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Figure 2.12 shows the transcription elongation complex (TEC) in the process of elongating the RNA transcript. Most of the features are mentioned above, including the approximately 17-bp transcription bubble where the two strands of DNA are separated, the approximately 8- to 9-bp RNA-DNA hybrid that forms in the active site is maintained, and the newly synthesized RNA strand separates from the DNA template strand and emerges through the RNA exit channel. The RNA polymerase is capable of synthesizing RNA at a rate of 30 to 100 nucleotides per second. However, it sometimes pauses and even slides backward (backtracks). This phenomenon often occurs when a helical domain, or hairpin, forms in the RNA as it exits the RNA exit channel, when the newly synthesized RNA contains inverted-repeated sequences. It is not clear why hairpins cause pausing and backtracking, but they may pull the RNA polymerase backward or bind to it and change its conformation. Backtracking creates special problems for the TEC. When the RNA polymerase is forced backward, it pushes the 3′ end of the newly synthesized RNA forward, driving it into the secondary channel through which the nucleotides enter, as shown in Figure 2.13. It would remain this way, permanently blocked, except for the action of two proteins called GreA and GreB. These proteins insert their N termini into the secondary channel and cleave the 3′ end of the RNA in the channel until it is in its proper place in the active site so that transcription can continue.

RNA polymerase pausing and backtracking reduce the rate of transcription overall and create the necessity for the Gre proteins. Selective pausing may help the folding of the newly synthesized RNA or the protein being translated from the RNA (see below). Some genes whose RNA products must be made in large amounts, such as the rRNA genes, have special mechanisms to reduce pausing and backtracking. The rRNA genes have sequences called antitermination sites that recruit protein factors that bind to the RNA polymerase and preempt the pausing effect of RNA hairpins that form in the emerging rRNA and avoid premature termination of transcription (see below). Pausing also plays an important role in a variety of mechanisms for gene regulation (see chapter 11).

Figure 2.10 Interactions between RNA polymerase subunits and promoter elements. (A) Interaction of σ⁷⁰ at –10 and –35 regions. (B) Flexible linkers between the α subunit carboxyl-terminal domain (αCTD) and the amino-terminal domain of α (αNTD) domains allow binding of αCTDs to UP elements in the DNA. (C) σ₃ binding to an extended –10 region. Modified from Dove SL, Hochschild A, in Higgins NP (ed), The Bacterial Chromosome (ASM Press, Washington, DC, 2005).