Reconstructing Life History Before LUCA

Fri 6 Dec 2019

Space Telescope Science Institute (STScI)
3700 San Martin Drive
Baltimore, MD 21218


12:00 PM - 2:30 PM


Gregory P. Fournier (Massachusetts Institute of Technology)

Origin of Life studies primarily consist of two sets of inferences:  bottom-up, which infer plausible scenarios of abiogenesis given our understanding of planetary, geological, and chemical processes, and top-down, which reconstruct the deepest evolutionary history of genes and genomes across the Tree of Life. A discontinuity exists between these narratives, however, as deterministic physiochemical processes must have given way to historic evolutionary processes long before extant lineages tracing back to the Last Universal Common Ancestor (LUCA) became established.  This gap in our knowledge represents a “dark age” during which evolutionary inference is especially challenging, and when most of the essential, life-defining biological processes on Earth arose.

The origin of the universally conserved genetic code and machinery of protein translation is perhaps the most remarkable invention during this dark age.  It seems especially remarkable that the genetic code inherited by LUCA was already “complete”, and pre-selected to be sufficient for the evolution of all future biological diversity, and the continued survival of life on Earth. This seems to suggest that the earliest living systems were separated in space, time, and ecology from LUCA, and that much biological diversification would have taken place before the common ancestor of extant life arose. Therefore, the genetic code itself would already have been selected for universal evolutionary robustness before it became “locked in”.

In our current work, we attempt to further narrow the interval of this “dark age” and constrain its physiological characteristics by reconstructing the history of ancient protein families that diversified before LUCA. Aminoacyl-tRNA synthetase proteins (aaRS) are ideal for these investigations, as they are currently essential for both defining the genetic code, and facilitating protein translation. The early divergences within each aaRS class represent very ancient events in the history of life, possibly even involved with the evolution of the genetic code itself. These large evolutionary distances are reflected by extensive sequence and structural diversity between related groups of aaRS, including recombination and domain shuffling, challenging conventional approaches to phylogenetic inference.  Taking these processes into account and generating a manually curated sequence alignment, a well-resolved pre-LUCA phylogeny of Class I aaRS protein families was generated.  Subsequent ancestral sequence reconstruction shows that the aaRS ancestor very likely already used all 20 amino acids in its sequence. This shows that the complete “modern” genetic code predated the proteins that currently define it, revealing that it must be the product of an even earlier system, for example, within the RNA world. Therefore, it seems that the earliest diversifications of life took place prior to the invention of much of the modern translational apparatus, although only one branch of this diversity survived to leave descendants, represented by LUCA.


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