Effect of R Factors on Rifampicm Resistance in <Emphasis Type="Italic">E. coli</Emphasis>

THE bactericidal effect of rifampicin, a semi-synthetic rifamycin, is due to its action on DNA-dependent RNA polymerase¹ and all rifampicin-resistant mutants of Escherichia coli contain an altered RNA polymerase with an increased resistance to rifampicin in vitro^2–4. While studying a possible curing effect of rifampicin on E. coli R factors, we observed that R⁺ recombinants of some rif-r mutants are more sensitive to rifampicin (Table 1). Of the cells harbouring certain R factors, less than 1% are able to form colonies on rifampicin-supplemented agar, while with certain others there is no detectable effect.     

Rifampicin-resistant bacteriophage PBS2 infection and RNA polymerase in Bacillus subtilis

Bacteriophage PBS2 replication is unaffected by rifampicin and other rifamycin derivatives, which are potent inhibitors of Bacillus subtilis RNA synthesis. Extracts of gently-lysed infected cells contain a DNA-dependent RNA polymerase activity which is specific for uracil-containing PBS2 DNA. The PBS2-induced RNA polymerase is insensitive to rifamycin derivatives which inhibit the host's RNA polymerase.     

The two effects of rifampicin on the RNA polymerase reaction.

At 25°C rifampicin strongly stimulates the synthesis of the dinucleotide pppA-U catalyzed by the DNA-dependent RNA polymerase from $\text{Escherichia coli}$. If the antibiotic is added to the enzyme during the synthesis of RNA the stimulatory effect on the dinucleotide synthesis is distinctly retarded as is its inhibitory action on RNA synthesis. It is proposed that this lag period is due to a retardation of the binding of rifampicin to RNA polymerase which is required for its action. Because of this slower binding rifampicin — although an inhibitor of RNA chain elongation — mimics the action of an inhibitor of RNA chain initiation.     

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.     

Physico-chemical properties of DNA-dependent RNA-polymerase from Escherichia coli and its subunits

CD and UV spectroscopy were employed to study at different temperatures the conformational states of the DNA-dependent RNA polymerase core- and holo-enzymes, as well as of its alpha and beta subunits. Both core- and holo-enzyme were shown to have a higher percentage of regular structures than the separate subunits. CD and fluorescence methods were used to monitor the complex formation between rifamycin SV or its derivative, rifampicin, with the RNA polymerase from the E. coli wild and mutant (Rpo B255) types, the former enzyme being sensitive and the latter being resistant to these antibiotics. Complexation led to concomitant changes in the conformation of antibiotics and local structural rearrangements of the protein in vicinity of the binding site which comprises at least one tryptophan residue in a hydrophobic microenvironment.     

Effect of Rifampicin on the Development of Tumours induced by Adenovirus in Male Hamsters

INITIAL in vitro studies established that rifampicin, one of a group of rifamycin SV derivatives^1,2, prohibits bacterial growth and phage replication by binding to a polypeptide component of the microbial DNA-dependent RNA polymerase^3–7. The trachoma agent and related psittacosis-lymphogranuloma agents are also inhibited in vitro and in embryonated eggs by this drug⁸. Further studies have shown that rifampicin is active against a number of bacteria in vivo, both after parenteral and oral administration^1,9,10. It also inhibits malaria in mice¹¹ and trachoma in monkeys^12,13 and is of special value in the treatment of human tuberculosis^14–16. The low toxicity of the rifamycins in mammals¹⁷ has been attributed to the observed relative insensitivity of mammalian RNA polymerase to the rifamycins in vitro^3,18.     

