Termination

RNA polymerase moves along the template, adding nucleotides to the 3' end of the growing RNA molecule until it transcribes a terminator. Most terminators are found upstream of the point of termination. Transcription therefore does not suddenly end when polymerase reaches a terminator, like a car stopping in front of a stop sign. Rather, transcription ends after the terminator has been transcribed, like a car that stops only after running over a speed bump. At the terminator, several overlapping events are needed to bring an end to transcription: RNA polymerase must stop synthesizing RNA, the RNA molecule must be released from RNA polymerase, the newly made RNA molecule must dissociate fully from the DNA, and RNA poly-merase must detach from the DNA template.

Bacterial cells possess two major types of terminators. Rho-dependent terminators are able to cause the termination of transcription only in the presence of an ancillary protein called the rho factor. Rho-independent terminators are able to cause the end of transcription in the absence of rho.

Rho-independent terminators have two common features. First, they contain inverted repeats (sequences of nucleotides on one strand that are inverted and complementary). When inverted repeats have been transcribed into RNA, a hairpin secondary structure forms (IFigure 13.14). Second, in rho-independent terminators, a string of approximately six adenine nucleotides follows the second inverted repeat in the template DNA. Their transcription produces a string of uracil nucleotides after the hairpin in the transcribed RNA.

The presence of a hairpin in an RNA transcript causes RNA polymerase to slow down or pause, which creates an opportunity for termination. The adenine - uracil base pairings downstream of the hairpin are relatively unstable compared with other base pairings, and the formation of the hairpin may itself destablize the DNA-RNA pairing, causing the RNA molecule to separate from its DNA template. When the RNA transcript has separated from the template, RNA synthesis can no longer continue (see Figure 13.14).

Rho-dependent terminators have two features: (1) DNA sequences that produce a pause in transcription; and (2) a DNA sequence that encodes a stretch of RNA upstream of the terminator that is devoid of any secondary structures. This unstructured RNA serves as binding site for the rho protein, which binds the RNA and moves toward its 3' end, following the RNA polymerase (I Figure 13.15). When RNA polymerase encounters the terminator, it pauses, allowing rt A rho-independent terminator contains an inverted repeat followed by a string of approximately six adenine nucleotides.

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