Recently, a novel type of regulatory mutation causing differential effects on the expression of virulence genes due to a slight overexpression of the RNA polymerase ␣ subunit (RpoA) was found in Bordetella pertussis (N. H. Carbonetti, T. M. Fuchs, A. A. Patamawenu, T. J. Irish, H. Deppisch, and R. Gross, J. Bacteriol. 176:7267-7273, 1994). To gather information on the molecular events behind this phenomenon, we isolated suppressor mutants of the RpoA-overexpressing strains after random mutagenesis. Genetic characterization of these suppressor strains revealed the existence of at least three distinct groups of dominant alleles. Mutations occurred either in the rpoA locus itself, in the bvg locus, or in unknown gene loci. One mutant of the latter group was further characterized. By the introduction of a cosmid library containing genomic B. pertussis DNA into this suppressor strain, we isolated a cosmid which suppressed the phenotype of the suppressor strain, thus restoring the negative effect on transcription of the ptx and cya toxin genes. Bordetella pertussis, the etiological agent of whooping cough (4), expresses a set of virulence-related factors such as several adhesins, e.g., filamentous hemagglutinin (FHA), pertactin (PRN), and fimbriae, and several toxins, e.g., pertussis toxin (PTX) and adenylate cyclase toxin (CyaA), which confers a hemolytic phenotype. The regulation of expression of these factors is coordinate and depends on the respective growth conditions; i.e., the virulence factors are expressed at body temperature but not at low temperature, a phenomenon termed phenotypic modulation (21, 43). The BvgAS two-component system is responsible for this coordinate regulation and controls virulence gene expression on the transcriptional level (1,3,17,18,27,40,41). The bvgAS locus is genetically unstable. Spontaneous mutations which inactivate the two-component system and thereby cause the lack of expression of the virulence genes can occur with a high incidence (25). Therefore, these mutations in the bvg locus lead to avirulent bacteria, the so-called phase variants (23). Despite the coordinate regulation mediated by this two-component system, differential regulatory phenomena such as different induction kinetics of transcription of the various factors or different expression patterns in the heterologous host Escherichia coli were noted, which led to the classification of the virulence factors into two groups, (i) the two toxins PTX and CyaA and (ii) the other factors (33,34,42). These differences in their expression are also reflected by differences in the promoter structures of the two groups. The upstream activating sequences present in these promoters are either close to the RNA polymerase binding region (bvg and fha promoters) or far upstream (ptx and cyaA promoters) (15,17,31). Recent work of several laboratories showed that the BvgA transcription factor directly interacts with the upstream activating sequences of both types of promoters, but transcription seems to be initiated differently in the va...