Subunit contacts of the rifamycin binding site of RNA polymerase (B. subtilis)

RNA polymerase (rpoB) mutants selected for increased resistance to gyrase inhibitors in Salmonella typhimurium

Some rifampicin-resistance (RifR) mutations make bacteria slightly resistant to the gyrase inhibitors novobiocin (Nov) and nalidixic acid (Nal). This suggested that it might be possible to isolate rpoB mutants using either drug for positive selection. In an initial test, we confirmed the presence of Rif-resistant isolates among clones selected for Nov resistance. These mutants are also more resistant to Nal. In a subsequent experiment, we found that mutants selected for low-level resistance to Nal include isolates harboring mutations genetically linked to the rpoB locus; of two such mutants studied, one is temperature-sensitive for growth. These two mutants, which are only marginally affected in their response to Nov, are normally sensitive to Rif and thus might be representative of a new class of rpoB alleles. The Rif-resistant and Rif-sensitive rpoB alleles that increase resistance to gyrase inhibitors have one property in common: they all suppress, to varying degrees, the defect in his operon regulation (transcriptional deattenuation) caused by a gyrase defect or inhibition by novobiocin. To further analyse the transcription-supercoiling relationships in these mutants, we examined the ability of RNA polymerase to recruit gyrase activity during transcription. This was done by two independent approaches: (i) observing transcription-induced accumulation of hyper-negatively supercoiled plasmid DNA in a topA mutant background and (ii) measuring transcription-induced plasmid DNA cleavage in the presence of oxolinic acid. Results indicate that the rpoB alleles described in this study diminish the recruitment of gyrase activity by the transcription process. This property correlates with a decrease in the rate of transcription initiation.(ABSTRACT TRUNCATED AT 250 WORDS)

Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance

Rifampicin is an antibiotic that inhibits the function of RNA polymerase in eubacteria. Mutations affecting the beta subunit of RNA polymerase can confer resistance to rifampicin. A large number of rifampicin-resistant (hereafter called Rifr) mutants have been isolated in Escherichia coli to probe the involvement of RNA polymerase in a variety of physiological processes. We have undertaken a comprehensive analysis of Rifr mutations to identify their structural and functional effects on RNA polymerase. Forty-two Rifr isolates with a variety of phenotypes were mapped to defined intervals within the rpoB gene using a set of deletions of the rpoB gene. The mutations were sequenced. Seventeen mutational alterations affecting 14 amino acid residues were identified. These alleles are located in three distinct clusters in the center of the rpoB gene. We discuss the implications of our results with regards to the structure of the rifampicin binding site.

The generation of the rifamycin binding site in the beta subunit of E. coli RNA polymerase through subunit interactions

Spectral studies were performed using rifampicin quinone to investigate the generation of the rifamycin binding site in the beta subunit of E. coli RNA polymerase due to subunit interactions. The spectrum of rifampicin quinone is not significantly altered in the presence of the beta subunit. In the case of the alpha 2 beta subassembly, a negative difference spectral band at 330 nm is observed for rifampicin quinone, whereas in the presence of either the holoenzyme or core polymerase a positive band at 348 and a negative one at 318 are observed. In affinity labeling studies using 3-(2-bromo[1-14C]acetamidoethyl)-thiorifamycin, it was demonstrated that the isolated beta subunit is nonspecifically modified by this reagent. However, in the case of both the alpha 2 beta subassembly and core polymerase, the beta subunit is specifically modified.

Quaternary structure of DNA-dependent RNA polymerase from Escherichia coli. Measurement of distances by fluorescence energy transfer

Distances between the subunits in Escherichia coli RNA polymerase (core and holo enzyme) and the rifamycin binding site have been determined using the nonradiative energy transfer technique. The appropriate donor and acceptor labels have been chosen in order to optimize the spectral overlap and maximize the energy transfer. Spacer linked derivatives of rifamycin SV possessing nitrobenzo-oxadiazole groups (energy acceptor) were synthesized for this purpose. The donor label, acetylaminoethylaminonaphthalene sulfonate, was introduced into the intact enzyme, and the subunits were separated. Enzyme molecules selectively labelled on one kind of subunit were produced by mixed reconstitution techniques employing labelled and non labelled subunits. The labelled beta'-subunit could not be prepared in sufficient amounts. Energy transfer distances between the enzyme-bound rifamycin derivative and the subunits were determined to be approximately 5.9 nm for sigma, 7.2 nm for alpha 2 and 6.1 nm for beta.