US researchers have repurposed the gene-repression tool CRISPRi (clustered regularly interspaced short palindromic repeats interference) to study which genes are targeted by particular antibiotics, providing information on how to improve existing antibiotics or develop new ones.
To make CRISPRi mobile, the researchers transferred the system from common lab models like E. coli to disease-causing species in a suite of CRISPRi systems, which combine modularity, stable genomic integration, and ease of transfer to diverse bacteria by conjugation.
Mobile-CRISPRi enables genetic dissection of non-model bacteria, facilitating analyses of microbiome function, antibiotic resistances and sensitivities, and comprehensive screens for host–microorganism interactions.
Basically, the new system allows researchers to identify how particular antibiotics inhibit the growth of pathogens by reducing the production of protein from targeted genes.
Focusing predominantly on human pathogens associated with antibiotic resistance, the researchers demonstrated the efficacy of Mobile-CRISPRi in gammaproteobacteria and Bacillales Firmicutes at the individual gene scale, by examining drug-gene synergies, and at the library scale, by systematically phenotyping conditionally essential genes involved in amino acid biosynthesis.
The researchers anticipate that Mobile-CRISPRi will be a transformative technology for non-model bacteria lacking genetic tools and will facilitate cross-species genetic analysis, complementing existing Transposon sequencing (Tn-seq) technology.
Their findings are published in Nature Microbiology.