Mode of Action of the Bordetella BvgA Protein: Transcriptional Activation and Repression of the Bordetella bronchiseptica bipA Promoter

Bordetella establishes respiratory tract infections by coordinately regulating the expression of several virulence factors including adhesins and toxins (21, 22). Similar to other bacterial systems, this regulation is mediated by initiating a signal transduction cascade in response to environmental fluctuations and is controlled by a two-component system encoded by the BvgAS locus (22, 31). BvgS functions as the sensor histidine kinase, which autophosphorylates in the presence of ATP in vitro and then transfers the phosphoryl group to BvgA, the cognate response regulator (4, 30). Genetic and biochemical evidence suggests that phosphorylation of BvgA leads to the alteration of its DNA binding affinity for target promoters, resulting in transcriptional activation or repression of Bvg regulon genes (3, 6, 11, 13, 19, 20). One of the striking features of the BvgAS signal transduction system is its ability to control at least three known (Bvg+, Bvg−, and Bvgi) and potentially multiple phenotypic states, as opposed to mediating a biphasic transition in response to environmental cues (22). The switch among different phenotypic phases is a direct consequence of differential expression of a distinct set of gene products. For example, when BvgAS is active, Bordetella cells are in the Bvg+ phase, which is characterized by maximal expression of Bvg-activated factors like adhesins and toxins and lack of expression of Bvg-repressed genes. Inactivation of BvgAS by modulating signals (sulfate anion, nicotinic acid, or growth at low temperature) results in the switch to the Bvg− phase, which is characterized by expression of Bvg-repressed factors (e.g., flagella in Bordetella bronchiseptica and outer membrane proteins of unknown function in Bordetella pertussis) and the repression of Bvg-activated genes (22). The Bvgi phase is expressed either as a result of specific genetic mutations in BvgS or by growth of wild-type Bordetella strains in the presence of semimodulating concentrations of chemical signals (9). The Bvgi phase is principally characterized by maximal expression of a set of antigens of which BipA is the first to be identified at the molecular level (13, 27). Expression of bipA is low in the Bvg+ phase, peaks in the Bvgi phase, and is at nearly background levels in the Bvg− phase (11, 13). Previously, we have shown that, depending on its phosphorylation state, BvgA binds with differential affinities to several sites located both upstream and downstream of the bipA transcription initiation site (Fig. ​(Fig.1)1) (11, 13). We demonstrated that, while the upstream site, IR1, is essential for transcriptional activation, the downstream sites IR2 and IR3 are involved in repression (Fig. ​(Fig.1)1) (11). Most importantly, we showed that the phase-specific expression of bipA can be altered by changes in the bipA promoter region, thereby providing direct evidence for the role of these sites in determining the expression profile of bipA (11, 12). Based on these results and other studies on Bvg-activated promoters, we proposed that, by adjusting the occupancy of various BvgA binding sites as a direct consequence of changes in BvgA-P levels, Bordetella cells display such variation in gene expression (8, 11, 12). The detailed mechanism of bipA regulation has not been elucidated, since the levels of BvgA-P inside the cell are unknown. FIG. 1. Arrangement and boundaries of different BvgA binding sites relative to the transcription initiation site (+1) encompassing the bipA promoter. IR1, -2, and -3 represent the three inverted repeat motifs. HS1 and HS2 denote the two half-site binding ... We are studying the mechanics of the phase-dependent expression profile of bipA as a model to understand how BvgAS is able to achieve and sustain such a precisely regulated program of gene expression. We believe that the bipA gene offers an excellent choice towards this end, since it displays a complex expression profile that involves interplay of transcriptional repression and activation. In this study, we have developed an in vitro transcription system that replicates the phase-dependent expression of bipA as a function of phosphorylated BvgA (BvgA-P) concentrations, providing direct in vitro evidence for the proposed model. We have previously invoked the possibility of the existence of a repressor that might act to efficiently repress bipA transcription in the Bvg+ phase (13). Our results using purified BvgA and RNA polymerase (RNAP) holoenzyme suggest that no other protein components are required for the dual activation-repression of bipA transcription. We have characterized the BvgA-RNAP interactions at the bipA promoter. Our results show that, at low concentrations of BvgA-P, conditions where transcription of bipA is activated in vitro, BvgA-P synergistically interacts with RNAP, leading to the stimulation of open complexes at the promoter. We further show that, at higher concentrations of BvgA-P, when bipA transcription is minimal, BvgA-P interferes with the binding of RNAP to the promoter. The results reported in this study describe the mechanism of BvgA in transcriptional repression of bipA and highlight the essential role of the downstream binding site IR2.