New light may have been shed on one of the most mysterious parts of the tree of life. The Last Universal Common Ancestor (LUCA) is a hypothetical single-celled species from which all of modern life is descended. If it ever existed, it lived approximately four billion years ago. Its physiology is a mystery, and its habitat has long been debated by experts.
In July, a team of researchers led by William F. Martin of Heinrich Heine University in Düsseldorf, Germany, attempted to uncover LUCA’s identity. In their paper published in Nature Microbiology, they describe using DNA samples from a wide variety of modern species to construct a crude model of LUCA’s genetic blueprint.
The tree of life is divided into three main branches or ‘domains’. They are the single-celled domains of bacteria and archaea and a younger sub-branch called eukaryota, which includes multicellular organisms like animals, plants, and fungi. LUCA sits near the very base of the tree of life, at the point where the first two branches meet. To get a look at this evolutionary intersection, the team traced backward.
Martin’s team analyzed over 6.1 million DNA sequences from thousands of primitive single-celled organisms, grouping together similar genes. Common traits are often a sign of relatedness, although genetic transfers can happen between unrelated species. This can make the tree of life difficult to piece together. To be considered, each group of genes required a wide distribution of representatives in both bacteria and archaea, as well as signs of its progress throughout the tree of life. Genes that appeared in unexpected places were eliminated from the study. In the end, the team could comfortably attribute 355 gene groups to a common ancestor, offering a glimpse at its nature.
According to the results, LUCA could assemble its own food substances, including sugars, fats, and proteins. Many of these proteins required a high quantity of iron, sulphur, and other metals. LUCA possessed the protein reverse gyrase, which protected its DNA from extremely high heat. It depended on hydrogen gas, nitrogen gas, and carbon dioxide for its respiration.
At the time when LUCA would have lived, its only available sources of hydrogen gas were geological. Hydrothermal vents — volcanic cracks along the ocean floor — produce it in high quantities. They also spew molten metal into the ocean floor — enough for LUCA to assemble its proteins. Only the hardiest of organisms can survive this sort of environment, and the presence of reverse gyrase suggests that LUCA may have been one of these organisms. Taking all of this into account, it seems possible that LUCA — and maybe even the earliest life forms — lived in hydrothermal vents.
Does this provide a definitive portrait of LUCA? Perhaps not. Microbiology expert and University of Toronto alumna Dr. Laura Hug describes the paper as “more a thought experiment than a truly conclusive study.” She also notes, “It is an interesting approach, but the suite of genomes used is composed only of relatively well-known and well-characterized groups, which limits the strength of the conclusions reached.”
To Hug, the study’s biggest weakness is its failure to consider ‘candidate phyla’. Candidate phyla are groups of single-celled organisms that have yet to be properly cultured and stored by scientists. Their existences are only known through the wide genetic analysis of environmental samples. Despite never having been officially discovered, many of their genes have been sequenced, covering “a wide swathe of the known diversity on the tree of life.” Failing to use “the most complete dataset available” is “problematic,” according to Hug.
“Many of the candidate phyla are highly divergent, and have unique metabolic features. Their inclusion might overturn some of the features of the model LUCA presented in this paper, or add new features,” explains Hug.
The researchers themselves acknowledge the uncertainty of their results. Several of the 355 gene groups code for oxygen-specific metabolic processes, even though oxygen gas was not abundant in Earth’s atmosphere during LUCA’s time. The paper addresses this discrepancy by suggesting that these genes were transferred between unrelated sections of the tree of life, and they proliferated as atmospheric oxygen rose, mimicking an evolutionary descent from LUCA.
Ultimately, according to Hug, the study is stronger at “narrowing the potential metabolic functions” of LUCA than it is at proving that “any pathway or gene is ancestral to all life on Earth.”
None of this negates the scientific value of the study. Hug notes, “The origin of life on earth and the characteristics of LUCA are of significant interest… and I think [the paper] is a valuable contribution from that perspective.”
