 by jt
08-23-2004 12:57 PM


Terse
Sorry, There was no intention to be 'terse' at all. It was just a simle attempt at informing.

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jt
Member (Idle past 5596 days)
Posts: 239
From: Upper Portion, Left Coast, United States
Joined: 04-26-2004


Message 24 of 58 (136360)
08-23-2004 4:51 PM
Reply to: Message 22 by pink sasquatch
08-23-2004 2:10 PM


Re: linear plasmids
This is a good discussion and I want to continue it, but unfortunately I'm in the process of moving my household, and so won't be able to contribute in the next two weeks.
Good luck moving! We'll be awaiting your return.
Though a word of advice: Throughout this discussion and others like it, try to come up with the simplest form of the process rather than looking to add complexity.
I'll try to do that, and the example you came up with is an interesting possibility that I need to think about...(I'll post about it when I've thought it through satisfactorily)

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jt
Member (Idle past 5596 days)
Posts: 239
From: Upper Portion, Left Coast, United States
Joined: 04-26-2004


Message 25 of 58 (136361)
08-23-2004 4:55 PM
Reply to: Message 23 by AdminNosy
08-23-2004 3:06 PM


Re: Terse
Sorry, There was no intention to be 'terse' at all.
No apology needed. M-w online defines "terse" as: "1 : smoothly elegant 2 : devoid of superfluity," both of which are good things. I didn't feel chastised, just corrected.

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 26 of 58 (136365)
08-23-2004 5:06 PM
Reply to: Message 21 by jt
08-23-2004 1:42 PM


Re: waiting ...
well it doesn't cover argument (1) of mine - that circular chromosomes broke open regularly and eventually one survived, or the element of (2) that the first chromosome (proto-chromosome?) was linear, from which the circular evolved as a more stable form, and therefore whatever system the original form used would still be available when circular ones broke open.
No hurry. I'm enjoying the read so far.

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

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Loudmouth
Inactive Member


Message 27 of 58 (136433)
08-24-2004 1:03 AM
Reply to: Message 20 by jt
08-23-2004 1:34 PM


quote:
If a circular chromosome broke, one of two things would happen to the cell: either it would survive, or it would die. There is no better/worse, faster/slower, it is pass/fail. If an enzyme was present which was not functional, even if it was extremely close, the cell would still die. There would be no co-evolution - since the cell would die if the enzyme was not working all the way, there would be no selective pressures able to keep around almost functional proteins.
I think someone mentioned stem-loops earlier, but I found an article (not primary) that discussed this process. In this article Dr. de Lange speaks about the use of telomeric loops (t-loops) as a means of stopping degradation of linear DNA. This type of end protection does not require telomerase or any enzymes at all. The mechanism relies on DNA bending back on itself forming a type of stem-loop. A few excerpts from the article:
But things started out very simply, de Lange says. She suggests that tiny structures called telomeric-loops (t-loops), which she and her collaborators discovered four years ago, are actually remnants of the original telomere system that served to protect the ends of the first linear chromosomes found in early microorganisms. The investigators have shown that without these little loops, cells mistake the exposed chromosome ends for sites of DNA damage and when they attempt to repair them, the cells die.
If the chromosomes of a microorganism, such as the bacterium that gave rise to eukaryotes, were linear, a t-loop could easily be formed from just a few repeats at the end of the chromosome, de Lange says. All the enzymes to make t-loops were already available; they were used for regular DNA replication in bacteria. When E. coli is replicating its DNA, occasionally the newly synthesized fork collapses, leaving the end of the new DNA hanging out of a half-replicated E. coli genome.
So it would seem that the telomeres and telomerases were not necessary for the formation of linear DNA. Also, de Lange also mentions that telomerases could have developed later as a more effecient and dynamic system (control by committee as de Lange puts it).
Also, we see other solutions in higher taxa, such as in Drosophila.
Annu Rev Genet. 2003;37:485-511.
Retrotransposons provide an evolutionarily robust non-telomerase mechanism to maintain telomeres.
Pardue ML, DeBaryshe PG.
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. mlpardue@mit.edu
Telomere molecular biology is far more complex than originally thought. Understanding biological systems is aided by study of evolutionary variants, and Drosophila telomeres are remarkable variants. Drosophila lack telomerase and the arrays of simple repeats generated by telomerase in almost all other organisms; instead, Drosophila telomeres are long tandem arrays of two non-LTR retrotransposons, HeT-A and TART. These are the first transposable elements found to have a bona fide role in cell structure, revealing an unexpected link between telomeres and what is generally considered to be parasitic DNA. In addition to providing insight into the cellular functions performed by telomeres, analysis of HeT-A and TART is providing insight into the evolution of chromosomes, retrotransposons, and retroviruses. Recent studies show that retrotransposon telomeres constitute a robust system for maintaining chromosome ends. These telomeres are now known to predate the separation of extant Drosophila species, allowing ample time for elements and hosts to coevolve interesting mechanisms. emphasis mine
The fruit fly actually uses viral genetic sequences to insert repetitive sequences at the end of their linear DNA. This is more evidence that telomerases are not needed and other solutions exist.
My conclusion is that assuming telomeres and telomerases are NECESSARY for linear DNA formation is not a correct assumption. Two other systems are found within nature, and possibly more exist that have not yet been discovered. Also, with a t-loop system in place it is very possible that another system was able to coevolve and replace the less ellegant system. As metazoans evolved they needed to control cell replication to prevent certain tissue types from dominating the organism. This requires a level of control not seen in the t-loop system, but is seen within a telomerase control system.

