How do the termination signals in the DNA stop the elongating polymerase? For most bacterial genes, a termination signal consists of a string of A-T nucleotide pairs preceded by a twofold symmetric DNA sequence, which, when transcribed into RNA, folds into a “hairpin” structure through Watson–Crick base-pairing (see Figure 6–11A). As the polymerase transcribes across a terminator, the formation of the hairpin helps to disengage the RNA transcript from the active site (step 7 in Figure 6–11A). The process of termination provides an example of a common theme in this chapter: the folding of RNA into specific structures affects many steps in decoding the genome.
As we have just seen, the processes of transcription initiation and termination involve a complicated series of structural transitions in protein, DNA, and RNA molecules. The signals encoded in DNA that specify these transitions are often difficult for researchers to recognize. Indeed, a comparison of many different bacterial promoters reveals a surprising degree of variation. Nevertheless, they all contain related sequences, reflecting aspects of the DNA that are recognized directly
Figure 6–11 The transcription cycle of bacterial RNA polymerase. (A) In step 1, the RNA polymerase holoenzyme (polymerase core enzyme plus σ factor) assembles and then locates a promoter DNA sequence (see Figure 6–12). The polymerase opens (unwinds) the DNA at the position at which transcription is to begin (step 2) and begins transcribing (step 3). This initial RNA synthesis (abortive initiation) is relatively inefficient as short, unproductive transcripts are often released. However, once RNA polymerase has managed to synthesize about 10 nucleotides of RNA, it breaks its interactions with the promoter DNA (step 4) and eventually releases σ factor—as the polymerase tightens around the DNA and shifts to the elongation mode of RNA synthesis, moving along the DNA (step 5). During the elongation mode, transcription is highly processive, with the polymerase leaving the DNA template and releasing the newly transcribed RNA only when it encounters a termination signal (steps 6 and 7). Termination signals are typically encoded in DNA, and many function by forming an RNA hairpin-like structure that destabilizes the polymerase’s hold on the RNA.
In bacteria, all RNA molecules are synthesized by a single type of RNA polymerase, and the cycle depicted in the figure therefore applies to the production of mRNAs as well as structural and catalytic RNAs. (B) Two-dimensional image of an elongating bacterial RNA polymerase, as determined by atomic force microscopy (see Figure 9–33). (C) Interpretation of the image in (B). (Adapted from K.M. Herbert et al., Annu. Rev. Biochem. 77:149–176, 2008.) frequency of nucleotide in each position (%) sequence and sequence logo for the major class of E. coli promoters.
(A) On the basis of a comparison of 300 promoters, the frequencies of each of the four nucleotides at each position in the promoter are given. The consensus sequence, shown below the graph, reflects the most common nucleotide found at each position in the collection of promoters. These promoters are characterized by two hexameric DNA sequences—the –35 sequence and the –10 sequence, named for their approximate location relative to the start point of transcription (designated +1). The sequence of nucleotides between the –35 and –10 hexamers shows no significant similarities among promoters.