Sequences in the 5' proximal segment of the paused transcript affect NusA-mediated enhancement of transcriptional...

NusA protein is a transcription elongation and termination factor that acts to enhance pausing of RNA chain growth by RNA polymerase at specific sites on DNA templates. We demonstrate that this enhancement of pausing in tR1, the transcription termination site between genes cro and cII of phage lambda, is inhibited by DNA oligonucleotides complementary to a segment of the nascent RNA just preceding the sequence that is thought to be a part of the stem of an RNA hairpin that is responsible for pausing, but not by oligonucleotides complementary to segments containing the boxA sequence or the sequences up to 40 nucleotides upstream from boxA. The results are consistent with a model proposed by Landick and Yanofsky (Landick, R., and Yanofsky, C. (1987) J. Mol. Biol. 196, 363-377) in which the NusA protein acting as a subunit of RNA polymerase in the elongation complex contacts a structure near the 3' end of the nascent transcript and uses the binding energy to shift the equilibrium between elongation and paused conformational isomers of the transcription complex in favor of the paused isomer.