A mutant of Escherichia coli capable of utilizing 3-deoxy-d-manno-2-octulosonic acid as sole carbon source

Abstract The hypothesis that rifampicin resistance mutations (possibly leading to altered RNA polymerases) have a pleiotropic effect on symbiotic nitrogen fixation was tested using the Rhizobium japonicum -soybean symbiosis. A total of 20 spontaneous rifampicin-resistant mutants of R. japonicum strain 110 were analyzed biochemically. RNA polymerase assays revealed that the enzyme from 15 mutants was indeed rifampicin-insensitive. Two of these mutants were found to possess an enzyme with an electrophoretically altered β subunit. All rifampicin-resistant mutants were able to form nodules on soybeans and fix nitrogen symbiotically; free-living nitrogen fixation under microaerophilic culture conditions was also unaffected.     

Symbiotic Properties of Antibiotic-Resistant and Auxotrophic Mutants of Rhizobium leguminosarum

A number of auxotrophic and antibiotic-resistant mutants of Rhizobium leguminosarum were isolated and their symbiotic properties examined. Among the auxotrophic mutants tested, only those with an adenine requirement were found to be symbiotically defective and these were all non-infective. Of the antibiotic-resistant mutants isolated, only a minority of the rifampicin-resistant mutants had a modified symbiotic phenotype and this was ineffective. Preliminary evidence suggests that the basis for the resistance in these mutants is a modified DNA-dependent RNA polymerase.     

Micro-analysis of pure deoxyribonucleic acid-dependent ribonucleic acid polymerase from Escherichia coli. Action of heparin and rifampicin on structure and function

By using micro disc electrophoresis and micro-diffusion techniques, the interaction of pure DNA-dependent RNA polymerase (EC 2.7.7.6) from Escherichia coli with the template, the substrates and the inhibitors heparin and rifampicin was investigated. The following findings were obtained: (1) heparin converts the 24S and 18S particles of the polymerase into the 13S form; (2) heparin inhibits RNA synthesis by dissociating the enzyme-template complex; (3) rifampicin does not affect the attachment of heparin to the enzyme; (4) the substrates ATP and UTP are bound by enzyme loaded with rifampicin; (5) rifampicin is bound by an enzyme-template complex to the same extent as by an RNA-synthesizing enzyme-template complex. From this it is concluded that the mechanism of the inhibition of RNA synthesis by rifampicin is radically different from that by heparin. As a working hypothesis to explain the inhibitory mechanism of rifampicin, it is assumed that it becomes very firmly attached to a position close to the synthesizing site and only blocks this when no synthesis is in progress.     

Genetical analysis of rifampicin resistant mutants of E. coli K 12

Summary E. coli rifampicin-resistant (rif-r) mutants were divided into two conventional groups: A, resistant to 50–100g/ml of rifampicin both on complete and minimal medium and B, sensitive to these concentrations of rifampicin on minimal, but resistant on complete medium. RNA polymerase from rif-r-A mutants is resistant to high concentrations of rifampicin in vitro while the enzyme from rif-r-B mutants but slightly if at all differs from the wild-type enzyme in its response to the drug.All rif-r-A and rif-r-B mutants are closely linked and map between argH and thi on E. coli K 12 chromosome. We failed to isolate any rifampicin-resistant mutants which would map outside this region.     

Inhibition of isolated yeast and mycelial phase RNA polymerases of Histoplasma capsulatum by rifamycin derivatives

Various derivatives of rifamycin were shown to inhibit the RNA polymerases of the yeast and mycelial phases of Histoplasma capsulatum. The relative potency of each of the derivatives against the isolated polymerases was the same as the potency of each against the viable organism. RNA polymerase PC III from the yeast phase was more susceptible to the rifamycin derivatives than yeast phase polymerases PC I and PC II and the biggest differences in susceptibility were seen with the derivative AF/ABDP (2,6-dimethyl-4-benzyl-4-demethyl-rifamycin). The susceptibility pattern of the mycelial polymerase activity was identical to the yeast polymerase PC III.     

