SummaryThe integration host factor (IHF) is a DNA-binding and -bending protein with roles in local DNA structural organization and transcriptional regulation in Gramnegative bacteria. This heterodimeric protein is composed of the two highly homologous subunits IHF a and IHF b . DNA microarray analysis was used to define the regulon of genes subject to IHF control in Salmonella enterica serovar Typhimurium ( S. Typhimurium). The transcription profile of the wild type was compared with those of mutants deficient in IHF a , IHF b , or both IHF a and IHF b . Our data reveal a new connection between IHF and the expression of genes required by the bacterium to undergo the physiological changes associated with the transition from exponential growth to stationary phase. When a mutant lacking IHF entered stationary phase, it displayed downregulated expression of classic stationary-phase genes in the absence of any concomitant change in expression of the RpoS sigma factor. Purified IHF was found to bind to the regulatory regions of stationary-phase genes indicating an auxiliary and direct role for IHF in RpoS-dependent gene activation. Loss of IHF also had a profound influence on expression of the major virulence genes and epithelial cell invasion, indicating a role in co-ordinating regulation of the pathogenic traits with adaptation to stationary phase. Although the three mutants showed considerable overlaps in the genes affected by the ihf lesions, the observed patterns were not identical, showing that S. Typhimurium has not one but three overlapping IHF regulons.

Campylobacter jejuni, a spiral-shaped Gram-negative pathogen, is a highly frequent cause of gastrointestinal foodborne illness in humans worldwide. Clinical outcome of C. jejuni infections ranges from mild to severe diarrheal disease, and some other complications including reactive arthritis and Guillain–Barré syndrome. This review article highlights various C. jejuni pathogenicity factors, host cell determinants, and proposed signaling mechanisms involved in human host cell invasion and their potential role in the development of C. jejuni-mediated disease. A model is presented which outlines the various important interactions of C. jejuni with the intestinal epithelium, and we discuss the pro’s and con’s for the “zipper” over the “trigger” mechanism of invasion. Future work should clarify the contradictory role of some previously identified factors, and should identify and characterize novel virulence determinants, which are crucial to provide fresh insights into the diversity of strategies employed by this pathogen to cause disease.

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Site-specific recombinases of the integrase family usually require cofactors to impart directionality in the recombination reactions that they catalyze. The FimB integrase inverts the Escherichia coli fim switch (fimS) in the on-to-off and off-to-on directions with approximately equal efficiency. Inhibiting DNA gyrase with novobiocin caused inversion to become biased in the off-to-on direction. This directionality was not due to differential DNA topological distortion of fimS in the on and off phases by the activity of its resident P fimA promoter. Instead, the leucine-responsive regulatory (Lrp) protein was found to determine switching outcomes. Knocking out the lrp gene or abolishing Lrp binding sites 1 and 2 within fimS completely reversed the response of the switch to DNA relaxation. Inactivation of either Lrp site alone resulted in mild on-to-off bias, showing that they act together to influence the response of the switch to changes in DNA supercoiling. Thus, Lrp is not merely an architectural element organizing the fim invertasome, it collaborates with DNA supercoiling to determine the directionality of the DNA inversion event.Site-specific recombinases of the integrase family are usually associated with the integration and excision of DNA sequences such as bacteriophage genomes from bacterial chromosomes or other replicons. The best-studied integrase is Int, the prototypic member of the family that catalyzes the integration and excision of bacteriophage lambda from the chromosome of Escherichia coli (33,40). Although the integration and excision reactions both require Int, an additional phage-encoded factor called the excisionase (Xis) confers directionality by being specific for the excision reaction. Despite its name, the excisionase has no enzymatic activity. Instead, it is an architectural element that helps to organize the local structure of lambda DNA in a way that favors the excision reaction. The Xis protein has been classified as a recombination directionality factor (RDF), and several other proteins have been identified that provide, or may provide, an analogous function in other integrase-dependent site-specific recombination reactions (23-25). The requirement for the RDFs arises due to the similarities of the DNA substrates and products of the integration and excision reactions. The RDF confers directionality by stimulating one reaction while inhibiting the other.An integrase-mediated site-specific recombination event controls the phase-variable expression of type 1 fimbriae in E. coli. A key difference between the fimbrial and phage recombination mechanisms is that the fimbrial system involves DNA inversion and not integration/excision. The promoter for fim operon transcription (P fimA ) is carried on a 314-bp invertible DNA element called the fim switch (fimS), and expression of the fim structural genes depends on its orientation (1, 15). With P fimA directed toward the fim operon, the genes are transcribed, and when it is inverted to the opposite orientation, the fim operon is silent (Fig. ...

The role of the HU nucleoid-associated proteins in gene regulation was examined in Salmonella enterica serovar Typhimurium. The dimeric HU protein consists of different combinations of its a and b subunits. Transcriptomic analysis was performed with cultures growing at 37 6C at 1, 4 and 6 h after inoculation with mutants that lack combinations of HU a and HU b. Distinct but overlapping patterns of gene expression were detected at each time point for each of the three mutants, revealing not one but three regulons of genes controlled by the HU proteins. Mutations in the hup genes altered the expression of regulatory and structural genes in both the SPI1 and SPI2 pathogenicity islands. The hupA hupB double mutant was defective in invasion of epithelial cell lines and in its ability to survive in macrophages. The double mutant also had defective swarming activity and a competitive fitness disadvantage compared with the wild-type. In contrast, inactivation of just the hupB gene resulted in increased fitness and correlated with the upregulation of members of the RpoS regulon in exponential-phase cultures. Our data show that HU coordinates the expression of genes involved in central metabolism and virulence and contributes to the success of S. enterica as a pathogen. INTRODUCTIONThe HU DNA-binding protein is one of approximately 12 nucleoid-associated proteins (NAPs) that have been described in Gram-negative bacteria such as Escherichia coli and Salmonella enterica. NAPs have the potential to influence the expression of large numbers of genes in bacteria and help to organize the nucleoid (Azam & Ishihama, 1999;Dorman & Deighan, 2003). In Salmonella, NAPs have been shown to influence virulence gene expression (Harrison et al., 1994; O'Byrne & Dorman, 1994a, b; Lucchini et al., 2006;Marshall et al., 1999; Navarre et al., 2006;Schechter et al., 2003). HU binds to DNA relatively non-specifically and influences many DNA-based transactions, including replication, transcription, site-specific-, general and illegitimate recombination, transposition and DNA repair (Kamashev et al., 2008;Li & Waters, 1998;Merickel & Johnson, 2004;Ryan et al., 2002;Semsey et al., 2004;Shanado et al., 1998;Signon & Kleckner, 1995). It also has RNA-binding activity (Balandina et al., 2001) and a preference for binding to unusual conformations in DNA such as four-way junctions and extruded cruciform structures (Kamashev et al., 1999;Pontiggia et al., 1993;Swinger & Rice, 2004).HU is a dimer composed of two closely related subunits, HU a and HU b (Guo & Adhya, 2007) and can exist in three forms, the HU ab heterodimer and the HU a 2 and HU b 2 homodimers. The relative abundances of the three forms vary with the phase of growth (Claret & Rouvière-Yaniv, 1997). The ab heterodimer is the dominant form of the protein at most stages of growth, except at the earliest stage of the exponential phase when the a 2 form predominates; the b 2 homodimer is detectable principally in late stationary phase. The presence of three forms of HU raises the question of w...