Genetics Home   Molecular Biology 2nd Edition               Robert F. Weaver
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Chapter 6

  1. Indirect evidence has strongly suggested that RNA polymerase causes DNA to rotate as it is transcribed. In this article the authors use real-time optical microscopy to detect and measure the DNA rotation directly. (Harada, Y., O. Ohara, A. Takatsuki, H. Itoh, N. Shimamoto, and K. Kinosita Jr. 2001. Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature 409:113-15)

  2. Rifampicin has been used as a tool to investigate bacterial RNA polymerases for decades. Now Campbell et al. have determined the crystal structure of Thermus aquaticus RNA polymerase in a complex with rifampicin. They find that the antibiotic binds in a pocket in the enzyme's subunit, within the DNA/RNA channel. This site is over 12 from the active site of the enzyme, and apparently allows rifampicin to block the exit of the product RNA when it reaches a length of 2-3 nt. (Campbell, E.A., N. Korzheva, A. Mustaev, K. Murakami, S. Nair, A. Goldfarb, and S.A. Darst. 2001. Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 104:901-12)

  3. The bacterial protein NusA normally enhances transcription pausing and termination. Toulokhonov et al. have used protein-RNA crosslinking studies, molecular modeling, and genetic studies to probe the role of hairpins in transcription pausing and termination by bacterial RNA polymerases. A flaplike domain covers the RNA exit channel of the polymerase. These investigators show that a short -helix at the tip of this flaplike domain interacts with the hairpin in a nascent transcript. Moreover, this same -helix is required for enhancement of pausing and termination by NusA. The authors suggest that the tripartite complex of hairpin, -helix, and NusA block the further addition of nucleotides to the growing RNA chain, and thereby causing pausing and, under the right conditions, termination. The distance between the tripartite complex and the enzyme's active site is 65 , so the effect appears to be allosteric. (Toulokhonov, I., I. Artsimovitch, and R. Landick. 2001. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 292:730-33)

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