Rifr Mutants Research Articles

Amino Acid Substitutions in the Two Largest Subunits of Escherichia coli RNA Polymerase That Suppress a Defective Rho Termination Factor Affect Different Parts of the Transcription Complex

Among the earliest rpoBC mutations identified are three suppressors of the conditional lethal rho allele, rho201. These three mutations are of particular interest because, unlike rpoB8, they do not increase termination at all rho-dependent and rho-independent terminators. rpoB211 and rpoB212 both change Asn-1072 to His in conserved region H of rpoB (betaN1072H), whereas rpoC214 changes Arg-352 to Cys in conserved region C of rpoC (beta'R352C). Both substitutions significantly reduce the overall rate of transcript elongation in vitro relative to wild-type RNA polymerase; however, they probably slow elongation for different reasons. The nucleotide triphosphate concentrations required at the T7 A1 promoter for both abortive trinucleotide synthesis and for promoter escape are much greater for betaN1072H. In contrast, beta'R352C and two adjacent substitutions (beta'G351S and beta'S350F), but not betaN1072H, formed open complexes of greatly reduced stability. The sequence in this region of beta' modestly resembles a region of Escherichia coli DNA polymerase I that contacts the phosphate backbone of DNA in co-crystals. Core determinants affecting open complex formation do not reside exclusively in beta', however, since the Rifr mutation rpoB2 in beta also dramatically destabilized open complexes. We suggest that the principal defects of the two Rho-suppressing substitutions may differ, perhaps reflecting a greater role of beta region H in nucleoside triphosphate-binding and nucleotide addition and of beta' region C in contacts to the DNA strands that could be important for translocation. Although both probably suppress rho201 by slowing RNA chain elongation, these differences may lead to terminator specificity that depends on the rate-limiting step at different sites.

A Mutant RNA Polymerase Reveals a Kinetic Mechanism for the Switch between Nonproductive Stuttering Synthesis and Productive Initiation during Promoter Clearance

A Mutant RNA Polymerase Reveals a Kinetic Mechanism for the Switch between Nonproductive Stuttering Synthesis and Productive Initiation during Promoter Clearance

Rifampin resistance in Neisseria meningitidis due to alterations in membrane permeability.

Rifampin-resistant (Rifr) Neisseria meningitidis strains are known to have single point mutations in the central conserved regions of the rpoB gene. We have demonstrated two distinct resistance phenotypes in strains with identical mutations in this region, an intermediate level of resistance in Rifr clinical isolates and a high level of resistance in mutants selected in vitro. The possible role of membrane permeability in the latter was investigated by measuring MICs in the presence of Tween 80; values for high-level-resistance mutants were reduced to intermediate levels, whereas those for intermediate-level-resistance strains were unaffected. The highly resistant mutants were also found to have increased resistance to Triton X-100 and gentian violet. Sequencing of the meningococcal mtrR gene and its promoter region (which determine resistance to hydrophobic agents in Neisseria gonorrhoeae) from susceptible or intermediate strains and highly resistant mutants generated from them showed no mutation within this region. Two-dimensional gel electrophoresis of two parent and Rif mutant strains showed identical shifts in the pI of one protein, indicating that differences between the parent and the highly Rifr mutant are not confined to the rpoB gene. These results indicate that both permeability and rpoB mutations play a role in determining the resistance of N. meningitidis to rifampin.

Suppression of Bacterial Wilt Disease of Tomato by Root-dipping with Pseudomonas fluorescens PfG32. The Role of Antibiotic Substances and Siderophore Production.

Pseudomonas fluorescens strain PfG32 isolated from the rhizosphere of the onion actively suppressed the occurrence of bacterial wilt disease of tomato (BWT) in vermiculite amended natural soil and produced antibiotic substance(s) and siderophore. To investigate the role of the substances in the biocontrol, several mutants defective in antibiotic substances or Siderophore production were isolated from spontaneous Rifr mutant, PfG32R, by Tn5 insertion. Based on pot experiment, the suppression of BWT by Ant-Sid+ (antibiotics non-producing but siderophore producing) mutants was lower compared to its parental strain and to Ant+Sid- (siderophore non producing but antibiotics producing) mutants. However, Ant-Sid+ mutants still express a significant effect. The suppression of BWT by PfG32R was correlated to the suppression of the population of the pathogen observed on the surface of root and to the delay of appearance of detectable population of the pathogen in root tissues. We consider that the ability of PfG32 to produce antibiotics and siderophore is the important factor on determining its biological control and other factor may act as secondary factor.

