Modulation of the structure of a leader RNA to control formation of an intrinsic termination signal is a common mechanism for regulation of gene expression in bacteria. Expression of the S box genes in Gram-positive organisms is induced in response to limitation for methionine. We previously postulated that methionine availability is monitored by binding of a regulatory factor to the leader RNA and suggested that methionine or S-adenosylmethionine (SAM) could serve as the metabolic signal. In this study, we show that efficient termination of the S box leader region by bacterial RNA polymerase depends on SAM but not on methionine or other related compounds. We also show that SAM directly binds to and induces a conformational change in the leader RNA. Both binding of SAM and SAM-directed transcription termination were blocked by leader mutations that cause constitutive expression in vivo. Overproduction of SAM synthetase in Bacillus subtilis resulted in delay in induction of S box gene expression in response to methionine starvation, consistent with the hypothesis that SAM is the molecular effector in vivo. These results indicate that SAM concentration is sensed directly by the nascent transcript in the absence of a trans-acting factor. A variety of mechanisms for control of gene expression by premature termination of transcription have been uncovered in bacteria (1, 2). Genes regulated in this way contain a transcription termination signal in the mRNA region upstream of the coding sequence of the regulated gene. The activity of this terminator can be controlled by modification of the activity of RNA polymerase (RNAP), blocking access of transcriptiontermination factor Rho, or by modulation of the leader RNA structure, commonly through alternate folding patterns. RNA folding can be controlled in turn through interaction with some regulatory factor, such as a translating ribosome, as in the Escherichia coli trp operon, or an RNA binding protein, as in the Bacillus subtilis trp operon or the E. coli bgl system. Modulation of RNA structure by an effector, in the absence of accessory proteins, has been demonstrated for the T box system, in which uncharged tRNA interacts directly with the leader RNA to promote antitermination (3, 4). Similar regulation by small molecules has recently been demonstrated for riboflavin and thiamin biosynthesis genes, by using flavin mononucleotide and thiamin pyrophosphate, respectively (5-7).The S box regulatory mechanism represents a system in which synthesis of the full-length transcript is determined by controlling whether the leader folds into the stem loop of an intrinsic terminator or a competing antiterminator structure (ref. 8 and Fig. 1). Formation of the antiterminator is inhibited by an alternative helical structure, which functions as an antiantiterminator. An anti-antiterminator element is also found in the B. subtilis pyr operon, in which leader RNA structure is controlled by binding of a regulatory protein (9). We initially identified the S box family by recognizing a high...