Systematic nomenclature for the RNA polymerase genes of prokaryotes

Trans-dominant mutations in the 3'-terminal region of the rpoB gene define highly conserved, essential residues in the beta subunit of RNA polymerase: the GEME motif

BACKGROUND

The multimeric DNA-dependent RNA polymerases are widespread throughout nature. The RNA polymerase of Escherichia coli, which is the most well characterized, consists of a holoenzyme with subunit stoichiometry of alpha2betabeta'sigma. The beta subunit is conserved and has been implicated in all stages of transcription. The extreme C-terminus of the beta subunit, which includes two well-conserved sequence segments, contributes to the active centre and has been proposed to act in transcriptional termination. We describe a genetic system for further characterizing the role of the extreme C-terminus of the beta subunit of E. coli RNA polymerase. This involves random, PCR (Polymerase Chain Reaction)-mediated mutagenesis of the 3' region of rpoB encoding the C-terminal 116 amino acids of beta, followed by the isolation and characterization of trans-dominant-negative mutations.

RESULTS

Substitutions of conserved residues in this region were obtained that exhibited different degrees of growth inhibition in a host expressing the chromosomal-encoded wild-type form of the beta subunit. A number of different substitutions were isolated within the highly conserved sequence motif GEME (residues 1271-->1274 of the E. coli beta subunit). In addition, substitutions were obtained in the extreme C-terminal (surface-exposed) region of beta and at two residues previously proposed to be in the active site (H1237, K1242). The properties of the purified mutant holoenzymes, assessed by transcription assays in vitro, suggested a promoter blockading action.

CONCLUSIONS

We have identified an important, highly conserved motif in the beta subunit, GEME (residues 1271-->1274). The nature and effect of the amino acid substitutions at the Gly residue in GEME emphasize the importance of a small, uncharged residue at this position. The in vitro properties of the most extreme trans dominant-negative mutants altered in the GEME motif (and the mutant characteristics in vivo) were similar to those of certain previously identified active-site mutants, suggesting that the altered RNA polymerases were capable of promoter binding and RNA chain initiation but were deficient in the subsequent transcriptional stage.

Identification of the sigma E subunit of Escherichia coli RNA polymerase: a second alternate sigma factor involved in high-temperature gene expression

The rpoH gene of Escherichia coli encodes sigma 32, the 32-kD sigma-factor responsible for the heat-inducible transcription of the heat shock genes. rpoH is transcribed from at least three promoters. Two of these promoters are recognized by RNA polymerase containing sigma 70, the predominant sigma-factor. We purified the factor responsible for recognizing the third rpoH promoter (rpoH P3) and identified it as RNA polymerase containing a novel sigma-factor with an apparent Mr of 24,000. This new sigma, which we call sigma E, is distinct from the known sigma factors in molecular weight and promoter specificity. sigma E holoenzyme will not recognize the sigma 70- or sigma 32-controlled promoters we tested, but it does transcribe the htrA gene, which is required for viability at temperatures greater than 42 degrees C. The in vivo role of sigma E is not known. The transcripts from the sigma E-controlled rpoH P3 and htrA promoters are most abundant at very high temperature, suggesting the sigma E holoenzyme may transcribe a second set of heat-inducible genes that are involved in growth at high temperature or in thermotolerance.

First committed step of lipid A biosynthesis in Escherichia coli: sequence of the lpxA gene

The min 4 region of the Escherichia coli genome contains genes (lpxA and lpxB) that encode proteins involved in lipid A biosynthesis. We have determined the sequence of 1,350 base pairs of DNA upstream of the lpxB gene. This fragment of DNA contains the complete coding sequence for the 28.0-kilodalton lpxA gene product and an upstream open reading frame capable of encoding a 17-kilodalton protein (ORF17). In addition there appears to be an additional open reading frame (ORF?) immediately upstream of ORF17. The initiation codon for lpxA is a GUG codon, and the start codon for ORF17 is apparently a UUG codon. The start and stop codons overlap between ORF? and ORF17, ORF17 and lpxA, and lpxA and lpxB. This overlap is suggestive of translational coupling and argues that the genes are cotranscribed. Crowell et al. (D.N. Crowell, W.S. Reznikoff, and C.R.H. Raetz, J. Bacteriol. 169:5727-5734, 1987) and Tomasiewicz and McHenry (H.G. Tomasiewicz and C.S. McHenry, J. Bacteriol. 169:5735-5744, 1987) have demonstrated that there are three similarly overlapping coding regions downstream of lpxB including dnaE, suggesting the existence of a complex operon of at least seven genes: 5'-ORF?-ORF17-lpxA-lpxB-ORF23-dnaE-ORF37-3 '.