The β Subunit Rif-cluster I Is Only Angstroms Away from the Active Center of Escherichia coli RNA Polymerase

Ribonucleotide analogs bound in the initiating site of Escherichia coli RNA polymerase-promoter complex were cross-linked to the beta subunit. Using limited proteolysis and chemical degradation, the cross-link was mapped to a segment of beta between amino acids Val516 and Arg540. This region (Rif-cluster I) is known to harbor many rifampicin-resistant (RifR) mutations. The results demonstrate that Rif-culster I is part of the "5'-face" of the active center and provide structural basis for the long-known effects of RifR mutations on transcription initiation, elongation, and termination.

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)

Spontaneous mutation in Escherichia coli containing the dnaE911 DNA polymerase antimutator allele.

We have previously isolated mutants of Escherichia coli that replicate their DNA with increased fidelity. These mutants have a mutation in the dnaE gene, encoding the alpha subunit of DNA polymerase III. They were isolated in a mismatch-repair-defective mutL background, in which mutations can be considered to represent uncorrected DNA replication errors. In the present study we analyze the effect of one of these alleles, dnaE911, on spontaneous mutagenesis in a mismatch-repair-proficient background. In this background, spontaneous mutations may be the sum of uncorrected replication errors and mutations resulting from other pathways. Hence, the effect of the dnaE allele may provide insights into the contribution of uncorrected DNA replication errors to spontaneous mutation. The data show that dnaE911 decreases the level of Rifr, lacI and galK mutations in this background by 1.5-2-fold. DNA sequencing of 748 forward mutants in the lacI gene reveals that this effect has a clear specificity. Transversions are decreased by approximately 3-fold, whereas transitions, frameshifts, deletions and duplications remain essentially unchanged. Among the transversions, A.T-->T.A are affected most strongly (approximately 6-fold). In addition to this effect on transversions within the lacI gene, one previously recognized A.T-->G.C base-pair substitution hotspot in the lac operator is also reduced (approximately 5-fold). The data are discussed in the light of the role of DNA replication errors in spontaneous mutation, as well as other possible explanations for the observed antimutator effects.

The frequency of MMS-induced, umuDC-dependent, mutations declines during starvation in Escherichia coli.

It has been found that the level of methyl methanesulfonate (MMS)-induced mutation in Escherichia coli is dependent on the level of UmuD(D')C proteins. The frequency of argE(ochre)-->Arg+ mutations (which occur predominantly by AT-->TA transversions) and RifS-->RifR mutations is much higher when UmuDC or UmuD'C are overproduced in the cell. When MMS-treated bacteria were starved for progressively longer times and hence the expression of mutations delayed, the level of mutations observed progressively declined. This same treatment had no effect on the degree of SOS induction. Examination of plasmid DNAs, isolated from MMS-treated cells, for their sensitivity to the specific endonucleases Fpg and Nth revealed that MMS causes formation of abasic sites, which are repaired during cell starvation. It is assumed that, in non-dividing cells, apurinic sites are mostly repaired by RecA-mediated recombinational repair. This pathway, which is error-free, is compared with the processing pathway in metabolically active cells, where translesion synthesis by the UmuD'2C-RecA-DNA polymerase III holoenzyme complex occurs; this latter pathway is error-prone.

Molecular characterization of rifampin-resistant Neisseria meningitidis

Primers were designed to amplify the rpoB gene of Neisseria meningitidis. The region of the gene amplified covered clusters I and II of the rifampin resistance (Rifr) mutation sites identified in Escherichia coli. DNAs from six Rifr isolates and 21 rifampin-susceptible isolates from the United Kingdom representing a number of serogroups were amplified and sequenced. All six Rifr isolates had identical DNA sequences and the same amino acid change, a His to an Asn change at position 35 (H35N). This His residue is equivalent to the His residue at position 526 in E. coli, one of the known Rifr mutation sites. DNAs from an additional six Rifr mutations generated in vitro were amplified and sequenced. Three had H35Y changes, one had an H35R change, one had an H35N change and one had an S40F change. The predominance of mutations at the His residue at position 35 in Rifr N. meningitidis isolates suggests that it plays a critical role in the selection of antibiotic-resistant variants. All six Rifr isolates belonged to the same clonal group when analyzed by restriction enzyme analysis and pulsed-field gel electrophoresis. These data suggest that a single clone of Rifr N. meningitidis is present and widespread throughout the United Kingdom.

