Evidence That a Nucleotide Sequence, "boxA," is Involved in the Action of the NusA Protein

We report the isolation of a mutation, boxA1, in the nutR region of the phage lambda genome. The nutR region, located downstream of the pR promoter, includes the site nutR where the lambda N protein is thought to act to render subsequent transcription termination-resistant. We have previously suggested that the boxA sequence, 5'CGCTCTTA3' (or its RNA analog), located 8 bp promoter-proximal to nutR, might be the recognition site for the E. coli host factor, NusA, which has been shown to be necessary for N action. The boxA1 mutation, an A:T to T:A transversion, results in a changed boxA sequence upstream of nutR, CGCTCTTT. This change is necessary for lambda to effectively use the NusA of Salmonella typhimurium, a NusA function not normally active with the N product of lambda. Other lambdoid phages with unique N functions and nut sites that are normally active with the NusA of Salmonella have boxA sequences with the terminal three Ts. Moreover, sequences closely resembling boxA have been found near transcription termination sequences in E. coli operons where NusA has been shown to be involved in termination. These findings identify boxA as an important recognition signal for the NusA protein.