Factor-Independent Termination of Transcription

In bacteria two distinct types of termination events have been identified-those that depend on the action of a protein termination factor, called (rho), and those that are factor-independent.

Factor-independent termination - Sequencing the 3' ends of genes that terminate in a factor-independent manner reveals the following two structural features shared by many such genes and illustrated in Figure 26.15:

1. Two symmetrical GC-rich segments in the transcript have the potential to form a stem--loop structure

2. A downstream run of four to eight A residues.

These features suggest the following as elements of the termination mechanism:

1. RNA Polymerase slows down, or pauses, when it reaches the first GC-rich segment, because the stability of G-C base pairs makes the template hard to unwind. In vitro, RNA polymerase does pause for several minutes at a GC-rich segment.

2. The pausing gives time for the complementary GC-rich parts of the nascent transcript to base-pair with one another. In the process, the downstream GC-rich segment of the transcript is displaced from its template (or from that part of the enzyme molecule to which it is bound; see Figure 26.8b). Hence, the ternary complex of RNA polymerase, DNA template, and RNA is weakened. Further weakening, leading to dissociation, occurs when the A-rich segment is transcribed to give a series of AU bonds (which are very weak), linking transcript to template.

The actual mechanism of termination is more complex than just described, in part because DNA sequences both upstream and downstream from the regions shown in Figure 26.15 also influence termination efficiency. Moreover, not all pause sites are termination sites.