Producer of Milk-Coagulating Enzyme Complex—Genetic Approach for Investigation and Stabilization

ABSTRACTThe subject of the present research is Bacillus subtilis 76, strain producer of milk-coagulating enzyme complex. The strain expresses the phenomenon of “bacterial dissociation”. The process is of a great importance for applying of industrial microorganisms. In the investigations reported, the results of enzyme productivity and stability of SmR and RifR mutants are shown. Mutant forms with high productivity and increased stability are obtained and discussed.

Direct, automated detection of rifampin-resistant Mycobacterium tuberculosis by polymerase chain reaction and single-strand conformation polymorphism analysis

A rapid screening test was recently established for the detection of mutations in the rpoB gene of Mycobacterium tuberculosis, a region identified as the locus for rifampin resistance (Rifr). The detection method involved the amplification by polymerase chain reaction (PCR) of the Rifr region and the identification of mutations by single-strand DNA conformation polymorphism analysis (SSCP) of the amplification products. Experience using two different PCR-SSCP formats for the evaluation of BACTEC cultures and sputum is presented here; the previously described manual procedure for the detection for the detection of radiolabelled amplification products and an automated SSCP by which fluorescein-labelled products were detected on a Pharmacia DNA sequencer apparatus. All 17 different Rifr mutations known to date were consistently detected. PCR-SSCP could be used for the evaluation of minimally grown cultures (BACTEC 12B medium with a growth index of < or = 100) and for direct screening of microscopically positive sputa with greater than 10 organisms per field (magnification, x250). Implementation of this technique could result in rapid detection of rifampin resistance in M. tuberculosis, a marker of multidrug-resistant tuberculosis.

Rifampicin region revisited. New rifampicin-resistant and streptolydigin-resistant mutants in the beta subunit of Escherichia coli RNA polymerase

Mutations to rifampicin resistance (RifR) in Escherichia coli alter the beta subunit of RNA polymerase (RNAP). A series of new point RifR mutations was isolated with the aid of random polymerase chain reaction-mediated mutagenesis followed by selection on rifampicin (Rif). All of the new RifR mutants, including changes in two novel positions, fell into the two principal clusters previously identified in the middle section of beta. Disruption of the spacer between the two clusters with deletions and insertions led to RNAP that was functional and sensitive to Rif in vitro, indicating that the spacer is not directly involved in Rif binding. However, most of the spacer mutants were strongly resistant to streptolydigin, suggesting that this area is involved in the binding of streptolydigin. An insertion of six consecutive histidines into the spacer was constructed that could be used to anchor RNAP on a Nichelate matrix without the loss of enzymatic activity, indicating that this region is looped out of the RNAP molecule.

Simultaneous gain and loss of functions caused by a single amino acid substitution in the beta subunit of Escherichia coli RNA polymerase: suppression of nusA and rho mutations and conditional lethality.

Transcript elongation and termination in Escherichia coli is modulated, in part, by the nusA gene product, an acidic protein that interacts not only with RNA polymerase itself but also with ancillary factors, namely the host termination protein Rho and phage lambda antitermination protein, N. The E. coli nusA1 mutant fails to support lambda development due to a specific defect in N-mediated antitermination. Certain rifampicin-resistant (rifR) variants of the nusA1 host support lambda growth. We report here the isolation and pleiotropic properties of one such rifR mutant, ts8, resulting from a single amino acid substitution mutation in rpoB, the structural gene for polymerase beta subunit. ts8 is a recessive lethal mutation that blocks cell growth at 42 degrees. Pulse-labeling and analysis of newly synthesized proteins indicate that the mutant cell is proficient in RNA synthesis at high temperature. Apparently, ts8 causes a loss of some specialized function of RNA polymerase without a gross defect in general transcription activities. ts8 is an allele-specific suppressor of nusA1. It does not suppress nusAsal, nusB5 and nusE71 mutations nor does it bypass the requirement for a functional N gene and the nut site for antitermination and lambda growth. A mutation in the N gene, punA1, that restores lambda growth in the nusA1 mutant host but not in the nusAsal host, compensates for the nusAsal allele in the ts8 mutant. This combined effect of two allele-specific suppressors suggests that they enhance some aspect of polymerase-NusA-N interaction and function. ts8 suppresses the rho15 mutation, but not the rho112 mutation, indicating that it might render RNA polymerase susceptible to the action of a defective Rho protein. Marker rescue analysis has localized ts8 to a 910-bp internal segment of rpoB that encodes the Rif domain. By amplification, cloning and sequencing of this segment of the mutant chromosome we have determined that ts8 contains Phe in place of Ser522, caused by a C to T transition. By gene conversion, we have established that the simultaneous gain and loss of three functions of polymerase is caused by this single amino acid substitution. Clearly, a site in the beta subunit critical for the functioning of both termination and antitermination factors is altered by ts8. The alteration, we imagine, might make this site on polymerase receptive to some factors but repulsive to others.

