Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS

et al. (2009) Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS. PLoS Genet 5(6): e1000513. doi:10.1371/journal.pgen.1000513 Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS Rosa C. Ban os 0 Aitziber Vivero 0 Sonia Aznar 0 Jesu s Garca 0 Miquel Pons 0 Cristina Madrid 0 Antonio Jua rez 0 Josep Casadesu s, Universidad de Sevilla, Spain 0 1 Institut de Bioenginyeria de Catalunya (IBEC), Parc Cient fic de Barcelona , Barcelona, Spain, 2 Departament de Microbiologia , Facultat de Biologia, Universitat de Barcelona , Barcelona , Spain , 3 Institute for Research in Biomedicine (IRB Barcelona), Parc Cient fic de Barcelona , Barcelona , Spain , 4 Departament de Qu mica Orga`nica, Universitat de Barcelona , Barcelona , Spain 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 R27encoded 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. - Funding: This work was supported by grants BIO2004-0247, BIO2007-63458, GEN2003-20234-C06-06, and CSD2008-00013 from Ministerio de Ciencia y Tecnologia, and SGR200500635 and IRB Barcelona from the Generalitat de Catalunya. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. Acquisition of DNA by horizontal gene transfer (HGT) is a crucial mechanism by which bacteria increase genetic variability. Among others, functions that enable bacterial cells to cause disease (virulence factors) as well as to overcome the effect of antimicrobial drugs are often encoded in HGT DNA (i.e., bacterial plasmids or genomic islands). While HGT DNA may provide a potential advantage in host colonization, the incorporation of foreign DNA may constitute a potential perturbation for the regulation of the core genome, resulting in a significant fitness cost. An efficient mechanism that enables the bacterial cell to control the expression of foreign DNA is exemplified by the H-NS protein [for a review see 1]. H-NS belongs to the superfamily of bacterial nucleoidassociated proteins and is involved in the adaptative response of bacterial cells to changes in environmental factors such as temperature or osmolarity. The regulatory region of H-NSmodulated genes usually contains two separated target sequences, which have often been characterized by being AT-rich curved DNA stretches [2]. Interaction of H-NS molecules with their target sequences results in protein oligomerization and the generation of a DNA loop. When this nucleoprotein complex is formed, transcription is switched off [24]. Silencing is relieved when changes in physicochemical parameters (i.e., temperature) affect either DNA properties or the capacity of H-NS to oligomerize [2,5,6]. In some instances, H-NS-mediated silencing requires the participation of proteins of the Hha/YmoA family [for a review see 7]. Hha-like proteins have been identified on the basis of their role in modulating several virulence determinants [8 11]. Their molecular mass is about half of that of H-NS-like proteins. They show structural mimicry to the H-NS oligomerization domain, bind to H-NS and appear to comodulate the expression of several genes with this latter protein [7]. H-NS targets both core genome and HGT genes [12,13] and provides an efficient mechanism that enables bacterial cells to control the expression of foreign DNA. Mapping of H-NS binding sites on the Salmonella enterica serovar Typhimurium chromosome by a ChlP on chip approach showed that H-NS binds preferentially to AT-rich HGT DNA [13,14]. This finding has been interpreted as H-NS playing a relevant role in the silencing of unwanted expression of these sequences and has led to the proposal of a predominant role of the H-NS protein as a genome sentinel [15]. Several conjugative plasmids, such as those of the IncH1 group, also encode plasmidic forms of H-NS and Hha. IncH1 plasmids are common in the causal agent of typhoid fever, Salmonella enterica Acquisition of DNA by horizontal gene transfer (HGT) significantly increases bacterial genetic variability. Relevant issues are the mechanisms that bacterial cells have evolved to efficiently integrate the newly acquired DNA into the host cell regulatory machinery. In Gram negative cells, the nucleoid associated protein H-NS has been shown to bind AT-rich sequences of HGT DNA and silence unwanted expression of these genes. This has led to consider H-NS as a genome sentinel. Nevertheless, this proposed role must be compatible with its role modulating core genome genes. Weak expression of recently transferred genes must be coordinated with proper expression levels of housekeeping genes. In this paper, we describe a strategy that enteric bacteria have developed to differentially modulate HGT and core genome genes. Two independent lines of experimental evidence suggest that the H-NS system of enteric bacteria may have evolved to discriminate between core genome and HGT DNA. The plasmid R27encoded H-NS protein selectively modulates HGT genes. This avoids plasmid-encoded H-NS interfering with modulation of core functions. We also show that, for efficient silencing of HGT genes, resident chromosomal H-NS recruits the Hha protein and forms heteromeric complexes with DNA. In contrast, housekeeping genes are modulated by H-NS alone. subsp. enterica serovar Typhimurium, and are associated with the multi-drug resistance (MDR) phenotype that some isolates exhibit [16]. A (...truncated)