DNAunion

DNAunion: Thanks. I looked up ftsZ and got a lot of good stuff.

“Tubulin from Ftsz”; “actin from MreB”

DNAunion: More interesting, ftsZ (the probably precursor to eukaryotic tubulin) is not confined only to prokaryotes. It is also found in eukaryotes: well, in eukaryotic organelles (chloroplasts and mitochondria).

DNAunion: The ftsZ genes are found in the nuclear genome, not in the genomes of the organelles. After transcription and translation, the proteins then are targeted to the organelles.

DNAunion: Ftsz in plant chloroplasts may form a cytoskeleton


DNAunion: Interesting stuff, many thanks. Best I can remember, my college biology texts – as well as the book by John Maynard Smith – stated that prokaryotes have no cytoskeleon or components of cytoskeletons. This is in line with the “long-standing dogma” mentioned in one of the quote above.

DNAunion: That “dogma” had me puzzled as it appeared that many things had to “pop into existence” when the first eukaryote arose. But now, I see that there are plausible precursors.


But I still didn't see any references to anyone actually finding fibers in the cytoplasm of prokaryotes. I am not talking about something like the transient Z ring, but some sort of stable, branching network of cytoskeletal fibers. Does anyone know of any such material?

[ March 16, 2002: Message edited by: DNAunion ]</p>

lpetrich

I'm only an amateur evolutionary biologist, but I disagree on Cavalier-Smith on the late origin of archaebacteria and eukaryotes. It requires some superfast "quantum evolution", which I find far from convincing, and C-S's dismissal of molecular-evolution rate inferences seems to me to be (pardon the pun) a bit cavalier.

It will be interesting to see how his views are received, however; there could well be some partial truth in them.

lpetrich

Here's a paper that suggests that eukaryotes are very old:

<a href="http://www.biomedcentral.com/1471-2148/1/4" target="_blank">http://www.biomedcentral.com/1471-2148/1/4</a>

Here's the scenario that this site proposes:

&gt; 4 Gya (billion years ago): divergence between eubacteria and archaebacteria.

~ 4 Gya: divergence between eukaryote ancestor and rest of archaebacteria (or perhaps somewhere deep in the tree of the known ones).

Oxygen levels low; Banded Iron Formations possibly produced by photosynthetic bacteria that performed Fe++ -&gt; Fe+++ to get electrons instead of extracting them from water and releasing O2.

~ 2.7 Gya: eubacterium symbiosis? Evidence of big gene transfers from certain eubacteria.

~ 2.5 Gya: divergence of cyanobacteria from other eubacteria.

2.4 Gya: super ice age like the late Precambrian one; the Earth got snowed over. Possibly because of reduction in greenhouse gases: methane (from reaction with oxygen) and carbon dioxide (from greater consumption by less-iron-dependent cyanobacteria).

~2.2 Gya: Giardia diverges from most of the rest of the eukaryotes

~1.8 Gya: Endosymbiosis: acquisition of mitochondrion ancestor: alpha-proteobacterium that is much like Rickettsia; most eukaryotes have descendants of this single ancestor, though some appear to have lost their mitochondria.

This would account for why fossil microoganisms start getting distinctly larger at around 1.5 Gya. That may be when eukaryotic algae emerged as a result of acquiring cyanobacteria to make chloroplasts and other plastids (they come in several colors); this enabled further proliferation.

I find that more convincing than Cavalier-Smith's scenario, because that avoids any truly unusual sort of evolution.

Cytochrome C, for example, indicates an animal-plant-fungus divergence something like twice as long ago as the insect-vertebrate divergence (about 600 mya), and that protein has a strongly-conserved function that would not be affected by the dramatic evolution that C-S requires not much before the I-V divergence.

