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Author Topic:   Evolution Before the Common Ancestor
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Message 1 of 4 (29555)
01-19-2003 7:12 AM

Over in this Internet Infidels thread, I had posted some interesting recent research into the evolution of life before the Last Universal Common Ancestor (LUA, LCA, LUCA) of all known cellular Earth life. To summarize, both papers I'd looked at point to the earliest Earth life as being closer to prebiotic chemistry than more recent life. And the second paper points to evidence of much less complexity in the earliest life.

The enormous volume of genetic data collected over the last few decades, including the sequencing of over 100 genomes, has made possible the reconstruction of several of the genes and proteins contained by the Last Universal Common Ancestor.

The amino-acid content of these proteins is interesting; according to the work of Brooks DJ, Fresco JR, Lesk AM, Singh M, the LUCA's proteins were enhanced in amino acids known to be produced in prebiotic-synthesis experiments, and depleted in amino acids known to be rare or absent in such experiments. This adds support to the hypothesis that the original source of amino acids was prebiotic synthesis; the earliest organisms simply eat some Primordial Soup.

By comparison, Brian K. Davis's work focuses on 10 proteins, and uses a different criterion for assigning amino-acid origin time; how many metabolic steps are necessary to produce some amino acid from a Krebs-Cycle predecessor. Aspartate and glutamate, for example, score very low, while lysine and arginine score very high. The low scorers are also those relatively abundant in prebiotic syntheses, which suggest that biosynthesis of them was developed as a substitute for Primordial-Soup eating (the Horowitz hypothesis).

The "code age" of a protein he determined by finding the average score of its amino acids; he used this to work out the proteins' order of appearance.

The oldest of these proteins was ferredoxin, a biosynthesis enzyme that contains iron-sulfur clusters and that transfers electrons (hydrogen-atom equivalents). This protein he reconstructs as having a negatively-charged tail; this can stick to positively-charged objects like mineral surfaces with their metal ions -- which is consistent with the view of Gunter Wachtershauser that life originated from iron-sulfur-associated chemical reactions on mineral surfaces, and that the Krebs Cycle dates from this time. Note that the Krebs Cycle's members are all acids -- negatively-charged ions -- meaning that they can stick to mineral surfaces.

This suggests that the earliest life had not had well-defined cells, that it had been a sort of Haeckelian Urschleim living in the mud of hydrothermal vents.

Not much younger than ferredoxin is a protein involved in cell division and an ATPase component that resides in cell membranes; as a consequence, nearly all the rest of Brian Davis's scenario takes place in distinct cells, including the acquisition of "difficult" amino acids like the benzene-ring and alkaline ones.

Also after the origin of cells but before the LUCA is the origin of DNA; enzymes for synthesizing DNA nucleotides from RNA ones, copying DNA to RNA, and copying RNA to DNA date from this period. So DNA is younger than both RNA and proteins.

However, DNA-to-DNA copying systems are much more difficult to place in this period, since those of the (eu)bacterial and the archaeo-eukaryotic lineages are very different, suggesting separate elaboration -- or even separate origin. The LUCA could have had a DNA-RNA genome, with DNA being copied to RNA and back.

Brian Davis's paper did not address the RNA-world question, but his work suggests that an RNA world, if it had existed, had been pre-cellular.

An interesting result is that the earliest Earth life is closer to various sorts of prebiotic chemistry than later Earth life. This poses an interesting conundrum for the hypothesis that some designer had "seeded" the Earth with some organism that became the ancestor of all its later life. Why this choice of "seed"? Why not a "seed" with a chemistry more like that of present-day organisms?

Also interesting is the absence from the earliest life of DNA, distinct cells, and several amino acids; this indicates the absence of the enzyme systems necessary for constructing and handling them. Thus, the origin of life has to account for much less complexity than one would expect from present-day cell architecture.


Brooks DJ, Fresco JR, Lesk AM, Singh M.
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
At this PubMed entry.

Davis BK.
Molecular evolution before the origin of species.
Prog Biophys Mol Biol 2002 May-Jul;79(1-3):77-133
At this PubMed entry.

