The quorum-sensing (QS) system present in the emerging nosocomial pathogen Stenotrophomonas maltophilia is based on the signaling molecule diffusible signal factor (DSF). Production and detection of DSF are governed by the rpf cluster, which encodes the synthase RpfF and the sensor RpfC, among other components. Despite a well-studied system, little is known about its implication in virulence regulation in S. maltophilia. Here, we have analyzed the rpfF gene from 82 S. maltophilia clinical isolates. Although rpfF was found to be present in all of the strains, it showed substantial variation, with two populations (rpfF-1 and rpfF-2) clearly distinguishable by the N-terminal region of the protein. Analysis of rpfC in seven complete genome sequences revealed a corresponding variability in the N-terminal transmembrane domain of its product, suggesting that each RpfF variant has an associated RpfC variant. We show that only RpfC-RpfF-1 variant strains display detectable DSF production. Heterologous rpfF complementation of ⌬rpfF mutants of a representative strain of each variant suggests that RpfF-2 is, however, functional and that the observed DSF-deficient phenotype of RpfC-RpfF-2 variant strains is due to permanent repression of RpfF-2 by RpfC-2. This is corroborated by the ⌬rpfC mutant of the RpfC-RpfF-2 representative strain. In line with this observations, deletion of rpfF from the RpfC-RpfF-1 strain leads to an increase in biofilm formation, a decrease in swarming motility, and relative attenuation in the Caenorhabditis elegans and zebrafish infection models, whereas deletion of the same gene from the representative RpfC-RpfF-2 strain has no significant effect on these virulence-related phenotypes. Q uorum sensing (QS) is a bacterial cell-cell communication process that allows bacteria to synchronize particular behaviors on a population-wide scale. Within current knowledge, QS in Stenotrophomonas maltophilia depends on the diffusible signal factor QS (DSF-QS) system, which is based mainly on the fatty acid DSF (cis-11-methyl-2-dodecenoic acid) (1, 2). DSF synthesis is fully dependent on RpfF, an enoyl coenzyme A hydratase encoded by the rpf (regulation of pathogenicity factors) cluster, a set of genes that includes all of the components necessary for the synthesis and detection of DSF molecules. In addition to RpfF, rpf encodes the aconitase RpfA, the fatty acid ligase RpfB, the two-component sensor-effector hybrid system RpfC, and the cytoplasmic regulator element RpfG (1, 2). The DSF-QS system was first described in the phytopathogen Xanthomonas campestris pv. campestris, where it plays an important role in virulence regulation (3). Since then, this system has been described in several members of the order Xanthomonadales, including the genera Xanthomonas, Xylella, and Stenotrophomonas, as well as in members of the order Burkholderiales (1, 3-5). The specific functions regulated by the DSF-QS system are dependent on the species, but it has been suggested that it controls several virulence-related phenotypes (6...

Helicobacter pylori encodes a large number of restriction–modification (R–M) systems despite its small genome. R–M systems have been described as ‘primitive immune systems’ in bacteria, but the role of methylation in bacterial gene regulation and other processes is increasingly accepted. Every H. pylori strain harbours a unique set of R–M systems resulting in a highly diverse methylome. We identified a highly conserved GCGC-specific m5C MTase (JHP1050) that was predicted to be active in all of 459 H. pylori genome sequences analyzed. Transcriptome analysis of two H. pylori strains and their respective MTase mutants showed that inactivation of the MTase led to changes in the expression of 225 genes in strain J99, and 29 genes in strain BCM-300. Ten genes were differentially expressed in both mutated strains. Combining bioinformatic analysis and site-directed mutagenesis, we demonstrated that motifs overlapping the promoter influence the expression of genes directly, while methylation of other motifs might cause secondary effects. Thus, m5C methylation modifies the transcription of multiple genes, affecting important phenotypic traits that include adherence to host cells, natural competence for DNA uptake, bacterial cell shape, and susceptibility to copper.

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6Helicobacter pylori encodes a large number of Restriction-Modification (R-M) systems despite its 1 7 small genome. R-M systems have been described as "primitive immune systems" in bacteria, but the 1 8 role of methylation in bacterial gene regulation and other processes is increasingly accepted. Every H.