Kinetic basis of sugar selection by a Y-family DNA polymerase from Sulfolobus solfataricus P2

DNA polymerases use either a bulky active site residue or a backbone segment to select against ribonucleotides in order to faithfully replicate cellular genomes. Here, we demonstrated that an active site mutation (Y12A) within Sulfolobus solfataricus DNA polymerase IV (Dpo4) caused an average increase of 220-fold in matched ribonucleotide incorporation efficiency and an average decrease of 9-fold in correct deoxyribonucleotide incorporation efficiency, leading to an average reduction of 2000-fold in sugar selectivity. Thus, the bulky side chain of Tyr12 is important for both ribonucleotide discrimination and efficient deoxyribonucleotide incorporation. Other than synthesizing DNA as the wild-type Dpo4, the Y12A Dpo4 mutant incorporated more than 20 consecutive ribonucleotides into primer/template (DNA/DNA) duplexes, suggesting that this mutant protein possesses both a DNA-dependent DNA polymerase activity and a DNA-dependent RNA polymerase activity. Moreover, the binary and ternary crystal structures of Dpo4 have revealed that this DNA lesion bypass polymerase can bind up to eight base pairs of double-stranded DNA which is entirely in B-type. Thus, the DNA binding cleft of Dpo4 is flexible and can accommodate both A- and B-type oligodeoxyribonucleotide duplexes as well as damaged DNA.     

An oligoribonucleotide polymerase from SV40-infected cells with properties of a primase

A transient decaribonucleotide (iRNA) is covalently linked to nascent eukaryotic DNA chains at their 5' end. Searching for the putative iRNA polymerase (primase), we detected in extracts from SV40-infected cells a DNA-dependent incorporation of UMP residues from UTP into free and DNA linked deca- or similarly sized ribonucleotides. Denatured salmon sperm DNA served as the standard template in this reaction. SV40 FIII DNA was also an effective template, SV40 FII DNA was ineffective while FI yielded mainly free decaribonucleotides. The incorporation depended on the other rNTPs and was resistant to high concentrations of alpha-amanitin and rifamycin AF/013, drugs inhibitory to RNA polymerases I, II and III. The results implicate the decaribonucleotide polymerase in the priming of nascent DNA chains and suggest that the unique size of iRNA is encoded within its primase.     

Fitness-compensatory mutations in rifampicin-resistant RNA polymerase

Mutations in rpoB (RNA polymerase β-subunit) can cause high-level resistance to rifampicin, an important first-line drug against tuberculosis. Most rifampicin-resistant (Rif(R)) mutants selected in vitro have reduced fitness, and resistant clinical isolates of M. tuberculosis frequently carry multiple mutations in RNA polymerase genes. This supports a role for compensatory evolution in global epidemics of drug-resistant tuberculosis but the significance of secondary mutations outside rpoB has not been demonstrated or quantified. Using Salmonella as a model organism, and a previously characterized Rif(R) mutation (rpoB R529C) as a starting point, independent lineages were evolved with selection for improved growth in the presence and absence of rifampicin. Compensatory mutations were identified in every lineage and were distributed between rpoA, rpoB and rpoC. Resistance was maintained in all strains showing that increased fitness by compensatory mutation was more likely than reversion. Genetic reconstructions demonstrated that the secondary mutations were responsible for increasing growth rate. Many of the compensatory mutations in rpoA and rpoC individually caused small but significant reductions in susceptibility to rifampicin, and some compensatory mutations in rpoB individually caused high-level resistance. These findings show that mutations in different components of RNA polymerase are responsible for fitness compensation of a Rif(R) mutant.     

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

The radiolabeled RNA polymerase inhibitors 3-(2-bromoacetamidoethyl)-thiorifamycin and 3-(2-acetamidoethyl)-thiorifamycin quinone have been prepared and covalently attached to the B. subtilis enzyme under mild conditions. Analysis of the subunits labeled indicates that regions of subunits sigma, beta, and beta-prime lie within about 7Å of the 3-position of rifamycin bound to the enzyme, while subunits $\text{alpha}$, beta, and beta-prime lie near the aromatic rings. The results of this work imply that the rifamycin binding site lies near the center of an arrangement involving at least four of the subunits of RNA polymerase. This idea is supported by the results of other studies involving cross-linking of subunits and also rifamycin binding to subunit complexes.