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

The integrase Intl1 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 (P-int) and of the cassette promoters (P-c and P-2) in the prototypical plasmid-borne class 1 integron, In2. Highly conserved P-int has near consensus -10 and -35 hexamers for sigma(70) RNA polymerase, but there are 11 naturally occurring arrangements of Pc alone or combinations of the P-c+P-2 cassette promoters (note that P-2 occurs with a 14 or 17 bp spacer). Using a bi-directional reporter vector, we found that P-int is a strong promoter in vivo, but its expression is reduced by converging transcription from P-c and P-2. 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 P-int and P-2 with the 14 bp spacer version of P-2 and FIS was necessary for maximum LexA repression; (3) IHF activated P-int when it faced the strong 17 bp spacer P-2 but did not elevate its expression versus LexA-repressed P-2 with the 14 bp spacer; and (4) H-NS repressed both P-int and the 14 bp P-2 but activated the 17 bp P-2 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.