Survival of rifampin-resistant mutants of Pseudomonas fluorescens and Pseudomonas putida in soil systems.

The fate of spontaneous chromosomal rifampin-resistant (Rifr) mutants of Pseudomonas putida and Pseudomonas fluorescens in sterile and live organic soil from which they were isolated was studied. In sterile native-soil assays, a Rifr mutant of P. putida showed no decrease in competitive fitness when compared with the wild-type parent. However, mutants of P. fluorescens were of two general categories. Group 1 showed no difference from the wild type in terms of growth rate, competitive fitness, and membrane protein composition. Group 2 showed a slower growth rate in both minimal and enriched media and an altered membrane protein profile. These mutants also demonstrated decreased competitive fitness compared with the wild-type strain. In live soil, the Rifr P. putida strain persisted throughout the 38-day test period with a decay rate of 0.7 log10 CFU/g of soil per 10 days. A group 1 Rifr P. fluorescens mutant maintained its inoculated titer for 7 to 10 days and then decayed at a rate of 0.2 to 0.4 log10 CFU/g of soil per 10 days. A group 2 Rifr P. fluorescens mutant remained at its titer for 1 to 5 days before decaying at a two- to threefold-faster rate. These findings indicate that rifampin resistance may not be an innocuous mutation in some pseudomonads and that marked strains should be compared with wild-type parents before being used as monitors of parental strain survival. Colonization of sterile soil with either the wild-type or mutant strain precluded normal colonization of the second added strain.(ABSTRACT TRUNCATED AT 250 WORDS)

Salmonella typhimurium mutants with altered expression of the pyrA gene due to changes in RNA polymerase.

Rifampicin-resistant mutants of Salmonella typhimurium were isolated and tested for pleiotropic defects in the regulation of pyr gene expression. Seven per cent of all the Rifr mutants were inhibited in growth by addition of uracil (uracil-sensitive). The uracil-sensitive phenotype ( UraS ) was reversed by arginine or citrulline, but not by ornithine, and it was suppressed by mutations in either argR or pyrH , which causes increased expression of pyrA . It was shown that the basal levels of carbamoylphosphate synthase (the pyrA gene product) was reduced to approximately 60% in the mutants, and that addition of arginine and/or uracil to the growth medium caused hyperrepression of pyrA expression. The expression of other genes of the arginine and pyrimidine biosynthetic pathways was not affected significantly in the mutants. The mutations were located in the rpoB gene coding for the beta-subunit of RNA polymerase, suggesting a regulatory function of RNA polymerase in the control of pyrA expression.

A possible role in transcription for the single-stranded DNA binding protein of bacteriophage T7.

A spontaneous rifampicin-resistant mutant of E. coli, RpoB26, which inhibits the growth of bacteriophage T7, has been described in the accompanying paper (Schwarz et al.). The rifr mutation appears to increase the rate of transcriptional termination in a rho-deficient strain. T7 mutants with the ability to grow (Gor+) on the Rifr mutant were isolated, and some of their properties were investigated. One of these Gor+ mutants has a small deletion, located between nucleotides 9694 and 9820 of the T7 DNA sequence (Dunn and Studier 1980), which affects the size of the T7 single-stranded DNA binding protein (ssDBP), the product of gene 2.5 (p 2.5) (Dunn and Studier 1980). The Gor+ phenotype was also mapped to this region by genetic methods. Gor+ is recessive to the wild-type (Gor-) phenotype. This suggests that the T7 ssDBP may normally increase the frequency of transcriptional termination in the early region by binding to single-stranded nucleic acid configurations, and so affecting molecular conformations involved in the termination process. Excessive termination in RpoB26 could therefore be compensated for by alterations of the ssDBP.

Altered stability and integration frequency of a F' factor in RNA polymerase mutants of Escherichia coli.

