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Environment and sustainability

Scientists use evolution to revive zombie genes

Bacteria have many pseudogenes that have lost their function, but researchers have learned how to use adaptive laboratory evolution to revive them. This discovery opens up great pharmaceutical possibilities.

The Technical University of Denmark has developed a method that speeds up evolution by pressuring bacteria and fungi to develop at a furious pace.

Researchers have now discovered that this method – adaptive laboratory evolution – can also revive pseudogenes.

The discovery is interesting because it indicates why evolution has retained these zombie genes that could otherwise easily have been discarded. The pseudogenes probably function like spare parts that keep an old car working so it can be used when the new one has broken down.

“This is fascinating. For the first time, we can show that pseudogenes can be repaired and probably have an evolutionary function we had not known about,” says a researcher behind the study, Bernhard Palsson, CEO, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark.

The new study was recently published in Nature Microbiology.

Pseudogenes are a legacy of the past

Understanding the new findings requires knowing what a pseudogene is.

A pseudogene is a gene that no longer functions and has shared ancestry with a functioning gene. For example, in evolutionary terms a bacterium may no longer require a specific protein coded by a specific gene and because this protein is not required for the organism to survive, the gene does not need to be repaired.

The pseudogenes are a legacy in the genome from a time when the bacteria functioned differently. Bacteria have up to 10,000 genes and also between 100 and 1000 pseudogenes that have no function and appear not to have any purpose.

The pseudogenes might be expected to disappear over time, but bacteria seem to retain them, which has long puzzled researchers.

They finally have an idea why the bacteria do not discard the pseudogenes.

Bacteria find new ways to absorb iron

The researchers investigated what happens to Escherichia coli if they gradually remove parts of the genes the bacterium uses to make proteins that draw iron into the bacterial cells.

When bacteria enter a host, they need iron to divide and proliferate, and they absorb the iron from their surroundings using specific proteins. When these proteins no longer function, the bacteria stop growing and dividing.

The researchers observed the same process in their evolution-accelerating process when they removed the genes from the bacteria. As expected, the bacteria stopped growing.

However, the researchers were also surprised to see that one of the bacterial cultures suddenly began to grow again, as if it still had fully functional versions of the genes the researchers had removed.

The researchers analysed the genome of the bacteria and discovered that the bacteria still lacked the gene that had been removed. Instead the bacteria had repaired a pseudogene, which caused the bacteria to produce a different protein that could enable the cells to absorb iron.

“The bacteria repaired a pseudogene that they were not using anymore. It was a minor repair. The bacteria needed to either remove two nucleotides from the DNA or insert four to activate the gene. The interesting thing is that they do this when we put the bacteria under evolutionary pressure during the evolution-accelerating process,” says Bernhard Palsson.

Forcing bacteria to evolve

The researchers have used adaptive laboratory evolution for some years. This enables them to apply strong selection pressure to bacteria by, for example, removing the type of sugar they normally metabolize. The bacteria then have to adapt to metabolize something else and the evolutionary process has to accelerate to achieve this

For example, some bacteria prefer to metabolize glucose, but if pressured because of the lack of their preferred food, they can develop the genetic basis to enable them to grow on other types of sugar.

This is like an evolutionary process providing people with the metabolic enzymes and proteins to enable them to live by eating grass or bark.

“Adaptive laboratory evolution enables us to observe evolution in action,” explains Bernhard Palsson.

Discovered several repaired pseudogenes

Based on numerous experiments, the researchers at the Technical University of Denmark examined the DNA sequences of 300,000 bacterial genomes in which bacteria have adapted to survive in ways for which they were not really designed.

One explanation may be that the researchers made them grow on new types of substrates, forced them to survive in various toxic chemicals or destroyed parts of their metabolism genetically.

If possible, the bacteria develop what they need to survive, and the researchers can genetically examine how they have done this.

After the researchers discovered the repaired pseudogenes, they returned to their database of 300,000 bacterial genomes to see whether any of the bacteria with which they previously had worked had also recreated lost functions by repairing pseudogenes. Here they found several other examples of bacteria that had taken old genes into use to survive.

“This provides fascinating insight into how evolution works. Organisms do not seem to discard pseudogenes because they provide opportunities to survive. This is a genetic reservoir that they can use if needed. This discovery is really interesting,” says Bernhard Palsson.

Can be used commercially

The insight into the evolutionary engine room and the development of adaptive laboratory evolution open up various commercial opportunities.

Researchers can use the method to force bacteria to produce things they would not normally. These could include various products of pharmaceutical interest, such as adrenaline, dopamine or melatonin, all of which are hormones in humans.

Researchers who know the evolutionary mechanisms of the bacteria can link a gene that produces one of these hormones to the metabolism of the bacteria, and although the bacteria do not normally produce the hormone, they are forced to do this to survive.

Further, the bacteria have to find evolutionary solutions to enable them to survive when producing the hormones. In this respect, nature and evolution are far better at finding solutions than researchers are.

“We can harness evolution to get bacteria to develop various molecules for us in many different ways. Adaptive laboratory evolution has developed from being a tool to study bacteria and fungi to becoming a tool to specifically design substances with the help of evolution,” says Bernhard Palsson.

Pseudogene repair driven by selection pressure applied in experimental evolution” has been published in Nature Microbiology. Several co-authors are employed by the Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby.

Bernhard O. Palsson
CEO
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.