Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS

Abstract

Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.

Figure 1. Effect of the presence of R27 in the transcriptome of an hns mutant strain.

Changes in expression of several gene groups in the hns mutant strain (SV5015AV) and in the hns strain harbouring R27 plasmid (SV5015AV(R27)) with respect to the wt strain (SV5015). (A,B) Percentage of genes belonging to each group that show altered expression in strain SV5015AV (A) and SV5015AV (R27) (B) with respect to the wt strain. Grey bars indicate the proportion of down-regulated genes (M<0) and open bars indicate the proportion of up-regulated genes (M>0). M is the fold change log₂ ratio. (C,D) M values of individual genes in the functional categories of pathogenicity islands SPI-1 to SPI-5 (C) and cell motility and secretion (D).

Figure 2. H-NS and H-NS_R27-depending expression of selected genes.

Expression of β-galactosidase from lac fusions to hilA, proV (Salmonella or E. coli), rcsA, and hlyA genes in wt, hns, hns (R27), and hns (R27Δhns) strains. Bars represent percentage of activity of each strain with respect to the activity of hns strain.

Figure 3. Differential affinity of H-NS and H-NS_R27 to hilA, proV, and rcsA gene promoters.

Competitive band shift assays showing differential affinity of H-NS_R27 to the hilA and rcsA promoters (A) and to the hilA and proV promoters (B). H-NS and H-NSR₂₇ purified proteins (1, 2, and 4 µM) were incubated with the mixture of both DNA fragments.