A number of spontaneous rifampicin-resistant (Rifr) mutants were isolated from a strain of E. coli having a deletion in the lac proA proB region of the chromosome. The stability of a F'lac proA proB episome in these mutants was determined by their sensitivity to acridine orange curing and the frequency of spontaneous loss of episomes. The Rifr mutants can be divided into three classes based on their ability to maintain the F'lac pro episome. Class I mutants (25% of the total Rifr mutants) showed high degree of spontaneous episome loss and high sensitivity to acridine orange curing. Class II mutants (55% of the total Rifr mutants), like the parent strains, showed intermediate sensitivity to acridine orange curing. Class III mutants (21% of the total Rifr mutants) showed high resistance to acridine orange curing and low frequency of spontaneous episome loss. Three-fourths of the Class II mutants were found to be Hfr as shown by their lack of the F'lac pro DNA band on agarose gel together with their ability to mobilize chromosomal markers in mating. Representative Rifr mutants from each class were selected and the Rifr mutants from each class were selected and the Rifr mutations were mapped within the proB gene for the beta beta' operon by P1 transduction. These results indicate that RNA polymerase, or the beta subunit of RNA polymerase, plays an important role in maintaining the F' lac pro episome and in the integration of the F' lac pro episome where no extensive sequence homology is involved.

A novel form of suppression due to an altered RNA polymerase.

A group of mutants isolated from E coli K12(tif-1) display a very pleiotropic phenotype. The main characteristic of these mutants, temporarily designated 'S' strains, is their ability to suppress a large number of mutations. High efficiency of suppression is correlated with increased thermolability of cellular proteins, indicating an impairment in the fidelity of protein synthesis. Efficient suppression is also accompanied by the appearance of new characteristics like simultaneous resistance to several antibiotic drugs (Sm, Spc, and Mer), and plasmid-like DNA circles. Genetic studies show that the suppressor character is located in the rpoBC region. In a large number of spontaneous Rifr mutants, isolated from these strains, suppression or resistance to drugs is lost. The findings suggest that the phenotype of 'S' strains is due to an altered RNA polymerase causing erroneous transcription.

A mutation suppressing the overproduction of RNA polymerase beta beta' subunits in the RpoC1 strain of Escherichia coli.

As has been shown previously, RNA polymerase β′ subunit ts-mutation rpoC1 results in an overproduction of RNA polymerase ββ′ subunits at nonpermissive temperature. The mutant enzyme shows low activity in vitro and a sedimentation coefficient 9S which is characteristic of immature core polymerase. In this paper we describe a mutation designated opr1 which suppresses RNA polymerase ββ′ subunit overproduction. The mutation was found among Ts+ revertants of the Ts double mutant carrying a rpoC1 mutation and a rif-r rpo B251 mutation. Opr1 is closely linked to the original rpo mutations and shows complete trans-dominance. Although opr1 seems to affect RNA polymerase, it does not suppress the accumulation of immature 9S RNA polymerase and does not restore the activity of the RpoC1 mutant enzyme. This and other results of a comparison of strains carrying different combinations of rpoC1, rpoB251 and opr1 mutations suggest that neither inhibition of total RNA and protein synthesis, nor the low RNA polymerase activity in vitro, nor the apparent defects in enzyme maturation, nor the enzyme degradation observed at 42°C are responsible for the ββ′ overproduction in RpoC1 strains.

On the fidelity of transcription by escherichia coli RNA polymerase

The enzymes that carry out template-directed synthesis of DNA (DNA polymerase and reverse transcriptase) were shown to participate in the selection of complementary nucleotides as proved by the effect of enzyme structure on the fidelity in copying polynucleotide templates [ 1,2]. Temperature-sensitive mutants affecting the structural gene of DNA polymerase are characterized by increased mutability [3-61. A difference has been observed between nucleotide misincorporation of in vitro DNA synthesis by normal and mutant enzyme [I]. Mutational alterations of DNA-dependent RNA polymerase have not revealed such a dependence [7]. No difference in the fidelity of in vitro transcription was observed when intrinsic Zn2+ of RNA polymerase was substituted by Co’+ [8]. The data available on the accuracy of base-selection during transcription are conflicting [7,9111. The values of misincorporation vary substantially in different reports. In the case of poly(AU) synthesis on a poly [d(AT) X d(AT)] template the frequency of GMP incorporation was shown to be 9.5 X lo4 [9] and 2.3 X IO-’ [IO]. The frequency of misincorporation of GMP into poly(A) synthesized on a poly(dT) template varies between 3.3 X lo-’ [l l] and 6.4 X lo4 [7]. With synthetic polyribonucleotides as a template, the variations are still greater. To study the role of RNA polymerase in ensuring the fidelity of transcription, in this work we chose RNA polymerase rifampicin resistant (rifr) mutants of Escher&h& coEi B/r, rpoB402, rpoB403 and rpoB409 [ 12,131, which are characterized by increased variance within one of the phenotypic parameters