Body and mind

Inserting human genes in Escherichia coli advances researchers’ knowledge on evolution

Researchers have inserted genes from humans into Escherichia coli bacteria and studied how the bacteria evolve to make these genes function. This insight gives researchers a better understanding of what being an organism means and can be used to further develop many biotechnological solutions.

Researchers have many good reasons to insert genes from some organisms into others.

An example is that they want bacteria to produce drugs or other biological molecules that may be useful in the health sciences.

Although researchers have been inserting genes from various organisms into bacteria for years, they have very limited understanding of what happens inside the bacteria when they have to adapt to completely new genes.

A new study recently published in Nature Ecology & Evolution has turned all this upside down.

The researchers show how bacteria evolve from being unable to utilize a foreign gene to assimilating it as one of their own.

“This requires understanding how organisms can differentiate between what is their own identity and what is foreign at the molecular level. Can a person’s genes, for example, function in a bacterium, or does the bacterium have to change them?” asks a researcher behind the new study, Bernhard Palsson, CEO, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark.

Swapping genes between bacteria and humans

The researchers answered Bernhard Palsson’s question in their study.

Organisms generally have more similarities than differences.

Many organisms have many genes in common that largely serve the same function and then a few small differences in genes.

Based on this, the researchers replaced genes encoding for enzymes that break down sugar in Escherichia coli (E. coli) with the corresponding gene from humans along with several other species from across the tree of life.

This is called gene-swapping, which has become a fast and simple process thanks to genetic engineering techniques like CRISPR.

After the researchers replaced the sugar-processing genes of E. coli with human equivalents, they let the bacteria grow using an adaptive laboratory evolution method that speeds up evolution by pressuring bacteria and fungi at a furious pace, enabling researchers to study evolution as it happens.

Mutations enable assimilation of human DNA

The result showed that the bacteria, as expected, had great difficulty in growing after a human gene replaced their own gene in the DNA.

However, over generations, the bacteria slowly adapted to the new gene, until they eventually grew just as quickly as they did before the researchers cut and pasted in their DNA.

The human gene could thus function just as well as the bacteria’s own gene, and that surprised the researchers.

The researchers were even more surprised when they discovered how the bacteria had been able to assimilate the foreign gene.

Instead of causing mutations in the foreign gene to make it similar to the gene the researchers had deleted from the bacteria to make room for the human DNA, the bacteria regulated the activity of the gene, which occurs in areas of the DNA outside the gene – the regulatory areas the researchers had not touched at all.

“These genes have been evolutionarily diverging for billions of years, and yet in such a foreign host they were able to go from completely non-functional to working without issue simply through mutations that increased the genes’ production levels,” says Troy Sandberg, first author and post. doc. at University of California San Diego.

“This type of adaptive laboratory evolution showed us what the bacteria had to do to make the gene function to enable them to grow. Regulating the extent to which the gene was expressed was easier than regulating its specific function,” explains Bernhard Palsson.

Affects how the whole system functions

The result of the experiment leads to a very important point in understanding identity at the molecular level.

Researchers often tend to examine the individual parts of an organism and determine how these function, such as how a gene functions in a person.

If a gene cannot immediately function in the same way in a bacterium, one can rapidly conclude that this is because it is a human gene and not a bacterium gene.

But instead of looking at things this way, the new study suggests viewing things from a systems biology perspective and focusing not on whether the individual gene functions or not in the given organism, but more on how the whole system interacts to make it work.

“Our experiments show that the gene functions quite well – even in bacteria. The interest is not whether the gene functions in the bacteria but how the bacteria get the gene to work,” says Bernhard Palsson.

Organisms adapt more rapidly to related genes

The researchers also inserted genes from other organisms into E. coli.

These experiments showed that the more closely related the organisms are, the easier it is for E. coli to make the genes function.

E. coli could relatively easily make the human gene function, but making genes from archaea function was difficult. Despite resembling bacteria in many ways, archaea are even more distantly related.

When the researchers investigated evolution in the various experiments using whole-genome sequencing, they saw how the bacteria tested billions and billions of mutations to make the genes function.

When they found something that worked, they optimized it until the gene eventually fulfilled the necessary function of promoting the growth of the bacteria.

Changing the regulatory areas of the genome is like turning the heat up and down. The bacteria needed to increase the amplification to express exactly the amount of the gene required.

The process took about 25 days for the human gene, and during this time, the bacteria assembled a handful of mutations to replicate the same function in the inserted gene as the gene that had been removed.

For the archaea, the bacteria often failed to find a solution.

“It was interesting that, in parallel experiments, we saw that the bacteria found different solutions to the problem. Sometimes they used different evolutionary steps to arrive at the same solution to the problem in relation to the choice of mutations, and other times they came up with a completely different solution,” says Bernhard Palsson.

Can be used in biotechnology

The discovery provides researchers with much greater understanding of how evolution works.

Although we humans do not exchange genes with each other, microorganisms often exchange genes in nature, and the new study provides insight into how an organism adapts to a new gene to enable it to function optimally.

The study also improves researchers’ understanding that systems biology is often much more important than discussing the extent to which something belongs to one or another organism. It instead focuses on how the organisms make a given gene function optimally in a specific situation.

Ultimately, the research also ushers in greater understanding of how to design bacteria biotechnologically to produce biomolecules that are of interest to researchers.

For example, this could involve getting bacteria to produce medicine. With the new knowledge in hand, researchers can now better understand what happens when they insert a gene intended to produce a drug into a bacterium. They can determine how the bacterium adapts to the gene and alters itself instead of changing the gene.

Importantly, the gene should not be altered, because researchers prefer that the genes intended for producing drugs are not altered once they have been inserted into the organism.

Another perspective is that researchers can use bacteria to, for example, produce enzymes that are involved in developing cancer.

Researchers often want to study how they can target a specific cancer protein with new medicine, and instead of taking proteins from humans, with all the complications this entails, they can get bacteria to produce them in volume.

“Many enzymes and proteins are targets for medicine. Our results show that bacteria can be made to produce enzymes that are identical to those found in cancer. This make it much easier to test the effectiveness of medicines to inhibit the enzymes without having to obtain them from people,” says Bernhard Palsson.

Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes” has been published in Nature Ecology & Evolution. Co-author Bernhard Palsson is the CEO of the Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby.

Bernhard O. Palsson
Bernhard Palsson is a Distinguished and the Galletti Professor of Bioengineering, Professor of Pediatrics, and the Principal Investigator of the Systems Biology Research Group in the Department of Bioengineering at the University of California, San Diego. Dr. Palsson has co-authored more than 500 peer-reviewed research articles and has authored four textbooks, with more in preparation. He is CEO at the Novo Nordisk Foundation Center for Biosustainability in Denmark. His research includes the development of methods to analyze metabolic dynamics (flux-balance analysis, and modal analysis), and the formulation of complete models of selected cells (the red blood cell, E. coli, CHO cells, and several human pathogens). He sits on the editorial broad of several leading peer-reviewed microbiology, bioengineering, and biotechnology journals. He previously held a faculty position at the University of Michigan for 11 years and was named the G.G. Brown Associate Professor at Michigan in 1989. He is inventor on over 40 U.S. patents, the co-founder of several biotechnology companies, and holds several major biotechnology awards. He received his PhD in Chemical Engineering from the University of Wisconsin, Madison in 1984. Dr. Palsson is a member of the National Academy of Engineering and is a Fellow of both the AAAS and the AAM.