Metabolically-targeted dCas9 expression in bacteria. Escherichia coli BL21(DE3)

The ability to specifically regulate metabolism in relevant bacterial species in complex microbiomes remains a significant challenge. In the context of the human microbiome, one relevant metabolic activity that is a target for down-regulation are glucuronide-utilization enzymes (GUS) that are implicated in the toxic re-activation of glucuronidated compounds in the human gastrointestinal (GI) tract, including the chemotherapeutic drug irinote-can. Here, we take advantage of the variable distribution of GUS enzymes in bacteria as a means to distinguish between bacteria with the relevant GUS activity, and re-purpose the glucuronide-responsive GusR transcription factor as a biosensor to regulate dCas9 expression in response to glucuronide inducers. We fused the E. coli gusA regulatory region to the dCas9 gene to create pGreg-dCas9, and showed that dCas9 expression is induced by glucuronides, but not other carbon sources. When conjugated from Escherichia coli to bacteria derived from human stool, dCas9 expression from pGreg-dCas9 was restricted to GUS-positive bacteria. dCas9-sgRNAs targeted to gusA specifically down-regulated gus operon transcription, with a resulting approximate 100-fold decrease in GusA activity. Our data outline a general strategy to re-purpose bacterial transcription factors responsive to exogenous metabolites for precise ligand-dependent expression of dCas9 or other genetic tools in relevant bacterial species.