Regulation of the integrase and cassette promoters of the class 1 integron by nucleoid-associated proteins

Abstract

The integrase IntI1 catalyses recombination of antibiotic-resistance gene cassettes in the integron, a widely found bacterial mobile element active in spreading antibiotic multi-resistance. We have previously shown that resistance cassette recombination rate and specificity depend on the amount of intracellular integrase. Here, we used in vivo and in vitro methods to examine convergent expression of the integrase promoter (Pint ) and of the cassette promoters (Pc and P2 ) in the prototypical plasmid-borne class 1 integron, In2. Highly conserved Pint has near consensus −10 and −35 hexamers for σ70 RNA polymerase, but there are 11 naturally occurring arrangements of Pc alone or combinations of the Pc +P2 cassette promoters (note that P2 occurs with a 14 or 17 bp spacer). Using a bi-directional reporter vector, we found that Pint is a strong promoter in vivo, but its expression is reduced by converging transcription from Pc and P2 . In addition to cis-acting convergence control of integrase expression, the regulator site prediction program, prodoric 8.9, identified sites for global regulators FIS, LexA, IHF and H-NS in and near the integron promoters. In strains mutated in each global regulator, we found that: (1) FIS repressed integrase and cassette expression; (2) LexA repressed Pint and P2 with the 14 bp spacer version of P2 and FIS was necessary for maximum LexA repression; (3) IHF activated Pint when it faced the strong 17 bp spacer P2 but did not elevate its expression versus LexA-repressed P2 with the 14 bp spacer; and (4) H-NS repressed both Pint and the 14 bp P2 but activated the 17 bp P2 cassette promoters. Mobility shift assays showed that FIS and IHF interact directly with the promoter regions and DNase I footprinting confirmed extensive protection by FIS of wild-type In2 integron promoter sequence. Thus, nucleoid-associated proteins, known to act directly in site-specific recombination, also control integron gene expression directly and possibly indirectly.