The FsrABC system of Enterococcus faecalis controls the expression of gelatinase and a serine protease via a quorum-sensing mechanism, and recent studies suggest that the Fsr system may also regulate other genes important for virulence. To investigate the possibility that Fsr influences the expression of additional genes, we used transcriptional profiling, with microarrays based on the E. faecalis strain V583 sequence, to compare the E. faecalis strain OG1RF with its isogenic mutant, TX5266, an fsrB deletion mutant. We found that the presence of an intact fsrB influences expression of numerous genes throughout the growth phases tested, namely, late log to early stationary phase. In addition, the Fsr regulon is independent of the activity of the proteases, GelE and SprE, whose expression was confirmed to be activated at all three time points tested. While expression of some genes (i.e., ef1097 and ef0750 to -757, encoding hypothetical proteins) was activated in late log phase in OG1RF versus the fsrB deletion mutant, expression of ef1617 to -1634 (eut-pdu orthologues) was highly repressed by the presence of an intact Fsr at entry into stationary phase. This is the first time that Fsr has been characterized as a negative regulator. The newly recognized Fsr-regulated targets include other factors, besides gelatinase, described as important for biofilms (BopD), and genes predicted to encode the surface proteins EF0750 to -0757 and EF1097, along with proteins implicated in several metabolic pathways, indicating that the FsrABC system may be an important regulator in strain OG1RF, with both positive and negative effects.Enterococcus faecalis is adapted to survive, persist, and proliferate in a wide range of environments as different as the gastrointestinal tract, heart valves, water, and soil. To do so, it is likely that E. faecalis has developed various mechanisms of adaptation. Examples include transcriptional regulators, such as hypR (47) or efaR (25); two-component systems (etaRS [46], croRS [9], vanSR [11], and RR1-13 [18]); and cell-cell signaling systems, including pheromone-inducible plasmid transfer (for a review, see reference 7), the Cyl system (8, 16), and the FsrABC system (30,31,34,35).The fsrABC operon, a homologue of agrABCD in Staphylococcus aureus, was originally shown by Qin et al. to activate, at the transcriptional level, the expression of two genes, gelE and sprE, coding for a metalloprotease and a serine protease, in addition to fsrBC (34, 35). Nakayama et al. and Qin et al. subsequently purified and characterized the FsrABC system pheromone as an 11-residue peptide lactone, produced from the C-terminal portion of the fsrB gene product and reaching peak levels at entry into stationary phase (ENT-stat) (30,31,35). Studies have also shown that, in the majority of the strains studied, a gelE ϩ genotype with a GelE Ϫ phenotype is associated with a 23.9-kb deletion, from ef1841 through part of ef1820 (ef1820 is fsrC). This deletion is found in many distinct clinical strains, as well as in isolates fr...