Replies to this message:
 Message 2 by Wounded King, posted 04-27-2003 9:56 AM lpetrich has not yet responded
 Message 3 by Coragyps, posted 04-27-2003 11:12 AM lpetrich has not yet responded

Wounded King
Member (Idle past 2439 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003

Message 2 of 4 (38145)
04-27-2003 9:56 AM
Reply to: Message 1 by lpetrich
01-19-2003 7:12 AM

Dear Ipetrich,

I saw a recent RNA world based paper suggesting, as you say, that it involves an acellular origin of life. It posits a form of protocell which is actually a sulphite precipitate which provides a catalytic surface.

Martin W, Russell MJ.
On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.
Philos Trans R Soc Lond B Biol Sci. 2003 Jan 29;358(1429):59-83

[This message has been edited by Wounded King, 04-27-2003]

This message is a reply to:
 Message 1 by lpetrich, posted 01-19-2003 7:12 AM lpetrich has not yet responded

Posts: 5414
From: Snyder, Texas, USA
Joined: 11-12-2002
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Message 3 of 4 (38148)
04-27-2003 11:12 AM
Reply to: Message 1 by lpetrich
01-19-2003 7:12 AM

LP, you might be interested in Kerner, et al., Nature 422, 150 - 154 (2003). It's a study showing the formation of cell-sized organic particles in a "post-biotic soup" - sterile river water. Abstract:
In aquatic systems, the concept of the 'microbial loop' is invoked to describe the conversion of dissolved organic matter to particulate organic matter by bacteria. This process mediates the transfer of energy and matter from dissolved organic matter to higher trophic levels, and therefore controls (together with primary production) the productivity of aquatic systems. Here we report experiments on laboratory incubations of sterile filtered river water in which we find that up to 25% of the dissolved organic carbon (DOC) aggregates abiotically to particles of diameter 0.4–0.8 micrometres, at rates similar to bacterial growth. Diffusion drives aggregation of low- to high-molecular-mass DOC and further to larger micelle-like microparticles. The chemical composition of these microparticles suggests their potential use as food by planktonic bacterivores. This pathway is apparent from differences in the stable carbon isotope compositions of picoplankton and the microparticles. A large fraction of dissolved organic matter might therefore be channelled through microparticles directly to higher trophic levels—bypassing the microbial loop—suggesting that current concepts of carbon conversion in aquatic systems require revision.

I think this may have some relevance to early cellular life, as the prebiotic soup likely had representatives of the same classes of compounds - fatty acids from basalt + water, amino acids, etc.

This message is a reply to:
 Message 1 by lpetrich, posted 01-19-2003 7:12 AM lpetrich has not yet responded

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Message 4 of 4 (39909)
05-13-2003 5:35 AM

Thanx. That "post-biotic" stuff suggests that bacteriumlike organisms could be difficult to identify. One has to look for things that such stuff would not typically produce, like strings of cells.

And I remember someone who worked on prebiotic-chemistry experiments for simulating the atmosphere of Titan, Saturn's largest moon. The experiments would produce a lot of particles of a reddish-brown goo ("tholin") that was about a micron in size or thereabouts. A goo that is the color of Titan's clouds!

And that Martin-Russell paper on the origin of cells looks interesting; I may want to purchase it. There is one curious possible discrepancy with Brian Davis's results.

BD concluded that cell membranes originated relatively early; he found that an ATPase subunit was the second oldest of his 10 proteins, and ATPases are adapted for residing in membranes -- they contain some hydrophobic (water-repellent) domains.

However, M&R conclude that the two branches of prokaryotes had emerged from a precellular state separately, because of their different membrane lipids.

I'm not sure how this work can be reconciled; perhaps the Last Universal Common Ancestor had not been "committed" to one type of membrane lipid.

And here's another one on this universal ancestor:

Di Giulio M.
The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence.
J Theor Biol 2003 Apr 7;221(3):425-36

One can work out a protein's "thermophily index" by correlating its amino-acid content with the owner organism's optimal growth temperature. This allows one to guess the optimal growth temperature of an organism from its protein content.

And Di Giulio estimated those temperatures for various ancestors by working from several of those ancestors' reconstructed protein sequences ("Archean Park"?). The results:

LUCA - hot (40 - 100+ C)
Bacteria / Eubacteria - hot (40 - 100+ C)
Archaea / Archaebacteria - hot (40 - 100+ C)
Eukarya - medium (10 - 40 C)

This is consistent with prokaryotes originating in hot springs and eukaryotes emerging away from those environments.

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