Katsuhiko Murakami

Single-Molecule Imaging of RNA Polymerase-DNA Interactions in Real Time

Using total internal reflection fluorescence microscopy, we have directly observed individual interactions of single RNA polymerase molecules with a single molecule of lambda-phage DNA suspended in solution by optical traps. The interactions of RNA polymerase molecules were not homogeneous along DNA. They dissociated slowly from the positions of the promoters and sequences common to promoters at a rate of approximately 0.66 s-1, which was more than severalfold smaller than the rate at other positions. The association rate constant for the slow dissociation sites was 9.2 x 10(2) bp-1 M-1 s-1. The frequency of binding to the fast dissociation sites was dependent on the A-T composition; it was larger in the AT-rich regions than in the GC-rich regions. RNA polymerase molecules on the fast dissociation sites underwent linear diffusion (sliding) along DNA. The binding to the slow dissociation sites was greatly enhanced when DNA was released to a relaxed state, suggesting that the binding depended on the strain exerted on the DNA. The present method is potentially applicable to the examination of a wide variety of protein-nucleic acid interactions, especially those involved in the process of transcription.

Transcription factor recognition surface on the RNA polymerase alpha subunit is involved in contact with the DNA enhancer element.

The carboxy‐terminal one‐third of Escherichia coli RNA polymerase alpha subunit plays a key role in transcription regulation by a group of protein transcription factors and DNA enhancer (UP) elements. The roles of individual amino acid residues within this regulatory domain of the alpha subunit were examined after systematic mutagenesis of the putative contact regions (residues 258–275 and 297–298) for the cAMP receptor protein (CRP). The reconstituted RNA polymerases containing the mutant alpha subunits were examined for their response to transcription activation by cAMP‐CRP and the rrnBP1 UP element. Mutations affecting CRP responsiveness were located on the surface of the putative CRP contact helix and most of these mutations also influenced the response to the rrnB UP element. These observations raise the possibility that the CRP contact surface is also involved in contact with the DNA UP element, although some amino acid residues within this region play different roles in molecular communication with CRP and the UP element. Among the amino acid residues constituting the contact surface, Arg265 was found to play a major role in response to both CRP and the DNA UP element. Judged by DNase I footprinting analysis, alpha mutants defective in transcription from the CRP‐dependent lacP1 promoter showed decreased activity in the cooperative binding of CRP. Likewise, mutants defective in rrnBP1 transcription showed decreased binding to the UP element. The amino acid residues important for contact with both CRP and DNA are conserved in the alpha subunits of not only bacterial, but also chloroplast RNA polymerases.

Transcription Activation by the Bacteriophage Mu Mor Protein Requires the C-terminal Regions of Both α and σ70 Subunits of Escherichia coli RNA Polymerase

Middle transcription of bacteriophage Mu requires Escherichia coliRNA polymerase and a Mu-encoded protein, Mor. Consistent with these requirements, the middle promoter, Pm, has a −10 hexamer but lacks a recognizable −35 hexamer. Interactions between Mor and RNA polymerase were studied using in vitro transcription, DNase I footprinting, and the yeast interaction trap system. We observed reduced promoter activity in vitro using reconstituted RNA polymerases with C-terminal deletions in α or σ70. As predicted if α were binding to Pm, we detected a polymerase-dependent footprint in the −60 region. Reconstituted RNA polymerases containing Ala substitutions in the α C-terminal domain were used to assay Mor-dependent transcription from Pm in vitro. The D258A substitution and α deletion gave large reductions in activation, whereas the L262A, R265A, and N268A substitutions caused smaller reductions. The interaction trap assay revealed weak interactions between Mor and both α and σ70; consistent with a key role of α-D258, the D258A substitution abolished interaction, whereas the R265A substitution did not. We propose that: (i) α-D258 is a Mor “contact site”; and (ii) residues Leu-262, Arg-265, and Asn-268 indirectly affect Mor-polymerase interaction by stabilizing the ternary complex via α-DNA contact.