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jt
Member (Idle past 5596 days)
Posts: 239
From: Upper Portion, Left Coast, United States
Joined: 04-26-2004


Message 28 of 58 (137116)
08-26-2004 3:32 PM
Reply to: Message 11 by Wounded King
08-23-2004 6:41 AM


Re: linear plasmids
Other proteins clearly exist which can resolve the cruciform Holliday junctions.
Could you quote some more of the article which supports that (I don't have access to the full article)? The part you quoted only said that the reaction mechanism was "similar," not that the proteins are identical. (I'm not trying to be pedantic - the context probably makes the meaning of that statement very clear, but without the context it is unclear)
The embo J. paper you go on to discuss may well be talking about a totally different 'telomere resolvase' it need not be the same as in the source paper, a similar possible confusion as to that between human and yeast telomerase.
Arggh! I made the same stupid mistake twice in a row. I will not do that again. But you are probably right; there are quite possibly telomere resolvases that are not site specific.

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jt
Member (Idle past 5596 days)
Posts: 239
From: Upper Portion, Left Coast, United States
Joined: 04-26-2004


Message 29 of 58 (137122)
08-26-2004 3:53 PM
Reply to: Message 26 by RAZD
08-23-2004 5:06 PM


Re: waiting ...
well it doesn't cover argument (1) of mine - that circular chromosomes broke open regularly and eventually one survived,...
If linear chromosomes evolved from circular chromosomes, it would have happened like that. What I am saying is that an occurence like that would be by complete chance - there could not be a gradual evolution of a system of preservation. If such a system was not present in full functionality when a cell's chromosome became linear, the cell would die.
Are you saying that even if the system was complex, it would have had enough chances to develop that odds are it would have?
...or the element of (2) that the first chromosome (proto-chromosome?) was linear, from which the circular evolved as a more stable form, and therefore whatever system the original form used would still be available when circular ones broke open.
Several things here; first, the protection system still would have had to evolve, which I think is implausible. If the protection of a linear chromosome is at its simplest a complex system, it evolving in the first cell with DNA is even more implausible than it evolving in a line of cells already having DNA. All you are doing is pushing the timeline back - it is not an explanation of how linear chromosomal protection could have evolved.
Second, even if such a system was present in extremely early cells, the chances of it surviving very long after it stopped being needed is low. Cells that didn't have to create/maintain the useless system would be less pressed for resources, and the system would soon degrade into non-functionality.
Well, I'm glad I only missed properly covering two points from your post. Two isn't a very big number, anyway...
No hurry. I'm enjoying the read so far.
Cool.

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Replies to this message:
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jar
Member (Idle past 393 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 30 of 58 (137123)
08-26-2004 4:01 PM
Reply to: Message 29 by jt
08-26-2004 3:53 PM


Re: waiting ...
Are you saying that even if the system was complex, it would have had enough chances to develop that odds are it would have?
IMHO, the issue of propabilities is simply another of the red herrings.
There are two bigg things. First when you start at one limit, as simple as things can get, the only direction that you can go is towards being more complex.
Second, you are dealing with very large numbers. The flask that contained whatever the initial broth was confined in was really, really big, with lots and lots of material.
Third, there is a filter. The things that work are kept, those random changes that don't work get discarded.

Aslan is not a Tame Lion

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