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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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.
The authors declare no competing financial interests.
Supplementary Figures 1–8, Note 1, Methods, Tables 1–4 and References. (PDF 1059 kb)
Analysis of LexA binding on the NA1000 chromosome by ChIPSEQ. (XLSX 67 kb)
Analysis of HigA binding on the NA1000 chromosome by ChIPSEQ. (XLSX 132 kb)
Validated HigB cleavage sites (5ʹ OH RNA ends) detected by nEMOTE. (XLS 154 kb)
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