Campylobacter jejuni is a gram-negative enteric organism causing gastroenteritis in humans (38). As a major food-borne pathogen, C. jejuni is well adapted in its mammalian and avian hosts, as well as in food animal production environments. So that it can survive in different conditions, C. jejuni has evolved multiple strategies for adaptation, including high rates of genetic variation (mediated by mutation and horizontal gene transfer) and differential gene expression (6, 11, 30). Indeed, previous analyses of the genomic sequences of C. jejuni revealed the presence of multiple genes encoding regulatory functions (9, 14, 32, 35). The majority of the transcriptional regulators have not been functionally characterized, but the two-component regulatory (TCR) systems in C. jejuni have recently received attention. In C. jejuni NCTC 11168 and RM1221, each system has nine response regulators and six histidine sensor kinases (9, 32). Several of the regulators or TCR systems, including DccRS (28), PhosSR (49), FlgSR (50), CbrR (36), RacRS (4), and CheY (53), have been studied, and all were found to be required for Campylobacter colonization in vivo. The RacRS system is responsive to temperature and controls the expression of multiple proteins in C. jejuni, while the PhosSR system senses phosphate conditions and modulates the expression of 12 genes that are involved in phosphate transport and utilization (4, 49). DccRS controls the expression of several genes encoding probable membrane-associated proteins and is required for Campylobacter colonization of mice and chickens, but the signals to which it responds and the functions of the DccR-regulated genes have not been defined (28). CbrR modulates the Campylobacter response to bile, but its cognate sensor kinase and the target genes controlled by it are unknown (36). The FlgSR system controls the flagellar regulon and affects the motility of Campylobacter (50). It was also found that FlaR undergoes phase variation due to the presence of homopolymeric tracts of adenine and thymine in the coding gene (13). These examples illustrate that C. jejuni utilizes multiple TCR systems for adaptation to different environments. In addition to the TCR systems, several non-TCR system regulators, including Fur, SpoT, HspR, and CmeR, have also been characterized in Campylobacter. Fur functions as a transcriptional repressor and controls iron homeostasis in C. jejuni (31, 45). Mutation of Fur affected the expression of 53 genes and significantly reduced the colonization of chickens by Campylobacter (31). HspR is a negative regulator for the heat shock response system in C. jejuni, and inactivation of HspR led to increased expression of several genes involved in the heat shock response and decreased expression of 17 genes (1). The HspR mutant showed decreased motility, increased sensitivity to temperature, and reduced adherence to and invasion of cultured epithelial cells (1). SpoT functions as a regulator for the stringent response in C. jejuni and is important for the survival of Campylobacter under various stress conditions (11). Deletion of spoT resulted in differential expression of multiple genes and reduced Campylobacter adherence, invasion, and intracellular survival in cell cultures (11). In a previous study by workers in our laboratory (21), a transcriptional regulator designated CmeR was characterized. CmeR belongs to the TetR family of transcriptional regulators and functions as a repressor of CmeABC, a resistance-nodulation-division-type efflux pump (23). The CmeABC pump is composed of three membrane components (CmeA, CmeB, and CmeC) and contributes to Campylobacter resistance to various antimicrobial agents and bile compounds present in the intestinal environment (23, 24). Inactivation of CmeABC abolished the ability of C. jejuni to colonize chickens (24), indicating that bile resistance is an important physiological function of CmeABC and that this efflux pump plays an important role in facilitating Campylobacter adaptation to the intestinal tract. CmeR is encoded by a gene located immediately upstream of the cmeABC operon and has two distinct domains, an N-terminal helix-turn-helix (HTH) DNA-binding motif and a potential ligand-binding domain in the C-terminal region (21). An in vitro electrophoretic mobility shift assay showed that CmeR binds specifically to the inverted repeat (TGTAAT) in the promoter region of cmeABC and represses the transcription of this efflux operon. Deletion of CmeR or mutation in the CmeR-binding site impedes the repression and results in overexpression of CmeABC (21). Importantly, the expression of cmeABC is strongly induced by bile salts in culture media (22). Since bile compounds are normally present in animal intestinal tracts, it is likely that CmeABC is upregulated during in vivo infection. Indeed, the DNA microarray work conducted by Stintzi et al. showed that cmeABC was significantly upregulated in rabbit ileal loops (40). Real-time quantitative reverse transcription-PCR (qRT-PCR) conducted in our laboratory also showed that there was a 14-fold increase in the expression of cmeABC in the chicken cecum compared with an in vitro culture (Y. W. Barton and Q. Zhang, unpublished data). Bile salts inhibit the binding of CmeR to the promoter DNA of cmeABC and thus release the inhibition of cmeABC by CmeR (22), resulting in overexpression of cmeABC. Recent protein crystallization studies confirmed the two-domain structure of CmeR and showed that CmeR functions as a homodimer (12). A striking feature of CmeR revealed by crystallization is the presence of a large ligand-binding pocket, which has the capacity and flexibility to accommodate diverse ligands, including bile salts. This finding suggests that CmeR may interact with multiple ligands in modulating gene expression in C. jejuni. Despite the recent advances in our understanding of the structure and function of CmeR and its transcriptional regulation of cmeABC, it is still unclear if CmeR regulates the expression of other genes in C. jejuni. It is also not known if CmeR is important for Campylobacter colonization in vivo. In this study, we compared the transcriptomes of C. jejuni NCTC 11168 and an isogenic CmeR mutant of this strain using a DNA microarray along with other molecular methods and identified multiple genes regulated by CmeR. We also characterized a gene (Cj0561c) that is highly repressed by CmeR and determined the role of CmeR in Campylobacter colonization in the chicken model system. Our new findings indicate that CmeR is a pleiotropic regulator modulating the expression of multiple genes with diverse functions in Campylobacter and is required for optimal colonization of chickens.