Bacteria use small molecules to slam the brakes on their own growth

Schematic Illustration of the Antitoxin Toxin System[2020-04-29] An international research team under the lead of scientists at the Umeå Center for Microbial Research (UCMR)  and The Laboratory for Molecular Infection Medicine Sweden (MIMS) have uncovered a new kind of regulatory system of toxin and antitoxin proteins in bacteria that could be a defense system against viral attack. The bioinformatic identification of the proteins and their experimental validation are now published in the high impact journal Proceedings of the National Academy of Sciences of the US (PNAS, 28 April 2020)

When bacteria get stressed e.g. through antibiotic treatment or the lack of nutrients, they slow down their growth mechanism by small signaling molecules called Alarmones. The Atkinson and Hauryliuk labs at Umeå University have worked on the proteins that make and degrade alarmones for over a decade. They previously revealed the ubiquitous presence of small proteins that make alarmones, called small alarmone synthetases or SASs, encoded in bacterial genomes.

It was an unanswered question why bacteria carry SAS proteins in addition to their standard tool-set for alarmone synthesis and degradation. Now, Gemma C. Atkinson, Vasili Hauryliuk and their colleagues found an explanation. They showed that some SASs are components of so-called toxin-antitoxin (TA) systems.

Toxin-antitoxins genes are enigmatic components of microbial genomes. What toxins of TA systems all have in common is that they slam the brakes on growth and reproduction. This is counteracted by their antitoxins which are encoded by adjacent genes. Antitoxins can also work in different ways, either binding to the toxin to stop its action, or counteracting the effect of the toxin in an indirect way.

Profilbild. Atkinson"It is almost paradoxical, but the very ability of an alarmone to down-regulate growth for continued survival is also what gives it toxic potential. In the case of toxic SASs (or toxSASs), these proteins produce a highly unusual alarmone – so-called ppApp – that inhibits growth so dramatically that it is essentially a poison", Atkinson explains.

"Importantly, this brake is reversible through the action of the antitoxins", she continues.

The biological function of toxin-antitoxin systems is a matter of much debate and controversy, but there is evidence that in the case of toxSASs, they may be a defence mechanism against viral attack, putting them in the same category as the CRISPR-Cas9 system. From earlier studies it was known that a protein – now known to be a toxSAS – encoded in virus DNA hiding in a bacterial genome could protect against infection by a second virus. The Umeå team has now discovered that many bacteria-infecting viruses carry toxSASs, and – even more often – small alarmone hydrolases, which would allow them to destroy the alarmone and bypass a toxSAS-based defense mechanism.

The initial discovery of toxSAS toxin-antitoxins was made possible using a tool made in the Atkinson group called FlaGs, standing for Flanking Genes. FlaGs analyses how gene neighbourhood changes or is kept the same (conserved) during evolution. It can be applied to any protein of interest to discover functional associations, not just toxin-antitoxin systems. The bioinformatics tool is available on, and a web server for online analyses is available at

Three members of the Umeå team share first-authorship on the PNAS paper: Steffi Jimmy, Chayan Kumar Saha and Tatsuaki Kurata. PhD student Chayan Kumar Saha carried out most of the bioinformatic analyses and drove the development of the FlaGs tool. Most of the validation of toxicity and neutralisation of toxSASs – and the discovery of the new ppApp alarmone as the toxic agent of toxSAS – was carried out by PhD students Steffi Jimmy and Sofia Oliveira (based in the University of Tartu), and post-doc Tatsuaki Kurata.

Many techniques which are used in genetic and molecular biological laboratories have been developed from discoveries of smart mechanisms in the toolbox of bacteria. The CRISPR-Cas9 system, the easy and precise tool now used for gene modification, is based on a mechanism which bacteria use to defend themselves against virus (phages) attacks.

"Who knows, maybe in the future we will see the toxSAS system in use as a tool for the therapeutic or biotechnological regulation of bacterial growth", Atkinson commented on the new findings.

This study also involved  researchers from the following organisations:

  • University of Tartu, Institute of Technology, Tartu, Estonia
  • Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
  • Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Belgium
  • Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
  • Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic

Original publication:

Steffi Jimmy, Chayan Kumar Saha, Tatsuaki Kurata, Constantine Stavropoulos, Sofia Raquel Alves Oliveira, Alan Koh, Albinas Cepauskas, Hiraku Takada, Dominik Rejman,Tanel Tenson, Henrik Strahl, Abel Garcia-Pino, Vasili Hauryliuk, Gemma C. Atkinson (2020): A widespread toxin-antitoxin system exploiting growth control via alarmone signaling. Proceedings of the National Academy of Sciences of the United States of America, PNAS, 28 April 2020,

About the Atkinson lab and the Hauryliuk lab

Gemma C. Atkinson and Vasili Hauryliuk are specialists in microbial protein synthesis, antibiotic resistance and stress responses. The great strength of the two research groups is that they both develop and use creative methods in bioinformatics combined with experimental methods in microbiology, molecular biology and biochemistry. They confirm in silico findings from bioinformatics with in vitro and in vivo studies in bacteria and yeast.

The Atkinson group has recently been granted funding from the Umeå University Medical Faculty for research into biotechnological applications of newly discovered TA systems.

Contact persons:
Gemma C. Atkinson, associate professor

Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University
This email address is being protected from spambots. You need JavaScript enabled to view it.
phone: +46 (0)706070315
Web page of the Atkinson Lab

Vasili HauryliukVasili Hauryliuk, associate professor
The Laboratory for Molecular Infection Medicine Sweden (MIMS)
Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University
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Webpage of the Hauryliuk lab


Picture for download: Gemma Atkinson, group leader and first senior author of the publication, picture by Susanna Bergström

Picture to the right: Vasili Hauryliuk, group leader second senior author of the publication, picture by Eva-Maria Diehl

Top Picture:  Illustration of the Toxin-Toxin System by Gemma Atkinson