Gene encoding the 37,000-dalton minor sigma factor of Bacillus subtilis RNA polymerase: isolation, nucleotide sequence, chromosomal locus, and cryptic function

We began an analysis of rpoF, the gene encoding the cryptic, 37,000-dalton minor sigma factor (sigma-37) of Bacillus subtilis RNA polymerase. Using antibody raised against sigma-37 holoenzyme to probe a lambda gt11 expression vector library, we isolated a 901-base-pair EcoRI fragment that expressed the COOH-terminal half of sigma-37 fused to lacZ. We used this fragment as a hybridization probe to isolate the entire rpoF gene and additional flanking sequences. Identity of the cloned gene was confirmed by the size and immunological reaction of its product expressed in Escherichia coli and, after DNA sequencing, by the homology of its predicted product (264 residues; 30,143 daltons) with other sigma factors. The DNA sequence also suggested that rpoF may lie in a gene cluster. Upstream of rpoF was an open reading frame that would encode a protein of 17,992 daltons; this frame overlapped the rpoF-coding sequence by 41 base pairs. Immediately following rpoF was a reading frame that would encode a protein of at least 20,000 daltons; expression of this region may be translationally coupled to that of rpoF. By plasmid integration and PBS1 transduction, we found the chromosomal locus of rpoF linked to ddl and dal at 40 degrees on the B. subtilis map and near no known lesions affecting growth regulation or development. Further, an rpoF null mutation resulting from gene disruption had no effect on cell growth or sporulation in rich medium, suggesting that sigma-37 may partly control a regulon not directly involved in the sporulation process.

Gene for the alpha subunit of Bacillus subtilis RNA polymerase maps in the ribosomal protein gene cluster

We isolated the gene encoding the alpha subunit of Bacillus subtilis RNA polymerase from a lambda gt11 expression vector library by using anti-alpha antibody as a probe. Four unique clones were isolated, one carrying a lacZ-alpha gene fusion and three carrying the entire alpha coding region together with additional sequences upstream. The identity of the cloned alpha gene was confirmed by the size and immunological reactivity of its product expressed in Escherichia coli. Further, a partial DNA sequence found the predicted NH2 terminus of alpha homologous with E. coli alpha. By plasmid integration and PBS1 transduction, we mapped alpha near rpsE and within the major ribosomal protein gene cluster on the B. subtilis chromosome. Additional DNA sequencing identified rpsM (encoding S13) and rpsK (encoding S11) upstream of alpha, followed by a 180-base-pair intercistronic region that may contain two alpha promoters. Although the organization of the alpha region resembles that of the alpha operon of E. coli, the putative promoters and absence of rpsD (encoding S4) immediately preceding the B. subtilis alpha gene suggest a different regulation.

Genetic analysis of two bacterial RNA polymerase mutants that inhibit the growth of bacteriophage T7

The Escherichia coli mutants 7009 and BR3 are defective in the growth of bacteriophage T7. We have previously shown that both of these mutant hosts produce an altered RNA polymerase which is resistant to inhibition by the T7 gene 2 protein (De Wyngaert and Hinkle 1979). In both strains, the mutation which prevents T7 growth is closely linked to rifA (rpoB). Both mutants are complemented by transformation with a multicopy plasmid carrying rpoB and rpoC but not by a plasmid carrying only rpoB. This indicates that the mutations reside in rpoC, the structural gene for the beta' subunit of RNA polymerase. When a single copy of the wildtype rpoC allele is introduced into the mutant using the transducing phage lambda drifd18, the mutant allele is dominant over wildtype. The lambda drifd18 transductant also remains unable to support the growth of T7 in the presence of rifampin. This supports our conclusion that the mutation is in rpoC. We have measured the growth of T7 phage, the kinetics of phage DNA synthesis, and the structure of replicative DNA intermediates in several transductants, and compared these results with those obtained in the original mutant strains.