However, that extrapolated A-P-F divergence time is about the right age for the proliferation seen in the fossil record about 1.5 Gya.

theyeti

Right, but that's exactly where whole genome duplication comes into play. While individual genes probably duplicate often enough to provide plenty of new material, the rare whole genome duplication doubles the number of genes immediately. There are also segmental duplications that add dozens of genes at a time. And of course whole or partial chromosome duplication certainly happens too. In fact, the problem with trying to infer whole genome duplication is that it can be easily confused with succesive rounds of chromosomal and segmental duplication (and the fact that after whole genome duplication, things will get rearranged over time). But when you have entire identical tandem arrays of genes showing up elsewhere, pseudogenes and retroviral inserts and all, it's pretty obvious that some sort of large scale duplication was at play.

I wouldn't be too hasty on that. I do know that segments of chromosomes can be translocated and still result in a functioning human being. The real problem is that their children might be missing part of a chromosome, and that is usually fatal. But this sort of thing shows that the arrangement of chromosomes can easily change during evolution, including the addition of small sections, even with us humans.

But humans shumumans. Lots of organisms are capable of surviving chromosome or genome duplications, even if we're not. One of the species of Rana, for example, has a triploidy male. Which reminds me that one of the "advantages" of whole genome duplication is that there are no triploidies -- everything doubles so that the genes remain in the same proportions. If we're going to consider the possibility of chromosome duplication in one of our deep ancestors, then what it does to us today is more or less irrelevant.

theyeti

DNAunion

DNAunion: Theyeti, are you intentionally missing my point and talking about something else? I keep talking about the addition of a WHOLE, COMPLETE chromosome, or the addition of a WHOLE, COMPLETE haploid set of chromosomes. And yet keep talking - mostly - about single gene duplications or other PARTIAL chromosome deviations (such as a translocation). Here's one example (anyone can look back and easily find others).

DNAunion: Yes, I know that too. But that does not deal with what I said.

Here, let me explain it a bit more.

MONOSOMY (having only one chromosome)
DNAunion: And the negative affects are not limited to just humans.

TRISOMY (having an three chromosomes)

DNAunion: The text then goes into the diseased related to trisomy.

trisomy 21: Down Syndrome
trisomy 18: Edwards Syndrome
trisomy 15: Patau Syndrome

DNAunion: I hope now that you can see the difference between what I am talking about, and about what you mostly talk about.

PS: All quotes from "Concepts of Genetics: Fifth Edition", William S. Klug & Michael R. Cummings, Prentice Hall, 1997


PPS: One more quote.

[ March 17, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: Many of my questions are still unanswered. So I'll ask them again.


1) What parts of eukaryotic cell division - as it currently occurs - can be eliminated without eliminating the function of cell division? Answering that question will help us strip away the "superfluous add-ons" to arrive at the simplest state of the system - its core - as it currently exists.


2) How was the cytoskeleton used to consume other bacteria?


3) DNAunion: That is, the centrosome of eukaryotes may have evolved from the attachment site of the origin of replication to the cell wall in prokaryotes; and the centromere may have evolved from the other attachement site to the cell wall in prokaryotes - that of the terminus (the point where DNA replication is complete). That suggests to me that the same proteins - or similar ones - specific to the centromere region (the protine disc called the kinetochore, where attachment of spindle fibers actually occurs) and the centrosome should be found in prokaryotes (functioning to anchor the origin and the terminus to the cell wall). Anyone know if this is so?


4) DNAunion: Aren't there multiple Cdk's that are highly conserved between organisms as distantly related as humans and yeasts? Anyone know of any findings the author might be basing his hunch on?


5) DNAunion: If eukaryotes evolved from prokaryotes, and prokaryotes don't have tubulin or cytoskeletons, then where would the preexisting tubulin for the mitotic spindle have come from? Wouldn't the first eukaryotes have needed a mitotic spindle?

***************************
Well, concering #5, we did see that there are two possible precursors: ftsZ for tubulin and Mreb for actin. But something about the proposed ftsZ-&gt;tubulin and Mreb1-&gt;actin (prokaryotic protein evolving into eukarytoic protein) has me a bit puzzled.

