Evolution is the accepted explanation for life's diversity today, but there are still some holes in the process that we don't understand. To peer back in time at certain key steps, scientists at the Scripps Research Institute have now engineered synthetic microorganisms designed to be similar to some that might have lived billions of years ago.

The team engineered two different types of synthetic microbes, each one designed to help them study a different stage in the evolution of life on Earth. The first is a chimera bacterium that has both RNA and DNA in its genome, to help study how life transitioned from one to the other. The second is a yeast species that's been modified to have a symbiotic bacterium inside its cells, which should shed light on how mitochondria – the powerhouses of living cells – evolved.

"These engineered organisms will allow us to probe two key theories about major milestones in the evolution of living organisms – the transition from the RNA world to the DNA world and the transition from prokaryotes to eukaryotes with mitochondria," says Peter Schultz, senior author on the two studies. "Access to readily manipulated laboratory models enables us to seek answers to questions about early evolution that were previously intractable."

RNA-DNA chimera

Today, lifeforms store their genetic information in DNA molecules, but it's been suggested for decades that life could have initially used the simpler RNA molecules for the same job, before eventually evolving to make use of the more stable DNA. Exactly how that switch was made remains a mystery, but one possibility is that at some point there existed a creature that used both at the same time.

So, the Scripps team set about engineering just such a bug to test its viability. The researchers modified E. coli so that it built its DNA out of ribonucleotides, which are normally used to construct RNA. Sure enough, the genome of the resulting microbes contained up to 50 percent RNA, and the bacteria were able to not only survive but replicate.

The researchers plan to use the new organism to test out other theories, including whether that much RNA would increase genetic drift and, as a result, speed up evolution.

Synthetic symbiosis

The second synthetic organism was designed to investigate the origins of our mitochondria. Found in the cells of complex organisms called eukaryotes, mitochondria are basically the energy generators of the body, converting oxygen into the molecule ATP.

Interestingly though, there are clues that these organelles were once independent organisms that were slowly absorbed by more complex creatures. Along with looking suspiciously like bacteria, mitochondria have their own DNA, and genetic analysis shows they might be related to Rickettsia, a bacterium that lives inside the cells of host organisms.

To test whether bacteria could evolve into a mitochondria-like role inside another organism's cells, the Scripps team engineered E. coli and baker's yeast so that they would have to depend on each other. The bacteria were modified to lack thiamin, meaning they had to source the vitamin from the yeast. The yeast, meanwhile, had been tweaked so that its existing mitochondria couldn't produce energy, meaning it had to rely on the ATP produced by the bacteria.

The team found that the symbiosis worked, with the bacteria surviving and proliferating for more than 40 generations with no sign of slowing down. Better yet, in that time they even seemed to be adapting to the unusual environment, supporting the idea that they could eventually evolve into something akin to mitochondria.

From there, the researchers plan to push the evolution along a bit, in particular by removing other unnecessary genes from the bacteria.

The new synthetic organisms were described in two papers, the first published in the journal PNAS and the second in the Journal of the American Chemical Society.