An amber mutation in the gene encoding the beta' subunit of Escherichia coli RNA polymerase

An Escherichia coli strain carrying an amber mutation (UAG) in rpoC, the gene encoding the beta prime subunit of RNA polymerase, was isolated after mutagenesis with nitrosoguanidine. The mutation was moved into an unmutagenized strain carrying the supD43,74 allele, which encodes a temperature-sensitive su1 amber suppressor, and sue alleles, which enhance the efficiency of the suppressor. In this background, beta prime is not synthesized at high temperature. Suppression of the mutation by the non-temperature-sensitive amber suppressor su1+ yields a protein which is functional at all temperatures examined (30, 37, and 42 degrees C).

Direct measurement of absolute suppressor efficiency

We have devised a system for measuring the degree of translational readthrough past a nonsense mutation which is based upon the quantitation of the two translation products, the suppressed polypeptide and the nonsense fragment. The absolute efficiency of four different amber suppressors (Su1, Su2, Su3, and Su7) has been determined at two unique amber sites in the structural gene for the beta subunit of Escherichia coli RNA polymerase.

Isolation of a second rifamycin-binding from Escherichia coli by affinity chromatography

When extracts of Escherichia coli are filtered through a Sepharose column containing covalently bound rifamycin a protein is bound which can be eluted either with a high concentration of urea or more specifically with low concentrations of rifamycins. Its Mr is 18,000 +/- 1,000 in the presence of dodecylsulfate, in its absence 36,000 +/- 3,000. The association constant of the protein for rifampicin is 2.4 +/- 0.5 x 10(-4) M with two binding sites per dimer as determined by equilibrium dialysis. Large amounts of this protein are released from the cells by an osmotic shock.

Rescue of abortive T7 gene 2 mutant phage infection by rifampin

Infection of Escherichia coli with T7 gene 2 mutant phage was abortive; concatemeric phage DNA was synthesized but was not packaged into the phage head, resulting in an accumulation of DNA species shorter in size than the phage genome, concomitant with an accumulation of phage head-related structures. Appearance of concatemeric T7 DNA in gene 2 mutant phage infection during onset of T7 DNA replication indicates that the product of gene 2 was required for proper processing or packaging of concatemer DNA rather than for the synthesis of T7 progeny DNA or concatemer formation. This abortive infection by gene 2 mutant phage could be rescued by rifampin. If rifampin was added at the onset of T7 DNA replication, concatemeric DNA molecules were properly packaged into phage heads, as evidenced by the production of infectious progeny phage. Since the gene 2 product acts as a specific inhibitor of E. coli RNA polymerase by preventing the enzyme from binding T7 DNA, uninhibited E. coli RNA polymerase in gene 2 mutant phage-infected cells interacts with concatemeric T7 DNA and perturbs proper DNA processing unless another inhibitor of the enzyme (rifampin) was added. Therefore, the involvement of gene 2 protein in T7 DNA processing may be due to its single function as the specific inhibitor of the host E. coli RNA polymerase.

A cold-sensitive beta subunit mutant RNA polymerase from Escherichia coli with defects in promoter opening in vitro

A cold-sensitive mutation in the rpoB gene for the RNA polymerase beta subunit increasing the temperature of promoter opening on T2 phage DNA was obtained in Escherichia coli. The mutation also affects the stages preceding promoter opening by increasing the dissociation rate of RNA polymerase--DNA closed complexes. The affinity of RNA polymerase to T2 and lambda DNA is differentially changed by the mutation. The relative efficiency of transcription of these two templates is also changed. These results suggest a participation of the RNA polymerase beta subunit in the interaction with promoters.

