In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to sialic acid (N-acetylneuraminic acid [Neu5Ac]). Transcriptome comparison of wild-type D39 grown in M17 medium with and without sialic acid revealed the elevated expression of various genes and operons, including the nan gene cluster (nan operon I and nanA gene). Our microarray analysis and promoter-lacZ fusion studies showed that the transcriptional regulator NanR acts as a transcriptional activator of nan operon I and the nanA gene in the presence of sialic acid. The putative regulatory site of NanR in the promoter region of nan operon I is predicted and confirmed by promoter truncation experiments. Furthermore, the role of CcpA in the regulation of the nan gene cluster is demonstrated through microarray analysis and promoter-lacZ fusion studies, suggesting that in the presence of sialic acid and glucose, CcpA represses the expression of nan operon I while the expression of the nanA gene is CcpA independent.T he low-GC Gram-positive bacterium Streptococcus pneumoniae is a major human pathogen and the causal agent of many diseases, including pneumonia, sepsis, meningitis, otitis media, and conjunctivitis, which result in over a million deaths each year worldwide (1, 2). S. pneumoniae colonizes the human nasopharynx during the first few months of life (3). For survival in the host, bacteria rely not only on the different virulence factors they possess but also on the appropriate use of nutrients available in their habitat (4, 5). The ability of S. pneumoniae to utilize a variety of carbohydrate sources is one of the crucial factors in successful colonization and in causing pneumococcal infections (6). Metabolic selection enables a bacterium to choose a preferred source of carbon over a nonpreferred one through a mechanism called carbon catabolite repression (CCR) (5). CcpA (carbon catabolite protein A) is a transcription factor that mediates CCR in the presence of a preferred sugar source, e.g., glucose, by binding to catabolite repression elements (cre boxes) found in the promoter regions of CcpA-targeted genes (5, 7-9). Despite the importance of carbohydrates in the pathogenesis of S. pneumoniae, research concerning metabolic pathways of S. pneumoniae still demands more attention.Sialic acid is one of the most important carbohydrates for S. pneumoniae, since it plays a vital role as a carbon/energy source, a receptor for adhesion and invasion, and a molecular signal for the promotion of biofilm formation, nasopharyngeal carriage, and invasion of the lungs (10). It has been shown that S. pneumoniae can utilize sialic acid as a carbon source, which results in improved pneumococcal biofilm formation in vitro, at concentrations comparable to those of free sialic acid in human saliva (11,12). Of the 43 known naturally occurring derivatives of the nine-carbon sugar neuraminic acid, N-acetylneuraminic acid (Neu5Ac) is the only one found in humans (13). Another form of sialic acid is N-glycolylneuraminic acid (Neu5Gc), which i...