Transcription of the pyelonephritis-associated pilus (pap) operon of Escherichia coli is subject to regulation by a phase variation control mechanism in which the pap pilin gene alternates between transcriptionally active (phase-on) and inactive (phase-off) states. Pap phase variation appears to involve differential inhibition of deoxyadenosine methylase (Dam) methylation of two pap GATC sites, GATC1028 and GATC113., located in the regulatory region upstream of the papBA promoter. DNA from phase-on cells contains an unmethylated adenosine in the GATC1028 site, whereas DNA from phase-off cells contains an unmethylated adenosine in the GATC130 site. papI and papB are two regulatory genes in the pap operon. Analysis of pap deletion mutants suggests that papI is required for methylation inhibition at the GATC1028 site; however, neither papl nor papB is required for inhibition of methylation at the GATC1130 site. We have identified a chromosomal locus, mbf (methylation-blocking factor), that is required for methylation protection of both the pap GATC1028 and GATC1130 sites. The mbflocus was identified after transposon mTnlO mutagenesis and mapped to 19.6 min on the E. coli chromosome. The effect of transposon mutations within mbf on pap pilin transcription was determined by using a papBAp-lac operon fusion which places lacZ under control of the papBA promoter. E. coli containing mbf::mTnlO and phase-off mbfr E. coli cells both expressed jI-galactosidase levels about 30-fold lower than the j-galactosidase level measured for phase-on mbft E. coli cells. These results indicated that mbf was necessary for pap pilin transcription and were supported by Northern (RNA) blotting and primer extension analyses. Moreover, transposon insertion within mbf greatly reduced Pap pilus expression. The mbf locus was isolated on a low-copy-number cosmid, pMBF1. Complementation analysis indicated that each of seven mbf::mTnlO mutants isolated contained a transposon insertion within the same gene or operon. The identification of the mbf locus, required for pap transcription, supports the hypothesis that pap phase variation is controlled by a mechanism involving alternation between different methylation states.Expression of Pap pili by uropathogenic Escherichia coli is subject to an on/off phase variation regulatory mechanism (7, 17). Studies carried out with a single-copy pap-lac operon fusion in E. coli K-12 indicate that alternation between the phase-on and phase-off states occurs at the level ofpap pilin transcription and is affected by both incubation temperature (13,32) and the carbon source used for growth of the bacteria (3, 7). Our recent studies indicate that pap pilin phase variation occurs through a novel mechanism involving the differential methylation of two DNA GATC sites (GATC1028 and GATC1130) near the papBA pilin promoter by deoxyadenosine methylase (Dam) (7). DNA isolated from phase-off E. coli populations contains an unmethylated GATC1130 site. Conversely, DNA isolated from phase-on populations contains an unmethylated G...