Genetic analysis of Staphylococcus aureus RNA polymerase mutants

Spontaneous mutants of Staphylococcus aureus resistant to rifampin, rifamycin SV, streptovaricin, or streptolydigin were isolated and shown to be resistant due to chromosomal rather than plasmid mutations. Based on data concerning spontaneous mutation rates, genetic cotransduction rates, and in vitro sensitivity studies, four major antibiotic cross-resistance patterns were found. The genetic markers responsible for these cross-resistance patterns were shown to be separable by transduction. Nonpurified RNA polymerase activity in lysates of mutants showed the same sensitivity to these antibiotics as shown by the mutants on solid media. A model is proposed explaining possible structure-function relationships involved in the binding of these antibiotics to the RNA polymerase molecule and the mutations resulting in resistance to these antibiotics. This model includes generally overlapping but different-sized binding sites on the RNA polymerase protein coded for by similarly arranged mutable sites on the DNA.

Over-synthesis and instability of sigma protein in a merodiploid strain of Escherichia coli

We have used two different methods to study the rates of RNA polymerase subunit synthesis in haploid Escherichia coli K12, and a KLF10 rPOB, C+ merodiploid derivative, when grown in glucose-minimal medium at 37 degrees C. Our results indicate that the haploid strain produces beta, beta', alpha and sigma in the molar ratios 1.01:0.99: less than or equal to 2.90:0.26; and that all these subunits are reasonably stable during subsequent growth. The merodiploid produces alpha at the same rate as the haploid, beta and beta' at a 42% higher rate, and sigma at twice the rate. Some 40% of the newly synthesised beta and beta' is degraded within one hour; the residuum is as stable as in the haploid. Alpha is stable throughout. By contrast, sigma is subject to a marked and continuous turnover in the merodiploid. These results are discussed in terms of gene dosage and regulatory effects.

Transformation of Escherichia coli by a specific DNA restriction fragment

Specific transformation of a rifampicin sensitive strain of Escherichia coli to rifampicin resistance has been performed by a single, defined DNA restriction fragment carrying the genetic information for the beta subunit of E. coli RNA polymerase. In this transformation the transforming genetic character has been substituted for the corresponding recipient gene locus by recombination. The value of the described transformation system for locating genetic markers on DNA restriction fragments is discussed in comparison to previously reported in vitro systems.

Lipiarmycin-resistant ribonucleic acid polymerase mutants of Bacillus subtilis

Lipiarmycin inhibited the activity of deoxyribonucleic acid-dependent ribonucleic acid (RNA) polymerase in vitro. We showed that inhibition was due to interference by lipiarmycin with the activity of sigma-containing molecules of RNA polymerase. Transcription by core enzyme was relatively resistant to the drug, but addition of sigma led to highly drug-sensitive RNA synthesis. We isolated lipiarmycin-resistant mutants of Bacillus subtilis and characterized them genetically and biochemically. Drug-resistant mutants contained an altered RNA polymerase that was resistant to the drug in vitro. By separation and mixed reconstitution of core and sigma fractions of mutant and wild-type RNA polymerase, we showed that lipiarmycin resistance in one mutant strain was a property of the core fraction. Genetic mapping experiments indicated that at least two lpm mutants are located between loci determining rifampin resistance and streptolydigin resistance.

Fine-structure mapping of the firA gene, a locus involved in the phenotypic expression of rifampin resistance in Escherichia

The firA (Ts)200 mutation not only eliminates the resistance to rifampin of certain genetically resistant strains, but, moreover, renders ribonucleic acid synthesis thermolabile. The firA gene has been mapped by P1 tranduction and is located extremely close to the structural gene for deoxyribonucleic acid polymerase III at 4 min on the Escherichia coli linkage map.

