A widespread toxin−antitoxin system exploiting growth control via alarmone signaling

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

Research output: Contribution to journalArticlepeer-review

38 Citations (SciVal)

Abstract

Under stressful conditions, bacterial RelA-SpoT Homolog (RSH) enzymes synthesize the alarmone (p)ppGpp, a nucleotide second messenger. (p)ppGpp rewires bacterial transcription and metabolism to cope with stress, and, at high concentrations, inhibits the process of protein synthesis and bacterial growth to save and redirect resources until conditions improve. Single-domain small alarmone synthetases (SASs) are RSH family members that contain the (p)ppGpp synthesis (SYNTH) domain, but lack the hydrolysis (HD) domain and regulatory C-terminal domains of the long RSHs such as Rel, RelA, and SpoT. We asked whether analysis of the genomic context of SASs can indicate possible functional roles. Indeed, multiple SAS subfamilies are encoded in widespread conserved bicistronic operon architectures that are reminiscent of those typically seen in toxin−antitoxin (TA) operons. We have validated five of these SASs as being toxic (toxSASs), with neutralization by the protein products of six neighboring antitoxin genes. The toxicity of Cellulomonas marina toxSAS FaRel is mediated by the accumulation of alarmones ppGpp and ppApp, and an associated depletion of cellular guanosine triphosphate and adenosine triphosphate pools, and is counteracted by its HD domain-containing antitoxin. Thus, the ToxSAS–antiToxSAS system with its multiple different antitoxins exemplifies how ancient nucleotide-based signaling mechanisms can be repurposed as TA modules during evolution, potentially multiple times independently.

Original languageEnglish
Pages (from-to)10500-10510
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number19
DOIs
Publication statusPublished - 2020
Externally publishedYes

Bibliographical note

Funding Information:
We are grateful to the Protein Expertise Platform Ume? University and Mikael Lindberg for constructing the plasmids used in this work, Mohammad Roghanian for purifying E. coli RelA, Victoriia Murina for assistance with setting up macromolecular labelling assays, and Ana?s Poirier for help with toxicity neutralization experiments. This work was supported by the Swedish Research Council (Vetenskapsr?det) (Grant 2017-03783 to V.H., and Grants 2015-04746 and 2019-01085 to G.C.A.); Molecular Infection Medicine Sweden (MIMS) (V.H.); Ragnar S?derbergs Stiftelse (V.H.); Kempestiftelserna (Grant SMK-1858.3 to G.C.A.); Carl Tryggers Stiftelse f?r Vetenskaplig Forskning (Grant 19-24 to G.C.A.); Jeans-sons Stiftelser grant to G.C.A.; Ume? Universitet Insamlingsstiftelsen f?r medicinsk forskning (G.C.A. and V.H.); Ume? Centre for Microbial Research (UCMR) gender policy program grant to G.C.A.; Biotechnology and Biological Sciences Research Council (BBSRC) New Investigator Award BB/S00257X/1 to H.S.; Czech Ministry of Education and Sport via the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) (Grant 8F19006 to D.R. and V.H.); Fonds National de Recherche Scientifique (grants FRFS-WELBIO CR-2017S-03, FNRS CDR J.0068.19, and FNRS-PDR T.0066.18 to A.G.-P.); The European Union from the European Regional Development Fund through the Centre of Excellence in Molecular Cell Engineering (award 2014-2020.4.01.15-0013 to T.T. and V.H.); and the Estonian Research Council (Grants PRG335 and IUT2-22 to T.T. and V.H.). Funding for open access charge is from Swedish Research Council (Grant 2019-01085 to G.C.A.).

Funding Information:
ACKNOWLEDGMENTS. We are grateful to the Protein Expertise Platform Umeå University and Mikael Lindberg for constructing the plasmids used in this work, Mohammad Roghanian for purifying E. coli RelA, Victoriia Murina for assistance with setting up macromolecular labelling assays, and Anaïs Poirier for help with toxicity neutralization experiments. This work was supported by the Swedish Research Council (Vetenskapsrådet) (Grant 2017-03783 to V.H., and Grants 2015-04746 and 2019-01085 to G.C.A.); Molecular Infection Medicine Sweden (MIMS) (V.H.); Ragnar Söder-bergs Stiftelse (V.H.); Kempestiftelserna (Grant SMK-1858.3 to G.C.A.); Carl Tryggers Stiftelse för Vetenskaplig Forskning (Grant 19-24 to G.C.A.); Jeans-sons Stiftelser grant to G.C.A.; Umeå Universitet Insamlingsstiftelsen för medi-cinsk forskning (G.C.A. and V.H.); Umeå Centre for Microbial Research (UCMR) gender policy program grant to G.C.A.; Biotechnology and Biological Sciences Research Council (BBSRC) New Investigator Award BB/S00257X/1 to H.S.; Czech Ministry of Education and Sport via the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) (Grant 8F19006 to D.R. and V.H.); Fonds National de Recherche Scientifique (grants FRFS-WELBIO CR-2017S-03, FNRS CDR J.0068.19, and FNRS-PDR T.0066.18 to A.G.-P.); The European Union from the European Regional Development Fund through the Centre of Excellence in Molecular Cell Engineering (award 2014-2020.4.01.15-0013 to T.T. and V.H.); and the Estonian Research Council (Grants PRG335 and IUT2-22 to T.T. and V.H.). Funding for open access charge is from Swedish Research Council (Grant 2019-01085 to G.C.A.).

Publisher Copyright:
© 2020 National Academy of Sciences. All rights reserved.

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

Keywords

  • Alarmone
  • Antitoxin
  • PpApp
  • PpGpp
  • Toxin

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