Freethought & Rationalism Archive

lpetrich · 10-31-2002, 08:30 PM

<a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=122257 77&dopt=Abstract" target="_blank">Another one from ISCID's most feared source</a>. By Brian K. Davis.

I've purchased the complete text of that article and of that early-protein article I'd mentioned in an earlier thread; it worked just like purchasing software online. But now for the nitty-gritty of that big article.

BD's paper used a smaller set of proteins than the first one, but examined them in more detail. The oldest one found was low-potential ferredoxin, which has an iron-sulfur cluster in it and one end strongly acidic. This protein uses mainly the simpler amino acids, which suggests that it dates back before the completion of the genetic code. A conclusion supported by the more detailed examination in BD's paper, which also points to evidence of a gene duplication early in that protein's history -- two copies became concatenated to produce one new protein.

That protein's structure fits in well with Wachterhauser's picture of prebiochemistry as taking place in clay-like materials and involving iron/sulfur chemistry; the clay's metal ions would make it positively charged, attracting the negatively-charged ferredoxin end. The rest of the molecule would remove the hydrogen from H2S and transfer it to CO2, helping make organic acids (with COOH groups) and the like. Which easily stick to those metal ions, keeping them easily available for more (pre)biosynthesis.

BD's paper scored amino acids by biosynthesis-step distance from the Krebs Cycle, which it used as a reference point in early metabolism. The best scorers are aspartate and glutamate, whose aspartate -> asparagine and glutamate -> glutamine reactions were inferred to be an early form of nitrogen fixing. These close ones are also acidic, enabling them to easily stick to metal ions, as are all of the Krebs Cycle members.

After those ones were those simpler amino acids, those easily formed in prebiotic-chemistry experiments, and then the more difficult ones, which include the ones with a benzene ring (phenylalanine, tyrosine) and the alkaline ones (lysine, arginine).

The other proteins examined included two that are intimately involved with cell structure:

Part of ATPase, an enzyme that sits on cell membranes, and that assembles ATP from the energy of membrane-crossing ions.
The protein FtsZ, which is involved with the splitting-in-two aspect (septation) of prokaryotic cell division.

These are younger than ferredoxin, suggesting that ferredoxin is older than distinct cells. Which is logical when one considers its adaptation to sticking to mineral surfaces.

The formation of distinct cells was followed by the biosynthesis of the more difficult amino acids -- and DNA. But although a DNA-to-RNA enzyme dates to before the last universal common ancestor (LCA, LUA, LUCA), the DNA-to-DNA enzymes are inferred to be younger on account of their very different structures between the bacterial and the archaeo-eukaryotic branches of the family tree of life.

Meaning that the LUCA may not have had DNA-to-DNA copying, but instead, DNA-to-RNA-to-DNA copying in its genome. With DNA-to-DNA copying being invented twice in its descendants.

BD's paper had not addressed the question of the origin of RNA, though it or some predecessor had been at least as old as ferredoxin -- and older than cells.

[ October 31, 2002: Message edited by: lpetrich ]

Nickle · 10-31-2002, 09:10 PM

Cool, just downloaded it. I'm amazed how fast they are breaking down the pathways in these early cells. Not that I understood the whole thing. Also lpetrich I sent you a PM.

Quetzal · 11-01-2002, 03:43 AM

lp: I'm sure you've seen this - but here's a group in the UK that's working on the exact sequence you're talking about (iron sulfide catalysis of ferredoxins) without the clay substrate: <a href="http://www.gla.ac.uk/projects/originoflife/html/2001/menu.htm" target="_blank"> University of Glasgow origin of life research</a>.

theyeti · 11-01-2002, 06:56 AM

Hey, thanks for that referrence LP!

I haven't gotten a copy of the paper, so I hope you can answer a question or two.

Quote:

Originally posted by lpetrich:
The best scorers are aspartate and glutamate, whose aspartate -> asparagine and glutamate -> glutamine reactions were inferred to be an early form of nitrogen fixing.

If I remember correctly, glutamine and asparagine are formed from ammonium ions in the cell reacting with glutamate or aspartate. How was atmosphereic N2 fixed to become ammonium way back when? Nowadays it's a pretty energy intensive process carried out by a few types of bacteria, but is there a prebiotic synthesis?

Quote:

Meaning that the LUCA may not have had DNA-to-DNA copying, but instead, DNA-to-RNA-to-DNA copying in its genome. With DNA-to-DNA copying being invented twice in its descendants.

I don't know why I never thought of this before, but a transcription / reverse transcription replication scheme makes a lot of sense. Are there any reverse transcriptases known that are as old as the RNA polymerase referrenced earlier?

theyeti

lpetrich · 11-01-2002, 10:51 AM

Thanx for pointing out that U of Glasgow link to me. However, that still seems a bit hand-waving to me, though in fairness, that paper is no worse than anyone else.

And as to the origin of the ammonia for the amine groups, this was likely a result of reducing-environent chemistry, such as

3H2 + N2 -> 2NH3

or oxidation of iron as described in <a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v395/n6700/full/395365a0_r.html" target="_blank">Abiotic nitrogen reduction on the early Earth</a>.

