Transcription terminators stop elongation of transcripts by DNA-dependent RNA polymerase and dissociate the ternary elongation complex. Antiterminators modify the elongation complex so that it no longer responds to terminators. Together, terminators and antiterminators are used to control the level of gene expression. We study antiterminators that are unusual in that they are embedded in the nascent transcript. These antiterminators are encoded by the put sites of E. coli bacteriophage HK022. A nascent put transcript modifies the enzyme molecule that catalyzed its synthesis, thus decreasing transcription termination and increasing bacteriophage gene expression. Other elongation complexes in the cell are unaffected. Antitermination requires persistent association of nascent put RNA with the elongation complex as it proceeds along the template. Indeed, the association of the antiterminator RNA with the elongation complex persists for many minutes after put is transcribed, as shown by suppression of terminators that are located as far as 10,000 base pairs from the put site. Since the intrinsic affinity of the two components is low, the basis of this persistence is an open question that is currently under investigation. Characterization of RNA polymerase mutants that specifically block put antitermination allowed identification of a put RNA binding site. This site is at the tip of a surface exposed loop known as the zinc binding domain that is located near the exit channel for nascent RNA. A mutation that alters a highly conserved residue in the zinc binding domain prevented both antitermination and put RNA binding. However, ablation of the entire zinc binding domain restored put-mediated antitermination, suggesting that put RNA can interact with a second site in the TEC. Our working model is that put RNA interacts with the zinc binding domain and then with the second site. Interaction with the zinc binding domain opens access to the second site, but ablation of the zinc binding domain obviates the need for the initial interaction by unmasking the second site. The location of the second site is not yet known. We have shown that put suppresses the pausing that occurs when the elongation complex synthesizes transcripts that are rich in U residues. Such U-rich sequences are essential components of intrinsic terminators. When the elongation complex is artificially halted within a U-rich sequence, it moves backwards on the template with consequent disengagement of the 3' end of the transcript from the active site, and concerted retreat of the RNA:DNA hybrid region and its associated transcription bubble from the 3'-end. Such retrograde movement also exposes upstream phosphodiester bonds to hydrolysis activated by the GreB protein and delays resumption of elongation until the 3' end is restored to the active site by forward movement of the elongation complex. We found that put modification changed the properties of a elongation complex that is artificially halted at a U-rich sequence by a protein roadblock. A modified elongation complex was less sensitive to GreB-mediated cleavage, had an altered pattern of cleavage of the transcription bubble by KMnO4, and resumed transcription more rapidly upon removal of the roadblock than did an unmodified elongation complex. We propose that modification by put RNA favors the posttranslocational state of the elongation complex; that is, the state in which the catalytic site of the enzyme is engaged with the next incoming templated substrate. This activity of put could, in principle, account for its ability to suppress pausing and termination.
