Preadaptations

[Techne]

Interesting article:
Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA)

By exploiting three-dimensional structure comparison, which is more sensitive than conventional sequence-based methods for detecting remote homology, we have identified a set of 140 ancestral protein domains using very restrictive criteria to minimize the potential error introduced by horizontal gene transfer. These domains are highly likely to have been present in the Last Universal Common Ancestor (LUCA) based on their universality in almost all of 114 completed prokaryotic (Bacteria and Archaea) and eukaryotic genomes. Functional analysis of these ancestral domains reveals a genetically complex LUCA with practically all the essential functional systems present in extant organisms, supporting the theory that life achieved its modern cellular status much before the main kingdom separation (Doolittle 2000). In addition, we have calculated different estimations of the genetic and functional versatility of all the superfamilies and functional groups in the prokaryote subsample. These estimations reveal that some ancestral superfamilies have been more versatile than others during evolution allowing more genetic and functional variation. Furthermore, the differences in genetic versatility between protein families are more attributable to their functional nature rather than the time that they have been evolving. These differences in tolerance to mutation suggest that some protein families have eroded their phylogenetic signal faster than others, hiding in many cases, their ancestral origin and suggesting that the calculation of 140 ancestral domains is probably an underestimate.

Mmm, "Functional analysis of these ancestral domains reveals a genetically complex LUCA with practically all the essential functional systems present in extant organisms"....

Let's see what they found:
From the conclusion:

From this annotation we know that the LUCA, or the primitive
community that constituted this entity, was functionally and genetically complex (Table 1, Fig. 1, Supplementary Table 3), supporting the theory that life achieved its modern cellular status long before the separation of the three kingdoms.
Contrary to analyses based purely on sequence conservation and universal ubiquity throughout all species, which suggested a simple LUCA with translation and few other genes (Koonin 2003), with the application of a more sensitive method to detect remote homology, we can affirm that the LUCA held representatives in practically all the essential functional niches currently present in extant organisms, with a metabolic complexity similar to translation in terms of domain variety.

What did this primitive clade of LUCAs have? What kind of machinery was present?
1) Replication, transcription, and translation
2) Repertoire of metabolic pathways coupled with the necessary machinery including;

• a) the use of glucose and other sugars
• b) the assimilation of amino acids and nucleosides/ base
• c) the synthesis of ATP both by substratelevel phosphorylation and through redox reactions coupled to membranes
• d) Signal transduction pathways controlling perception.
• e) These pathways are linked to gene regulation and protein modification, protein signal recognition, transport, and secretion, protein folding assistance
• f) And then of course the self-replication machinery.

With all these present in the LUCA, all that is needed is a little time for functional diversification and genetic expansion. The inevitable and repeated emergence of eyes, body plans, toolkits for body plans etc. should not be a problem, even expected if the tape of life was to be replayed even if randomness was taken into consideration.

But... it gets more interesting:
A minimal estimate for the gene content of the last universal common ancestor—exobiology from a terrestrial perspective

Using an algorithm for ancestral state inference of gene content, given a large number of extant genome sequences and a phylogenetic tree, we aim to reconstruct the gene content of the last universal common ancestor (LUCA), a hypothetical life form that presumably was the progenitor of the three domains of life. The method allows for gene loss, previously found to be a major factor in shaping gene content, and thus the estimate of LUCA's gene content appears to be substantially higher than that proposed previously, with a typical number of over 1000 gene families, of which more than 90% are also functionally characterized. More precisely, when only prokaryotes are considered, the number varies between 1006 and 1189 gene families while when eukaryotes are also included, this number increases to between 1344 and 1529 families depending on the underlying phylogenetic tree. Therefore, the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth, with profound repercussions for planetary exploration and exobiology.

If you think the LUCA was just a simple self-replicator, think again: From the article the following conclusions were drawn:
The gene content of LUCA with respect to
A) DNA processing (replication, recombination, modification and repair) contains a wide range of functions including;
DNA polymerase
excinuclease ABC
DNA gyrase
topoisomerase
NADdependent DNA ligase
DNA helicases
DNA mismatch repair MutS and MutT
endonucleases
RecA
chromosome segregation SMC
methyltransferase (Epigenetics related enzyme)
methyladenine glycosylase and adenine glycosylase
adenine phosphoribosyltransferase
deoxyribodipyrimidine photolyase
integrase
HAM1 Sir2 involved invarious aspects of genomic stabilit)
TatD—a recently discovered DNase
histone deacetylase (More epigentically related enzymes)

These are just replication related machinery.
Next is:
Transcription/regulation
Translation/ribosome
RNA processing (No, it is not junk DNA, RNA processing was there from the beginnig)
Cellular processes (e.g. cell division control)
Transport/membrane
Electron transport
Metabolism
And several with unknown function...

How deep does the rabbit hole go?

Time will tell I guess....
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[Walter L. Wagner]

Interesting article about the LUCA. It's what I teach in my biology classes. Keep the posts coming!

 

[iceaura]

I agree, and think that preadaptation does not differ from exaptation.

It's fascinating stuff, and it's too bad you have chosen such a misleading term to label it.

Most native English speakers familiar with the words regard preadaptation and exaptation to be directly opposed in their implications - almost opposites.

(Bateson called it "abduction", from its logical structure: compare deduction, induction. I find that convenient and accurate)