Journal
NATURE MICROBIOLOGY
Volume 6, Issue 2, Pages 162-+Publisher
NATURE RESEARCH
DOI: 10.1038/s41564-020-00822-7
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Funding
- Marsden Fund from the Royal Society of New Zealand
- School of Biomedical Sciences Bequest Fund from the University of Otago
- University of Otago Doctoral Scholarships
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Bacteria have multiple immune mechanisms against phages and foreign genetic elements. The study found that pathways like the Rcs pathway can simultaneously regulate innate and adaptive CRISPR-Cas immunity to suppress phage infection and facilitate plasmid acquisition.
Bacteria harbour multiple innate defences and adaptive CRISPR-Cas systems that provide immunity against bacteriophages and mobile genetic elements. Although some bacteria modulate defences in response to population density, stress and metabolic state, a lack of high-throughput methods to systematically reveal regulators has hampered efforts to understand when and how immune strategies are deployed. We developed a robust approach called SorTn-seq, which combines saturation transposon mutagenesis, fluorescence-activated cell sorting and deep sequencing to characterize regulatory networks controlling CRISPR-Cas immunity in Serratia sp. ATCC 39006. We applied our technology to assess csm gene expression for similar to 300,000 mutants and uncovered multiple pathways regulating type III-A CRISPR-Cas expression. Mutation of igaA or mdoG activated the Rcs outer-membrane stress response, eliciting cell-surface-based innate immunity against diverse phages via the transcriptional regulators RcsB and RcsA. Activation of this Rcs phosphorelay concomitantly attenuated adaptive immunity by three distinct type I and III CRISPR-Cas systems. Rcs-mediated repression of CRISPR-Cas defence enabled increased acquisition and retention of plasmids. Dual downregulation of cell-surface receptors and adaptive immunity in response to stress by the Rcs pathway enables protection from phage infection without preventing the uptake of plasmids that may harbour beneficial traits.
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