[ November 01, 2002: Message edited by: lpetrich ]

lpetrich · 11-01-2002, 09:31 PM

I've had some broader thoughts.

The idea of a pre-cellular phase of life that lived amidst rocky material brings to mind Ernst Haeckel's Urschleim ("original slime"). Which was "found" in the late 19th cy. on the ocean floor and named Bathybius haeckelii. However, Bathybius turned out to be produced by the preservative that was applied to the ocean-floor samples.

Maybe we can revive this genus name and name this phase Bathybius siderothiophilus ("iron-sulfur loving").

Another interesting circumstance is the drastic revision of our picture of what the earliest organisms were like. Older discussions, like Carl Sagan's earlier books, pictured the earliest ones as being much like Clostridium, an anaerobic eater of organic molecules.

Although that is still likely true of the absolute earliest organisms, the LUCA is more likely chemolithotrophic/autotrophic, living off of chemical reactions like

H2 + S -> H2S

fixing carbon dioxide, and building all its organic molecules. Heterotrophy, like the metabolism of Clostridium itself, would later be re-invented as a way of taking advantage of other organisms' biosyntheses.

lpetrich · 11-26-2002, 08:21 AM

Quote:

Originally posted by theyeti:
I don't know why I never thought of this before, but a transcription / reverse transcription replication scheme makes a lot of sense. Are there any reverse transcriptases known that are as old as the RNA polymerase referrenced earlier?

Sorry for not responding in a more timely fashion, but one of the proteins discussed in Brian Davis's paper was a reverse transcriptase. Which makes me wonder what "normal" cellular function involves RNA-to-DNA transcription, because there would otherwise be no "incentive" to keep it.

Here are all the proteins discussed, in order of the "code age" of its amino acids:

"Code Age" = 7
Ferredoxin (electron transfer)
Proteolipid h1 (part of ATPase)

"Code Age" = 8 to 11
FtsZ (involved in cell division)
FEN-1 (flap exonuclease; digests RNA)
RNAP-beta (DNA-dependent RNA polymerase: DNA to RNA)
Reverse transcriptase (RNA to DNA)

"Code Age" = 12 to 13
Topoisomerase-I (involved in DNA supercoiling)
RNR (Ribonucleotide reductase: RNA to DNA nucleotides)

An amino acid's "code age" is determined by the number of metabolic steps needed to make it from a Krebs-Cycle precursor:

2: Aspartate, Glutamate, Asparagine, Glutamine
4: Alanine, Proline, Serine, Valine
5: Cysteine, Glycine
6: Threonine
7: Isoleucine, Leucine, Methionine
9: Arginine
10: Lysine
11: Phenylalanine, Tyrosine
13: Histidine
14: Tryptophan

The upper ones are inferred to be used before the lower ones.

And from that Brooks et al. paper on the LUCA's amino-acid content, here are the most abundant prebiotic amino acids:

Alanine, Aspartate, Glutamate, Glycine, Isoleucine, Leucine, Proline, Serine, Threonine, Valine

Dr.GH · 11-26-2002, 12:08 PM

Thanks for the ref.s.

Brooks DJ, Fresco JR, Lesk AM, Singh M. take a slightly different approach in Evolution of amino Acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol Biol Evol. 2002 Oct;19(10):1645-55.

Here is their abstract:

To understand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral genome. Estimates are based upon the composition of conserved residues in descendant sequences and empirical knowledge of the relative probability of conservation of various amino acids. Simulations are used to model and correct for errors in the estimates. The method was used to infer the amino acid composition of a large protein set in the Last Universal Ancestor (LUA) of all extant species. Relative to the modern protein set, LUA proteins were found to be generally richer in those amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those amino acids that are believed to have been unavailable or scarce. It is proposed that the inferred amino acid composition of proteins in the LUA probably reflects historical events in the establishment of the genetic code.

[ November 26, 2002: Message edited by: Dr.GH ]

