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

Jimmy, Steffi ; Saha, Chayan Kumar LU orcid ; Kurata, Tatsuaki LU ; Stavropoulos, Constantine ; Oliveira, Sofia Raquel Alves ; Koh, Alan ; Cepauskas, Albinas ; Takada, Hiraku ; Rejman, Dominik and Tenson, Tanel , et al. (2020) In Proceedings of the National Academy of Sciences of the United States of America 117(19). p.10500-10510
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... (More)

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.

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publishing date
type
Contribution to journal
publication status
published
keywords
Alarmone, Antitoxin, PpApp, PpGpp, Toxin
in
Proceedings of the National Academy of Sciences of the United States of America
volume
117
issue
19
pages
10500 - 10510
publisher
National Academy of Sciences
external identifiers
  • scopus:85084503982
  • pmid:32345719
ISSN
0027-8424
DOI
10.1073/pnas.1916617117
language
English
LU publication?
no
additional info
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.
id
abba6482-627c-411e-9213-c539d49843bd
date added to LUP
2021-09-24 20:32:29
date last changed
2024-06-16 19:30:41
@article{abba6482-627c-411e-9213-c539d49843bd,
  abstract     = {{<p>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.</p>}},
  author       = {{Jimmy, Steffi and Saha, Chayan Kumar and Kurata, Tatsuaki and Stavropoulos, Constantine and Oliveira, Sofia Raquel Alves and Koh, Alan and Cepauskas, Albinas and Takada, Hiraku and Rejman, Dominik and Tenson, Tanel and Strahl, Henrik and Garcia-Pino, Abel and Hauryliuk, Vasili and Atkinson, Gemma C.}},
  issn         = {{0027-8424}},
  keywords     = {{Alarmone; Antitoxin; PpApp; PpGpp; Toxin}},
  language     = {{eng}},
  number       = {{19}},
  pages        = {{10500--10510}},
  publisher    = {{National Academy of Sciences}},
  series       = {{Proceedings of the National Academy of Sciences of the United States of America}},
  title        = {{A widespread toxin−antitoxin system exploiting growth control via alarmone signaling}},
  url          = {{http://dx.doi.org/10.1073/pnas.1916617117}},
  doi          = {{10.1073/pnas.1916617117}},
  volume       = {{117}},
  year         = {{2020}},
}