Features of how DNA, RNA, and proteins are built and metabolized are common to every living thing we've looked at, suggesting they were inherited through common descent. While life may have arisen more than once, it appears that only one lineage has survived down to the present day.

If you could trace living lineages back far enough, you'd arrive at an organism that's the ancestor to every living thing: the last universal common ancestor, or LUCA. This idea has naturally led to a lot of speculation about what LUCA might have looked like. In the latest effort to offer some informed opinion, scientists have performed a clever genomic analysis to identify some of the genes that were probably in LUCA. Those genes, in turn, allow us to infer something about how LUCA lived and what environments it inhabited.

Building trees

Various analyses have indicated that organisms with complex cells (eukaryotes) are a relatively recent development on Earth—assuming you're willing to call something over two billion years old "recent." Two other lineages, bacteria and archaea, go back much further. LUCA sits at the point where bacteria and archaea started to diverge. So if you can identify genes that have been inherited by both of these lineages, they probably were present in LUCA's genome as well.

But performing that sort of analysis turns out to be complicated by the fact that both of these groups of single-celled organisms will happily exchange genes through a process known as horizontal gene transfer. If a gene provides a big advantage to an organism, it's likely to spread widely in both bacteria and archaea. Thus, it will look like all of them have inherited the gene from an ancient common ancestor when in fact it was a recent development that has spread through horizontal gene transfer.

Complicating matters further, some genes that were useful in LUCA might have been lost when its descendants occupied different habitats—it's even possible to lose a gene and then pick up a replacement through horizontal gene transfer. Looking at where genes are now doesn't necessarily tell you much about where they were in the past.

The new work relied on the fact that we've sequenced nearly 2,000 bacterial genomes, along with 134 archaeal ones. The researchers involved in the work, all from the Heinrich Heine University in Düsseldorf, identified over 6.1 million protein-coding genes in these genomes. The researchers grouped the genes into families of related genes, which left them with about 285,000 gene families to analyze.

The analysis then focused on those that were widely distributed in modern organisms. To make the final cut, genes had to appear in at least two major groups of both archaea and bacteria. And when an evolutionary tree is built using the DNA sequences, it had to resolve into a single tree with separate branches for bacteria and archaea, suggesting an ancestor in the distant past. When all this was done, there were only 355 families of genes left.

Is this everything? Definitely not. Some genes that had to have been around in LUCA have also been lost from some lineages and/or handed around through horizontal gene transfer at later times, and those might not show up in this analysis. For instance, all indications are that LUCA had a protein-making machinery of some sort, but only a few (25) of its components came out of this work. And there are definitely some false positives, such as seven genes that are involved in oxygen metabolism, which didn't exist at the time LUCA was around.

In the vents

So some of the results are a bit off. But many of the genes that came out of this analysis tell a consistent story: LUCA probably lived in an anaerobic environment at a geothermal vent.

For example, there's one protein (with the catchy name "reverse gyrase") that is only found in organisms that live at extreme temperatures, where it helps stabilize their DNA. Many of the enzymes that the analysis identified are oxygen-sensitive, supporting the idea that the organism was anaerobic.

More critically, LUCA only had one energy-generating metabolic pathway. That pathway relies on a relatively rare commodity: hydrogen. The one significant source of hydrogen on Earth is provided by hot geothermal water reacting with iron-containing rocks. The analysis suggests that LUCA could also use CO 2 as a carbon source and could break down nitrogen molecules for use in proteins and nucleic acids.

Other things that can be inferred from this data: the organism relied heavily on iron and other metals as co-factors for its enzymes, and it used methane derivatives (methyl groups) for both metabolism and for modifying nucleic acids.

The last thing that came out of the analysis was the identification of the lineages that have the greatest genetic affinity for LUCA. On the archaeal side, this is the methanogens, a large group that still lives in anaerobic conditions and (as their name implies) has methane playing a central role in their metabolism. For bacteria, it's the clostridia, home to familiar organisms like the ones that cause gangrene, food poisoning, tetanus, and botulism (though most of them live harmlessly in the soil). These organisms are also anaerobic, which is why they can thrive in places like wounds. Both of these groups use versions of the same hydrogen-dependent metabolic pathway that the research suggests was present in LUCA.

To some extent, that's not surprising; one would expect that organisms residing in similar environments might evolve similar solutions to the metabolic challenges the environment presents. So it's not entirely clear whether this idea really represents a genetic affinity or simply a good solution to a set of shared environmental challenges. What it does suggest, however, is that LUCA had already come about a general solution that has stood the test of time for several billion years.

It's important to emphasize that this data doesn't mean life was started at a geothermal event; the origin of life was well before LUCA. But it does suggest that geothermal vents provided life an environment in which it could thrive long enough to start evolving some of the genetic toolkit that it still relies on today.

Nature Microbiology, 2016. DOI: 10.1038/NMICROBIOL.2016.116 (About DOIs).