Monday, August 10, 2020

Evolutionary assimilation of foreign DNA in a new host


We know from decades of biological study that all living beings share many similar genes. We also know that these genes are subject to evolution, from mutations that change the DNA sequence of an organism’s offspring, or through horizontal gene transfer (HGT), the acquisition of DNA from a creature other than a parent, and even of a different species.

This got a team of bioengineers at UC San Diego wondering: could a human gene function in other organisms? And if it does function, what evolutionary changes are happening to the DNA to allow it to work properly in a new host species?

Bioengineers in Professor Bernhard Palsson’s Systems BiologyResearch Group used genetic engineering and laboratory evolution to test the functionality of DNA placed into a new species and study how it can mutate to become functional if given sufficient evolutionary time. They published their results on August 10 in Nature Ecology and Evolution.

Schematic of the experimental workflow. Native E. coli glycolytic isomerases pgi and tpiA were replaced with the coding sequence of foreign orthologues and subjected to laboratory evolution for improved exponential phase growth rate. Ma, million years ago.

The researchers used the bacteria E.coli to answer these questions. They took two common genes from the human genome involved in sugar metabolism, and used CRISPR to swap them into a commonly used laboratory strain of E. coli.

The two genes used—pgi and tpiA-- cripple E. coli when removed, causing the bacteria to grow about 5 times slower. Initially, following the gene swap, E. coli’s growth rate did drop, signaling that the genes weren’t functioning properly. But then, the researchers subjected the transformed E. coli strain to a laboratory “evolution machine”—a robotic system used to study how engineered bacteria adapt to changes. After thousands of generations of evolution, the new genes started to function properly. The human genes could serve just the same function in the bacterium as its own genes.

The automated evolution system enabled a large-scale study, generating hundreds of mutant strains evolved for more than 50,000 cumulative generations, something that would take decades rather than months if performed manually.

How was it possible that the human genes were fulfilling the same role in E.coli?  The researchers sequenced the genomes of the evolved strains to find out.

For every strain that successfully evolved, the critical factor was one or more mutations increasing gene expression level. Most of these mutations did not occur within the foreign gene, but rather in regions of E. coli’s DNA controlling regulation of the gene, with their nature depending sensitively on the gene’s specific DNA sequence and location in the chromosome. Some of these mutations occurred with shocking regularity, including one observed independently more than 20 times, demonstrating that evolutionary outcomes can be (probabilistically) predicted to the single DNA basepair.

“This result shows the importance of systems biology,” said Professor Bernhard Palsson, principal investigator of the study. “Namely, biological function, in this case, is not so much about the parts of the cell, but how they come together to function as a system.”

The original motivation for the study was to determine ’self’ versus ’non-self’ at the molecular biology level. The surprising answer is that even if human enzymes are foreign entities to the E. coli bacterium, they are not recognized as such, and the bacterium adopts their function by simply adjusting their abundance to achieve balanced phenotypic state.

This study establishes the influence of various DNA and protein features on cross-species genetic interchangeability and evolutionary outcomes, with implications for both natural horizontal gene transfer and strain design via genetic engineering.