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Growth control switch by a DNA-damage-inducible toxin–antitoxin system in Caulobacter crescentus

Nature Microbiology volume 1, Article number: 16008 (2016) Cite this article

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Abstract

Bacterial toxin–antitoxin systems (TASs) are thought to respond to various stresses, often inducing growth-arrested (persistent) sub-populations of cells whose housekeeping functions are inhibited. Many such TASs induce this effect through the translation-dependent RNA cleavage (RNase) activity of their toxins, which are held in check by their cognate antitoxins in the absence of stress. However, it is not always clear whether specific mRNA targets of orthologous RNase toxins are responsible for their phenotypic effect, which has made it difficult to accurately place the multitude of TASs within cellular and adaptive regulatory networks. Here, we show that the TAS HigBA of Caulobacter crescentus can promote and inhibit bacterial growth dependent on the dosage of HigB, a toxin regulated by the DNA damage (SOS) repressor LexA in addition to its antitoxin HigA, and the target selectivity of HigB's mRNA cleavage activity. HigB reduced the expression of an efflux pump that is toxic to a polarity control mutant, cripples the growth of cells lacking LexA, and targets the cell cycle circuitry. Thus, TASs can have outcome switching activity in bacterial adaptive (stress) and systemic (cell cycle) networks.

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Figure 1: Loss of function of the antitoxin HigA improves ΔtipN Nal tolerance.
Figure 2: HigBA is auto-regulated but also subject to hierarchically superior repression by LexA.
Figure 3: HigB preferentially cleaves at UCG-Ser codons.
Figure 4: Quinolone antibiotics identified from high-throughput chemical screening simultaneously activate the SOS response, higBA and acrAB2nodT.
Figure 5: HigB activity exacerbates loss of viability during the SOS response, increases cell filamentation and decreases G1 cell accumulation in ΔlexA cells with constitutively activated SOS response.

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Acknowledgements

This work was supported by grant no. SNF#31003A_143660 to P.H.V. and a grant from the Société Académique de Genève to C.L.K. The authors acknowledge SNF/NCCR Chemical Biology for support of the chemical screening experiments and S. Kicka, V. Trofimov, D. Moreau and H. Riezman for advice and assistance with high-throughput screening. The authors thank P. Linder for discussions and funding contributions (SNF#31003A_149228/1) for the nEMOTE experiments, G. Panis for assistance with flow cytometry data acquisition and interpretation, C. Menck for the PimuA-lac290 and pNPTSΔlexA plasmids, L. Théraulaz for technical assistance, H. Yasrebi for nEMOTE data tabularization and J. Prados for assistance with R programming.

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Author notes

  1. Antonio Frandi & Johann Mignolet

    Present address: † Present addresses: Department of Fundamental Microbiology, University of Lausanne, Quartier UNIL-Sorge, CH-1015 Lausanne VD, Switzerland (A.F.). Institute of Life Sciences, Université catholique de Louvain, Place Croix du Sud 5, 1348 Louvain-La-Neuve, Belgium (J.M.).,

Authors and Affiliations

  1. Department of Microbiology & Molecular Medicine Institute of Genetics & Genomics in Geneva (iGE3), Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel-Servet 1, 1211 Genève 4, Switzerland

    Clare L. Kirkpatrick, Daniel Martins, Peter Redder, Antonio Frandi, Johann Mignolet & Patrick H. Viollier

  2. Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland

    Julien Bortoli Chapalay, Marc Chambon & Gerardo Turcatti

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Contributions

C.L.K. and P.H.V. conceived and designed the study and wrote the manuscript. D.M. performed experiments (reported in Figs 1, 2 and Supplementary Figs 1–4) under the guidance of C.L.K. and P.H.V. P.R. designed, performed and analysed the nEMOTE experiments and wrote the corresponding sections of the manuscript. J.M. designed, performed and analysed the Tn-SEQ experiment. A.F. and J.B.C. contributed data analysis tools and analysed ChIP-SEQ and codon usage (A.F.) and high-throughput screening (J.B.C.) data. C.L.K., G.T., J.B.C. and M.C. designed the high-throughput screening experiments and C.L.K. performed these and all other experiments. M.C. and J.B.C. co-wrote the high-throughput screening section of the manuscript.

Corresponding authors

Correspondence to Clare L. Kirkpatrick or Patrick H. Viollier.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1–8, Note 1, Methods, Tables 1–4 and References. (PDF 1059 kb)

Supplementary Data 1

Analysis of LexA binding on the NA1000 chromosome by ChIPSEQ. (XLSX 67 kb)

Supplementary Data 2

Analysis of HigA binding on the NA1000 chromosome by ChIPSEQ. (XLSX 132 kb)

Supplementary Data 3

Validated HigB cleavage sites (5ʹ OH RNA ends) detected by nEMOTE. (XLS 154 kb)

Supplementary Data 4

Relative synonymous codon usage (RSCU) of the UCG-Ser codon per ORF in the NA1000 genome. (XLSX 220 kb)

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Kirkpatrick, C., Martins, D., Redder, P. et al. Growth control switch by a DNA-damage-inducible toxin–antitoxin system in Caulobacter crescentus. Nat Microbiol 1, 16008 (2016). https://doi.org/10.1038/nmicrobiol.2016.8

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