A new multipurpose on-off switch for inhibiting bacterial growth

A new multipurpose on-off switch for inhibiting bacterial growth
Figure 1. The domain DUF4065/Panacea is found in a wide variety of TA-like loci across bacteria, archaea, and bacteriophages. Branches of the IQTree maximum likelihood phylogenetic tree of representative PanA sequences are colored by major taxonomic groupings as per the upper left key with an additional symbol to highlight bacteriophages. Rectangles in the outer and inner rings indicate the presence and absence of N-terminal domains in the PanA sequences and predicted associated toxin groups, respectively, according to the left-hand keys. Colored circles between the rings indicate putative TA pairs that have been tested in toxicity neutralization assays and the results of those assays. “TA” means the expression of the toxin compromises E. coli growth, and coexpression of the antitoxin either fully or partially counteracts the toxicity. “Toxic” means toxicity is confirmed, but the cognate PanA sequence does not rescue in this E. coli system. “Stuck in cloning” refers to cases in which the putative toxin genes could not be successfully chemically synthesized and plasmid subcloned, potentially because of the toxicity being too severe. Gray circles on the branches indicate branch support from IQTree ultrafast bootstrapping (53). Tree annotation was carried out with iTOL (54). Credit: DOI: 10.1073/pnas.2102212119

Researchers in Lund have discovered an antitoxin mechanism that seems to be able to neutralize hundreds of different toxins and may protect bacteria against virus attacks. The mechanism has been named Panacea, after the Greek goddess of medicine whose name has become synonymous with universal cure. The understanding of bacterial toxin and antitoxin mechanisms will be crucial for the future success of so-called phage therapy for the treatment of antibiotic resistance infections, the researchers say. The study has been published in PNAS.

So-called toxin-antitoxin systems, a kind of on-off switch in many bacterial DNA genomes, are increasingly being found to defend against attack by bacteriophages—viruses that infect bacteria. Activation of toxins allows bacterial populations to go into a kind of lockdown that limits growth and therefore the spread of the virus. As such, understanding the diversity, mechanisms and evolution of these systems is critical for the eventual success of to treat antibiotic resistance infections.

"Toxin-antitoxin pairs consist of a gene encoding a toxin that dramatically inhibits and an adjacent gene encoding an antitoxin that counteracts the toxic effect. It is like keeping a bottle of poison on a shelf next to a bottle of the antidote. While toxin-antitoxin pairs have been seen to evolve to associate with new toxins or antitoxins before, the scale of the neutralization ability seen with Panacea—so called hyperpromiscuity—is unprecedented," explains researcher and group leader Gemma Atkinson at Lund University, who has led the study

Ph.D. student and co-first author Chayan Kumar Sahamade a computer program for analyzing the kinds of genes that are found next to each other in bacterial genomes. The team then used this tool to predict new antitoxin genes found next to some very potent toxins that they have previously worked on.

The researchers were startled by the discovery that one particular antitoxin protein fold can be found in toxin-antitoxin-like arrangements with dozens of different kinds of toxins. Many of these toxins are new to science. The other first author, Tatsuaki Kurata, Lund University, has confirmed experimentally that several of these systems are genuine toxins neutralized by the neighboring antitoxin genes.

The study shows that what we know so far about the diversity of toxin-antitoxin systems probably is just the tip of the iceberg, and that there could be a range of similar systems that have gone under the radar until now.

As well as being important for understanding bacterial biochemistry, the discovery of new toxin-antitoxin systems is important for so-called therapy against antibiotic resistant infections. As bacteria have increasingly become resistant to antibiotics, other approaches are needed for eliminating infections.

The principle of phage therapy is to treat patients with cocktails of bacteriophages—viruses that infect bacteria—in order to kill the bacteria causing infection. However, bacteria carry various defense systems to protect themselves from phages, and this includes toxin-antitoxin systems.

"Thus identifying toxin-antitoxin systems of pathogens may help us in the future design phage therapy that can counter this layer of defense," explains Gemma Atkinson.

So, what is the next research step? "We are now trying to find novel toxin-antitoxin systems on a universal scale, and understand their involvement in phage defense. We are also interested in possible biotechnological applications of toxin-antitoxin systems, given that these systems can be thought of as on-off switches of core aspects of bacterial biology. The full set of toxin-antitoxin systems could be a molecular toolbox for tweaking bacterial metabolism and controlling bacterial cell resources. This can be important in industrial and pharmaceutical manufacture situations where bacteria are used to produce molecules of interest."


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More information: Tatsuaki Kurata et al, A hyperpromiscuous antitoxin protein domain for the neutralization of diverse toxin domains, Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2102212119
Provided by Lund University
Citation: A new multipurpose on-off switch for inhibiting bacterial growth (2022, February 9) retrieved 6 July 2022 from https://phys.org/news/2022-02-multipurpose-on-off-inhibiting-bacterial-growth.html
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