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Scientists have engineered a self-destruct button in bacteria

Sneaky molecular biology tricks bacteria into killing themselves, in place of antibiotics

Molly Sargen

Bacteriology

Harvard University

Overuse of antibiotics has escalated the emergence of antibiotic-resistant bacteria. Unfortunately, the growth of resistance has outpaced the development and discovery of new antibiotics and limited the treatment of bacterial infections. 

Now, scientists are turning to a uniquely human advantage, the ability to think and reason, to solve the issue. Now, we're tricking pathogenic microbes into killing themselves.

In April, a team of French scientists published a new kind of molecular trickery that selectively kills harmful and antibiotic-resistant bacteria without traditional antibiotics. The research, led by genomicist Rocío López-Igual and colleagues at the Pasteur Institute capitalized on mechanisms of gene regulation to trick Vibrio cholerae into producing self-destructive toxins. This approach could be adapted to target other microbes and reduce the need for antibiotics.

Antibiotic-resistant bacteria are a major threat to human health

 Photo by freestocks.org on Unsplash 

V. cholerae, which causes cholera, encodes multiple toxins in its genome. Bacterial toxins inhibit vital processes like DNA replication or cell division. Typically, anti-toxins – that the bacteria also produce themselves – protect bacteria from poisoning themselves. Stress activates the toxins, often leading to cell death. Although exactly why bacteria maintain deadly toxin genes is still puzzling, we know that artificially activating the toxins provides a route to kill bacteria. The star of López-Igual and her colleagues' method is a toxin that inhibits DNA gyrase, an important bacterial enzyme. Normally, DNA gyrase relieves stress from twisted DNA strands, so preventing DNA gyrase activity causes breaks in DNA. And like in human cells, such severe DNA damage is also fatal to bacterial cells. 

The researchers manipulated the DNA sequences of V. cholerae to create a code for production of the toxin in specific kinds of bacteria. The specificity of bacterial gene regulation ensures that only certain bacteria can interpret this code. Bad news for the ones that can: they end up triggering their own death. 

In the new antimicrobial system, the expression of the toxin is controlled by a protein that also activates expression of V. cholerae’s virulence genes. Virulence describes a pathogen’s ability to make you sick. And since the virulence protein is present only in virulent bacteria, the antimicrobial will only harm virulent bacteria. So, the more dangerous the bacteria, the more likely it is to fall prey to its own toxin.

Scientists say that initiating what can be thought of as bacterial suicide by modifying their DNA might be the next workable solution to antibiotic resistance. In fact, a similar mechanism for killing the tuberculosis bacteria is currently being explored. 

DNA-based antimicrobials like the one developed by Lopez-Igual and her colleagues avoid using antibiotic drugs that might only work temporarily. Because of the specificity of the antimicrobial, bacteria face less pressure to escape death and would need to change drastically in order to survive this self-destruct mechanism. While resistance to the antimicrobial could still arise, such resistance is much less likely than resistance to traditional antibiotics. 

petri dish with growth

This new method harnesses microbial biology to protect us from harmful bacteria

 Photo by Michael Schiffer on Unsplash 

Additionally, this DNA-based method provides a platform for targeting other pathogens, like Staphylococcus aureus (which causes skin infections) and Streptococcus pneumoniae (pneumonia). The toxin from this paper targets V. cholerae using DNA sequences from V. cholerae’s own genome. Building from this model, scientists could manipulate the sequences from other bacterial genomes with similar results. 

Finally, targeting specific bacteria also protects the natural microbiome. Traditional antibiotics used to treat infections kill everything in their paths, beneficial and harmful bacteria alike. Consequently, they impair common bacterial processes that keep our bodies working smoothly, like the digestion of fiber. Since depletion of the microbiome can be just as devastating as an infection, maintaining a healthy microbiome during the treatment of infections could improve recovery. 

