Zombie bacteria keep building DNA after death - Biology Cell & Microbiology - Biotechnology

Gabriel Antonio Minero in the laboratory, illustrating the experiment using props he has sewn and built himself. The orange soft toy represents DNA, the blue one is a bacteriophage, and the LEGO flower represents the flower-like structures of crystallized DNA. But where are the zombie bacteria? They are hiding in the biofilm sample under the microscope right next to him, where they are busy producing the flower-like DNA structures. Credit: Peter F. Gammelby, Aarhus University

Researchers at Aarhus University have discovered that bacteria can continue producing DNA after they die. And they have found a way to control what gets produced. The discovery could eventually contribute to the development of new biological materials.

Researchers at Aarhus University have found something that could belong in a horror film: bacteria that continue producing DNA after they are dead. Or rather, the machinery they leave behind carries on working. And behind it all are viruses that both kill the bacteria and provide some of the equipment.

The researchers have even worked out how to get the bacteria's "zombie factories" to produce DNA according to a particular blueprint.

They have published both the discovery and the method in Angewandte Chemie.

Viruses on standby

Bacteria often live in communities known as biofilms. They are surrounded by a sticky substance that contains DNA, among other things. It serves as both building material and protection—for example, in the plaque we brush off our teeth.

This illustration, which covers the entire back cover of Angewandte Chemie, shows how bacteriophages—viruses that infect bacteria—can trigger the production of new DNA in a biofilm. The blue bacteria are alive, while the green ones are dead but have not become zombies. The pink, ladder-like structures represent dead "zombie bacteria" producing special DNA structures called G-quadruplexes. The red circle shows a bacteriophage that can lie dormant inside a bacterium. When activated, it can cause the bacterial cell to burst, releasing enzymes that continue producing DNA outside the cell. At the bottom right, a light-blue enzyme is shown repeatedly copying an artificially created ring of DNA. This produces long DNA strands (red) containing G-quadruplexes (pink), which can assemble into the red, flower-like structures seen in the biofilm and give it new chemical properties. Parts of the illustration were created using BioRender. Credit: Gabriel Antonio Minero / Angewandte Chemie

Many bacteria also carry what are known as bacteriophages—viruses that infect only bacteria. Some bacteriophages can lie dormant as part of a bacterium's genetic material.

The researchers deprived two bacterial species, Shewanella oneidensis and Bacillus subtilis, of nutrients. This caused some of the dormant viruses to wake up and multiply. Eventually, they burst the bacterial cells open.

You might think that would bring all work to a halt.

But when the cells burst, both the building blocks of DNA and specialized enzymes were released. And the enzymes continued making DNA outside the dead bacteria—out in the biofilm.

"In a way, life goes on after the bacterium has died," says the study's first author, assistant professor Gabriel Antonio Minero from the Department of Biology at Aarhus University.

Flowers from the dead

To find out whether they were really seeing newly produced DNA—rather than merely remnants of the burst cells—the researchers added a small, artificially made ring of DNA to the bacterial cultures. 

One of the red, flower-like structures, captured under a microscope. It formed in a biofilm of the bacterium Shewanella oneidensis. Credit: Gabriel Antonio Minero / Angewandte Chemie

The ring served as a blueprint that the enzymes could copy over and over again. The new DNA had a distinctive structure that could be detected using fluorescent dyes.

Under the microscope, the DNA combined with other substances to form shapes resembling flowers in one bacterial species and long strands in the other. And when the researchers used a bacterial strain that lacked the relevant viruses, none of this particular DNA was produced.

Minero calls the bacteriophages nano-architects. Although they kill some of the bacteria, they also supply part of the molecular machinery that makes it possible to keep building the biofilm.

Zombies with special powers

The researchers have done more than get the machinery of dead bacteria to produce DNA. They have also worked out how to change the blueprint and thereby determine which type of DNA the machinery produces.

"What matters most to me is that we can hijack the process," says Minero.

Among other things, the researchers got the zombie factories to produce what are known as G-quadruplexes. These are DNA structures that fold into particular shapes, allowing them to bind other molecules and act rather like enzymes, speeding up certain chemical reactions.

Minero likens this to giving the zombies armor or a weapon, equipping the biofilm with new properties.

The armor has not, of course, been shown to protect against antibiotics or other attacks. But the researchers have demonstrated that this special DNA can act as a catalyst and alter the biofilm's electrical properties.

An evolutionary puzzle

The discovery also raises an intriguing question: why do some bacteria harbor dormant viruses in their genetic material?

Is it mere coincidence that bacteriophages can help build on the bacterial community after killing some of its members? Or has this interaction evolved because, under certain conditions, it benefits the bacteria?

The researchers cannot yet answer that.

What can the zombies be used for?

The discovery opens up some intriguing possibilities. After all, DNA is not just a blueprint for life. It can also have chemical properties that make it useful for other purposes.

One area of potential interest is environmental biotechnology, where researchers are already trying to harness bacteria for wastewater treatment and bioenergy production.

In the longer term, Minero envisions programming the bacteria's DNA production to create different materials that could help break down pollutants. Instead of making the biological materials in a factory, perhaps the bacteria could be made to produce them wherever they are needed.

But there is still a long way to go

The experiments were carried out in the laboratory with two bacterial species and DNA blueprints supplied by the researchers themselves.

They have shown that they can control which DNA is produced and give it particular chemical properties. They have not yet demonstrated that the technology can clean up polluted water or improve the practical production of bioenergy.

The study thus raises many new questions and possibilities for the researchers to explore.

And if all this has left you thinking that bacteria in biofilms are so well protected that they are practically immortal, think again:

The bacteria really are dead. It's just that some of their machinery hasn't gotten the message. 

Provided by Aarhus University 

by Aarhus University

edited by Sadie Harley, reviewed by Robert Egan 

Source: Zombie bacteria keep building DNA after death