The transcription termination factor Rho associates with most nascent bacterial RNAs as they emerge from RNA polymerase. However, pharmacological inhibition of Rho derepresses only a small fraction of these transcripts. What, then, determines the specificity of Rho-dependent transcription termination? We now report the identification of a Rho-antagonizing RNA element (RARE) that hinders Rho-dependent transcription termination. We establish that RARE traps Rho in an inactive complex but does not prevent Rho binding to its recruitment sites. Although translating ribosomes normally block Rho access to an mRNA, inefficient translation of an open reading frame in the leader region of the Salmonella mgtCBR operon actually enables transcription of its associated coding region by favoring an RNA conformation that sequesters RARE. The discovery of an RNA element that inactivates Rho signifies that the specificity of nucleic-acid binding proteins is defined not only by the sequences that recruit these proteins but also by sequences that antagonize their activity.T ranscription factors recognize sequence and structural elements in DNA and RNA to turn genes on or off. The transcription termination factor Rho is responsible for the majority of factor-dependent termination events in enteric bacterial species (1). Rho prevents the production of dysfunctional, and potentially dangerous, RNAs (2). For instance, Rho implements transcriptional polarity, a process whereby compromised translation of a promoter-proximal gene reduces transcription of downstream genes in an operon (3-5).Rho is a hexameric helicase that binds RNA and translocates in the 5′-to-3′ direction using the energy derived from ATP hydrolysis. Initially, RNA is anchored to Rho primary binding sites on the surface of the hexamer. Rho recruitment sites tend to be rich in Cs and Us and free of strong secondary structures (6-8). Interaction with a recruitment site causes the Rho hexamer to open briefly, allowing the RNA 3′ region to pass through the center, where secondary binding sites are located (9, 10). Further contact between the RNA and the secondary binding sites stimulates Rho's ATPase activity (11). Using the energy derived from ATP hydrolysis, Rho translocates along an RNA until it reaches a paused RNA polymerase (RNAP) and promotes transcription termination (12).The specificity of Rho-dependent transcription termination has remained enigmatic because Rho associates with many newly transcribed RNAs in Escherichia coli (13), but only a portion of these messages is affected when bacteria are treated with bicyclomycin (BCM) (1), a Rho-specific inhibitor (14). In other words, binding of Rho to a particular RNA is not sufficient for subsequent transcription termination.Rho-dependent terminators are typically found at the end of operons; however, they can also be present in the leader region of mRNAs, where they perform regulatory functions (15)(16)(17)). This appears to be the case for the 296-nt-long leader region of the mgtCBR transcript from Salmonella enteri...