10-31-2002, 08:30 PM	#1
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	Molecular Evolution Before the Origin of Species <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=122257 77&dopt=Abstract" target="_blank">Another one from ISCID's most feared source</a>. By Brian K. Davis. I've purchased the complete text of that article and of that early-protein article I'd mentioned in an earlier thread; it worked just like purchasing software online. But now for the nitty-gritty of that big article. BD's paper used a smaller set of proteins than the first one, but examined them in more detail. The oldest one found was low-potential ferredoxin, which has an iron-sulfur cluster in it and one end strongly acidic. This protein uses mainly the simpler amino acids, which suggests that it dates back before the completion of the genetic code. A conclusion supported by the more detailed examination in BD's paper, which also points to evidence of a gene duplication early in that protein's history -- two copies became concatenated to produce one new protein. That protein's structure fits in well with Wachterhauser's picture of prebiochemistry as taking place in clay-like materials and involving iron/sulfur chemistry; the clay's metal ions would make it positively charged, attracting the negatively-charged ferredoxin end. The rest of the molecule would remove the hydrogen from H2S and transfer it to CO2, helping make organic acids (with COOH groups) and the like. Which easily stick to those metal ions, keeping them easily available for more (pre)biosynthesis. BD's paper scored amino acids by biosynthesis-step distance from the Krebs Cycle, which it used as a reference point in early metabolism. The best scorers are aspartate and glutamate, whose aspartate -> asparagine and glutamate -> glutamine reactions were inferred to be an early form of nitrogen fixing. These close ones are also acidic, enabling them to easily stick to metal ions, as are all of the Krebs Cycle members. After those ones were those simpler amino acids, those easily formed in prebiotic-chemistry experiments, and then the more difficult ones, which include the ones with a benzene ring (phenylalanine, tyrosine) and the alkaline ones (lysine, arginine). The other proteins examined included two that are intimately involved with cell structure: Part of ATPase, an enzyme that sits on cell membranes, and that assembles ATP from the energy of membrane-crossing ions. The protein FtsZ, which is involved with the splitting-in-two aspect (septation) of prokaryotic cell division. These are younger than ferredoxin, suggesting that ferredoxin is older than distinct cells. Which is logical when one considers its adaptation to sticking to mineral surfaces. The formation of distinct cells was followed by the biosynthesis of the more difficult amino acids -- and DNA. But although a DNA-to-RNA enzyme dates to before the last universal common ancestor (LCA, LUA, LUCA), the DNA-to-DNA enzymes are inferred to be younger on account of their very different structures between the bacterial and the archaeo-eukaryotic branches of the family tree of life. Meaning that the LUCA may not have had DNA-to-DNA copying, but instead, DNA-to-RNA-to-DNA copying in its genome. With DNA-to-DNA copying being invented twice in its descendants. BD's paper had not addressed the question of the origin of RNA, though it or some predecessor had been at least as old as ferredoxin -- and older than cells. [ October 31, 2002: Message edited by: lpetrich ]</p>

11-01-2002, 10:51 AM	#5
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	Thanx for pointing out that U of Glasgow link to me. However, that still seems a bit hand-waving to me, though in fairness, that paper is no worse than anyone else. And as to the origin of the ammonia for the amine groups, this was likely a result of reducing-environent chemistry, such as 3H2 + N2 -> 2NH3 or oxidation of iron as described in <a href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v395/n6700/full/395365a0_r.html" target="_blank">Abiotic nitrogen reduction on the early Earth</a>. [ November 01, 2002: Message edited by: lpetrich ]</p>

11-26-2002, 12:08 PM	#8
Dr.GH Veteran Member Join Date: Jul 2001 Location: Dana Point, Ca, USA Posts: 2,115	Thanks for the ref.s. Brooks DJ, Fresco JR, Lesk AM, Singh M. take a slightly different approach in Evolution of amino Acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code. Mol Biol Evol. 2002 Oct;19(10):1645-55. Here is their abstract: To understand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral genome. Estimates are based upon the composition of conserved residues in descendant sequences and empirical knowledge of the relative probability of conservation of various amino acids. Simulations are used to model and correct for errors in the estimates. The method was used to infer the amino acid composition of a large protein set in the Last Universal Ancestor (LUA) of all extant species. Relative to the modern protein set, LUA proteins were found to be generally richer in those amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those amino acids that are believed to have been unavailable or scarce. It is proposed that the inferred amino acid composition of proteins in the LUA probably reflects historical events in the establishment of the genetic code. [ November 26, 2002: Message edited by: Dr.GH ]</p>

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10-31-2002, 09:10 PM	#2
Nickle Regular Member Join Date: Oct 2001 Location: Texas Posts: 385	Cool, just downloaded it. I'm amazed how fast they are breaking down the pathways in these early cells. Not that I understood the whole thing. Also lpetrich I sent you a PM.

11-01-2002, 03:43 AM	#3
Quetzal Senior Member Join Date: Nov 2001 Location: Ecuador Posts: 738	lp: I'm sure you've seen this - but here's a group in the UK that's working on the exact sequence you're talking about (iron sulfide catalysis of ferredoxins) without the clay substrate: <a href="http://www.gla.ac.uk/projects/originoflife/html/2001/menu.htm" target="_blank"> University of Glasgow origin of life research</a>.

11-01-2002, 09:31 PM	#6
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	I've had some broader thoughts. The idea of a pre-cellular phase of life that lived amidst rocky material brings to mind Ernst Haeckel's Urschleim ("original slime"). Which was "found" in the late 19th cy. on the ocean floor and named Bathybius haeckelii. However, Bathybius turned out to be produced by the preservative that was applied to the ocean-floor samples. Maybe we can revive this genus name and name this phase Bathybius siderothiophilus ("iron-sulfur loving"). Another interesting circumstance is the drastic revision of our picture of what the earliest organisms were like. Older discussions, like Carl Sagan's earlier books, pictured the earliest ones as being much like Clostridium, an anaerobic eater of organic molecules. Although that is still likely true of the absolute earliest organisms, the LUCA is more likely chemolithotrophic/autotrophic, living off of chemical reactions like H2 + S -> H2S fixing carbon dioxide, and building all its organic molecules. Heterotrophy, like the metabolism of Clostridium itself, would later be re-invented as a way of taking advantage of other organisms' biosyntheses.

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