Here are a some points from the quotes I present below.

ACTIN
1) Present in virtually all eukaryotic cells (animals, plants, algae, and fungi) and is the most abundant intracellular protein in eukayrotice cells.

2) Actin genes are the most highly conserved of the genes encoding cytoskeletal proteins, and in fact, are one of the most highly conserved genes in the cell, comparable to histones: about 99% identity between those in vertebrates; 90% identity between yeast and chicken; 80% identity between amebas and animals.


TUBULINS
1) Found in all eukaryotic cells.

2) Tubulin genes are highly conserved. 70% identity between yeast and chicken. Alpha- and beta- subunits from any two different species will combine to form microtubules.


This paints a picture (although the painting may turn out to be an abstract). There seems to be a sharp divide between eukaryotes and prokaryotes in relation to these two cytoskeletal proteins. All eukaryotes have actin and tubulin genes – no prokaryotes do. Furthermore, the tubulin and especially the actin genes of eukaryotes - as distantly related as humans, chickens, yeast, and amebas - are highly conserved.

Why the dichotomy?

ACTIN

TUBULIN

[ March 17, 2002: Message edited by: DNAunion ]</p>

theyeti

So how is a whole genome duplication not a duplication of WHOLE, COMPLETE chromosomes? Whole genome duplication duplicates every chromsome at once, and it's a well known phemomenon. Does it happen often? No. But then again, to explain the number of genes that we see in modern metazoans, it's only had to have happened a handful of times over the last several hundred million years. Individual and segmental gene duplication take care of the rest.

And whole or partial chromosomal duplication is known to occur too. Yes, most of the time it's probably bad for you, at least if you're human. But it does not follow that this is always the case, and the fact that we see such things as trisomy males in Rana shows us that it's deffinately not always the case. Are you claiming that they can't occur? If you're just claiming that they're rare, then I'm in complete agreement with you. It would be hard to explain the lack of genes otherwise.

theyeti

DNAunion

DNAunion: See, you are still doing it!

Show me where I said that whole genome duplications were NOT duplications of whole, complete chromosomes? You can't, because I didn't.

And I didn't "complain" about your talking about them either.

My complaint specifically addressed your repeatedly addressing mere gene duplications or PARTIAL chromosome aberrations, such as translocations. Those are not what I am talking about.

[ March 17, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: Theyeti, do you plan to stop playing games any time soon?

DNAunion: Do I claim that what can't occur? You mentioned BOTH whole and partial chromosomal duplication. Let's look at them one at a time, shall we.

I never said or even implied that "partial chromosomal duplication" can't occur. Where did you get that from?

As far a "whole choromosomal duplication", I quoted my biology texts that said that trisomy does not have as drastic of effects as does monosomy; and it even said that trisomy of all human chromosomes have been recovered (whereas this is not so for monosomy). Besides that, I mentioned that the biology texts discussed diseases that result from trisomy (Down Syndrome, Patau Syndrome, and Edwards Sysndrome). So again, I never said or even implied that "whole chromosomal duplication" can't occur, and in fact, actually discussed them. Where did you get that from?

[ March 17, 2002: Message edited by: DNAunion ]</p>

theyeti

No, you asked for examples of how chromosomes could be replicated, and I provided whole genome duplication as an example. I also included the example of partial chromsome duplication, because I think it's an important thing to take into consideration -- since the real issue it gene duplication, at least as a means of generating redundancies that can lead to IC systems, etc., then all forms of gene duplication should be considered, IMO. This includes things like single duplication, and also things like whole genome duplication, and the whole wide range of things in between. It just doesn't do for you to accuse me of not answering your question because partial chromosomal duplication doesn't meet your criteria (and I don't know why it should matter), but I clearly mentioned the fact of whole genome duplications, which does meet that criteria.

theyeti