Streptococcus pneumoniae encounters a number of environmental niches in the body, including the nasopharynx, lungs, blood, middle ear, and brain. Recent studies have identified 13 putative two-component signal-transduction systems in S. pneumoniae, which are likely to be important for gene regulation in response to external stimuli. Here, we present conclusive evidence for the regulation of choline binding protein A (CbpA), a major pneumococcal virulence factor and protective antigen, by one of these two-component signal-transduction systems. We have demonstrated divergent expression of cbpA in unmarked hk06 and rr06 deletion mutants relative to wild-type S. pneumoniae D39 by using Western immunoblotting and real-time RT-PCR. Electrophoretic mobility-shift and solid-phase binding assays have demonstrated the binding of RR06 to the promoter region of cbpA, suggesting that RR06͞HK06 directly regulates cbpA transcription. We have also shown that this system is important for the ability of the pneumococcus to adhere to epithelial cells in vitro and to survive and proliferate in an in vivo mouse model. Thus, the RR06͞HK06 system has a significant role in pathogenesis, both in colonization and invasive disease.adherence ͉ two-component system ͉ pneumococcus ͉ colonization T he major human pathogen Streptococcus pneumoniae is responsible for diseases, including pneumonia, sepsis, meningitis, and otitis media. During the course of an infection, the pneumococcus encounters a number of different environmental niches, including the nasopharynx, lungs, blood, and potentially the brain. Thus, the regulation of virulence factors in response to external stimuli may be a principal determinant of the success or failure of the infection. Recently, several virulence-associated genes of S. pneumoniae have been shown to be differentially expressed in varying in vitro and in vivo conditions, but the underlying mechanism is unknown (1, 2). Two-component signal-transduction systems (TCSTSs) control the expression of virulence factors in a wide range of bacterial species in response to external stimuli (reviewed in ref.3). The typical TCSTS consists of a His kinase (HK) and a response regulator (RR). The HK, usually present in the cell membrane, responds to external stimuli by autophosphorylating a conserved His residue, with subsequent transfer of this phosphate group to the RR. The resultant conformational change enables the RR to bind to the promoter region of target gene(s) and act as a transcription factor.The S. pneumoniae genome sequence contains 13 putative TCSTSs, along with one orphan RR (4, 5). The best characterized of these is ComDE, which activates the genetic competence system in response to a competence-stimulating peptide (6, 7). Another system, CiaRH, also affects competence and has been shown to control a novel virulence factor, HtrA (8, 9). More recently, HK͞RR04 has been linked to the control of the Mn transporter PsaA, although this regulation was apparently strainspecific (10). In this study, we used unmarked dele...