The team of French scientists warn that several obstacles must be overcome before employing this type of targeted-antimicrobial to treat human infections. First, they need an effective method to deliver the antimicrobial DNA to bacteria throughout the human body. Scientists also need to address the stability of the antimicrobial DNA, since mutations in the toxin could prevent it from functioning properly. Lastly, like current drugs, targeted antimicrobials will need to be assessed for safety. However, it is unlikely that human cells would be at risk.

Overcoming these barriers to the application of targeted-antimicrobials will provide us with a new weapon in the fight against antibiotic-resistant bacteria. As pathogens devastate human health, it might be time to turn the tables on them with a little deception. 

Comment Peer Commentary

We ask other scientists from our Consortium to respond to articles with commentary from their expert perspective.

Maddie Bender

Ecology & Evolutionary Biology

Yale University

Great article! Finding alternatives to antibiotics is critical in this day and age, and I think you did a really nice job explaining the mechanism of this technique without getting too jargony. I wanted to draw attention to one of the obstacles you note:

“First, they need an effective method to deliver the antimicrobial DNA to bacteria throughout the human body.”

In the paper, it looks like the researchers delivered the plasmid  (what you aptly called “molecular trickery”) through bacterial  conjugation, and then selected for transconjugants. They themselves  admit that even when they used every tool in their antimicrobial toolbox to increase that conjugation rate, they couldn’t get the plasmid into all of the bacteria.

In other words, it’s very promising how well the self-destruct button works when it’s been installed, but how can we make sure it’s installed in the first place?

Molly Sargen responds:

Great anology about installing the self-destruct button, Maddie. Since studying installation of the antimicrobial is the next step, I don’t have an answer to your question yet. For now, I can offer a few thoughts.

It’s difficult to efficiently deliver DNA to bacteria in a laboratory setting, so delivering DNA throughout a human body is likely to be much more challenging. Unlike in the lab, we can’t manipulate temperatures, chemicals, nutrients, and electricity to make it easier for bacteria to install the DNA. Consequently, laboratory DNA delivery techniques like electroporation and heat-shock cannot be used in the body. Conjugation, such as these researchers used, may be the best currently available method although there are still major limitations. However, like you mentioned, current conjugation methods are not efficient enough. Furthermore, conjugation involves multiple bacteria, which would be difficult to control in the body. The authors noted that phages (bacterial viruses that naturally deliver DNA) might be used, but phages don’t infect 100% of bacteria either.

Finding solutions to obstacles like these can come from or lead to major changes in the techniques researchers use regularly. I’m excited to see what these or other researchers can do.

Lauren Gandy

Biochemistry, Microbiology, and Chemical Biology

Rensselaer Polytechnic Institute

Fascinating read, Molly! You did an excellent job summarizing Lopez-Igual et al.’s work and the future challenges that  remain from their study. One tidbit in particular caught my eye: when you referred to the toxin/anti-toxin system that V. cholerae has (Type II), it reminded me of the natural toxin/anti-toxin systems that some gut microbes have.

For example, in the gut Bacteroides species, there is a defense mechanism called the Type VI protein secretion system, similar to V. cholerae ’s Type II but with a different mode of attack. In Type VI, the toxin is always active – and therefore Bacteroides bugs must constantly produce the anti-toxin to protect themselves from their own antibacterial mechanism. Do you think that by manipulating the native antibacterial products from our own body, we can create more “natural” antibiotics for foreign pathogens, that are not only tuned to  an individual, thereby not affecting the already protected gut  microbiome, but also eliminate the invaders?

Molly Sargen responds:

 Hi, Lauren. Thanks for your comment. The type II and type IV secretion systems are a little different from the toxin-antitoxin systems this method would target. However, researchers are already searching for  antibiotics made by common inhabitants of the microbiome like you suggested. While these are probably more specific for targeting pathogens vs. commensals, these molecules would create many of the same  selective pressures as traditional antibiotics. Eventually, pathogens would become resistant to these too. Furthermore, every individual’s microbiome is unique. A molecule produced by my microbiome might act very differently when applied to your microbiome. Overall, I think finding new antibiotics can delay the development of totally resistant bacteria, but it won’t solve the problem.