Recent genome-scale studies have begun to establish the scope and magnitude of the impacts of carbohydrate source and availability on the regulation of gene expression in bacteria. The effects of sugars on gene expression are particularly profound in a group of lactic acid bacteria that rely almost entirely on their saccharolytic activities for energy production and growth. For Streptococcus mutans, the major etiologic agent of human dental caries, sucrose is the carbohydrate that contributes in the most significant manner to establishment, persistence, and virulence of the organism. However, because this organism produces multiple extracellular sucrolytic enzymes that can release hexoses from sucrose, it has not been possible to study the specific effects of sucrose transport and metabolism on gene expression in the absence of carbohydrates that by themselves can elicit catabolite repression and induce expression of multiple genes. By employing RNA deep-sequencing (RNA-Seq) technology and mutants that lacked particular sucrose-metabolizing enzymes, we compared the transcriptomes of S. mutans bacteria growing on glucose, fructose, or sucrose as the sole carbohydrate source. The results provide a variety of new insights into the impact of sucrose transport and metabolism by S. mutans, including the likely expulsion of fructose after sucrose internalization and hydrolysis, and identify a set of genes that are differentially regulated by sucrose versus fructose. The findings significantly enhance our understanding of the genetics and physiology of this cariogenic pathogen.N early all isolates of the primary etiologic agent of human dental caries, Streptococcus mutans, encode at least five secreted enzymes that act on sucrose in the extracellular environment, including three glucosyltransferases (GtfB, GtfC, and GtfD) that incorporate the glucose moiety of sucrose into high-molecular-mass ␣1,3-and ␣1,6-linked homopolymers of glucose that promote biofilm formation (1, 2); a fructosyltransferase (Ftf) that catalyzes the incorporation of fructose into 2,1-and 2,6-linked homopolymers of fructose (fructans) that serve as extracellular stores of carbohydrate within the biofilm matrix (3, 4); and a fructan hydrolase (FruA) that releases fructose from fructans, sucrose, and other -fructosides (4, 5). While these exoenzymes contribute significantly to the virulence of S. mutans, most of the sucrose presented to S. mutans is rapidly internalized by a highaffinity, high-capacity sugar-phosphotransferase system (PTS) (6,7). A single open reading frame (ORF), scrA, encodes the enzyme II permease of a sucrose-specific PTS, which internalizes and concomitantly phosphorylates sucrose. Transcribed divergently from scrA are two genes that encode a sucrose-6-PO 4 (S-6-P) hydrolase (scrB), which cleaves S-6-P into glucose-6-PO 4 (G-6-P) and fructose, and a transcriptional regulator (scrR) that represses the expression of both scrA and scrB (6,8,9). In addition, the multiplesugar metabolism (msm) ABC transporter and a trehalose-PTS e...