The firA gene, a locus involved in the expression of rifampicin resistance in Escherichia coli. II. Characterisation of bacterial proteins coded by lambdafirA transducing phages

The firA gene probably codes for an essential component of the transcription machinery in E. coli. Bacterial proteins coded by lambdafirA transducing phages have been examined after infection of a UV-irradiated lambda lysogen, and 2 major fir-specific proteins have been characterized. The larger protein has a molecular weight of 27,000 daltons. The smaller protein, of 17,000 daltons, is produced in a considerable molar excess over the larger protein, is basic and binds strongly to DNA-, to DEAE- and to phospho-cellulose. This protein is clearly visible upon 2-dimensional gel electrophoresis of unfractionated E. coli protein, showing that it is present in the cell in large quantities. Evidence is presented to suggest that this protein may be identical to the Kappa factor of Schäfer and Zillig (1973).

The firA gene, a locus involved in the expression of rifampicin resistance in Escherichia coli. I. Characterisation of lambdafirA transducing phages constructed in vitro

The firA200 mutation of E. coli not only renders RNA synthesis thermosensitive but also eliminates the high-level resistance to rifampicin associated with certain mutations in the beta subunit of the RNA polymerase. A priori, the firA gene is likely to code for an essential component of the transcription apparatus. The isolation is reported of transducing phages for the firA gene, constructed in vitro by fusing fragments of the E. coli chromosomes into a lambdoid bacteriophage. Such phages carry at least two essential genes and are able to suppress both the thermosensitivity and abnormal rifampicin sensitivity associated with the firA200 allele. The finding that some, but not all, of the lambdafirA phages have a temperature dependent growth defect is discussed.

Identification of an amber fragment of the beta subunit of Escherichia coli RNA polymerase: a yardstick for measuring controls on RNA polymerase subunit synthesis

An amber fragment of the beta subunit of Escherichia coli RNA polymerase has been recovered from strains carrying the rpoB12 amber mutation, indicating that the B12 mutation resides in the structural gene for the beta subunit. The fragment is readily assayed and can be used to determine the degree of expression of a single rpoB cistron in strains haploid or diploid for this region. These studies confirm that the bacterial mechanism, which can compensate for reduced translation of the beta message, operates by the co-ordinate induction of rpoB and rpoC. Furthermore, I show that rpo control depends upon cistron(s) located on the F' factor, KLF10, whose product(s) can act negatively in trans on rpoBC expression.

DNA blockade by rifampicin-inactivated Escherichia coli RNA polymerase, and its amelioration by a specific mutation

1. Partially diploid strains of Escherichia coli containing both rifampicin-sensitive and rifampicin-resistant RNA polymerase are, in general, sensitive to the drug: of the two copies of the rpoB gene present in such strains, that which codes for sensitive enzyme is dominant. 2. RNA polymerase purified from a normal sensitive strain of E. coli, and inactivated by rifampicin, can "blockade" bacteriophage T7 DNA in vitro, inhibiting its transcription by drug-resistant enzyme molecules. 3. A mutation, rcs-40, reverses the normal dominance relationship in vivo, without detectably affecting the concentrations of resistant and sensitive RNA polymerase in the diploid cell. I show that rcs-40 is closely linked to the rpoB gene which codes for the rifampicin-sensitive enzyme. 4. Rifampicin-sensitive RNA polymerase purified from E. coli rcs-40, although indistinguishable from the normal enzyme by many criteria, is significantly less efficient in the production of drug-dependent DNA blockade.

Temperature-sensitive ribonucleic acid polymerase mutant of Salmonella typhimurium with a defect in the beta' subunit

Localized mutagenes of Salmonella typhimurium followed by a [3H]uridine enrichment procedure yielded a temperature-sensitive strain with a mutation in the rpo region of the chromosome. Ribonucleic acid (RNA) polymerase (EC 2.7.7.6; nucleoside triphosphate: RNA nucleotidyltransferase) purified from this mutant was considerably less active at the nonpermissive temperature than wild-type enzyme. Furthermore, the enzyme from this mutant, unlike RNA polymerase of previously isolated temperature-sensitive mutants, was as thermostable as wild-type enzyme when preincubated at 50 degrees C. Subunit reconstitution experiments have shown that the temperature sensitivity is caused by an alteration in the beta' subunit of the enzyme.