Last universal common ancestor (LUCA) between ancient Earth chemistry and the onset of genetics

There was a time when there was no life on Earth (i.e. only the environment). And there was a time when there were DNA-inheriting cells (i.e. there were gene-environment interactions). Transitioning from the former to the latter is difficult to imagine. Earth is 4.54 billion years old. By 4.2 to 4.3 billion years ago, Earth had cooled sufficiently so that there was liquid water; subsequently, hydrothermal convection currents started sequestering water to the primordial crust and mantle. First signs of life appear as carbon isotope signatures in rocks 3.95 billion years ago. Thus –– somewhere on the ocean-covered early Earth, and in a narrow window of time of “only” ~200 million years –– the first cells came into existence.

Because the genetic code and amino acid chirality (asymmetrical mirror images, of a chiral molecule or ion, are called enantiomers or optical isomers, and cannot be superimposed on one another) are universal, all modern life forms ultimately trace back to that phase of evolution –– which was the time during which the last universal common ancestor (LUCA) of all cells lived. [LUCA is a theoretical construct, which might or might not have been something we today would call an organism; but it helps to bridge the conceptual gap between rocks and water on the early Earth and ideas about the nature of the first cells.] Opinions about LUCA have spanned many decades. These concepts are traditionally linked to our ideas about the overall tree of life and where “its root” might lie. However, phylogenetic trees are temporary and of course undergo change as new data and new methods of phylogenetic inference emerge.

The familiar three-domain tree of life presented by ribosomal RNA [Carl Woese, 1990] depicted LUCA as the last common ancestor of archaea, bacteria, and eukaryotes. But we were confronted with two recurrent and fundamental problems: 1) How are the three domains related to one another (so that gene presence patterns would really trace genes to LUCA) as opposed to another evolutionarily more derived branch? 2) Does presence of a gene in two domains (or three) indicate that it was present in the common ancestor of those domains, or could it have reached its current distribution via late creation in one domain, and horizontal gene transfer (movement of genetic material between unicellular and/or multicellular organisms other than by transmission of DNA from parent to offspring) from one domain to another?

With the availability now of so many genome sequences, authors [see attached paper] ask what genes are ancient –– by virtue of their phylogeny –– rather than by virtue of being universal. This approach, undertaken recently, leads to a different view of LUCA than we have had in the past. In this insightful review, authors argue that this approach (ancient genes as a consequence of their phylogeny) fits better with the harsh geochemical setting of early Earth and resembles more the biology of prokaryotes that today inhabit Earth’s crust.

Did the origin of genetics hinge upon hydrothermal chemical conditions that gave rise to the first biochemical pathways that, in turn, gave rise to the first cells? Genes that trace to LUCA, ancient biochemical pathways, and aqueous reactions of CO2 with iron and water –– all seem to converge on similar sets of simple, exergonic (reaction accompanied by release of energy) chemical reactions –– such as those that occur spontaneously in hydrothermal vents. From the standpoint of genes, physiology, laboratory chemistry, and geochemistry, it is therefore looking more and more like LUCA was rooted in rocks and hydrothermal vents., i.e. Life was based on CO2 with iron and water.


PLoS Genet Aug 2o18; 14: e1007518

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