Subunits of RNA polymerase in function and structure; Maturation in vitro of core enzyme from Escherichia coli

Free sigma subunit of Bacillus subtilis RNA polymerase binds to DNA

The affinity of Bacillus subtilis RNA polymerase sigma and delta subunits to DNA was examined by a non-denaturing polyacrylamide slab gel electrophoresis method which made it possible to resolve DNA-bound and free subunits. The results revealed that sigma subunit, but not delta subunit had a relatively high affinity for double stranded DNA. The sigma subunit was bound maximally to super-coiled pGR1-3 plasmid DNA at a mass ratio of sigma/DNA of 0.7. With B. subtilis double stranded linear DNA one sigma subunit was bound per approximately 1,000 base pairs. The sigma-DNA complex was sufficiently stable for isolation by a molecular gel filtration column. The sigma subunit had much higher affinity for super-coiled than for linear pGR1-3 DNA or for linear double stranded or denatured DNA from B. subtilis, E. coli, and calf thymus. These results indicate that the free B. subtilis sigma subunit, in contrast to the E. coli sigma subunit, can bind by itself to DNA.

Amber mutations in the structural gene for RNA polymerase sigma factor of Escherichia coli

Amber mutants of Escherichia coli K-12 affected in the structural gene (rpoD) for the sigma subunit of RNA polymerase have been obtained from a strain harboring a temperature-sensitive amber suppressor (supF-Ts6) which is active only at low temperatures. These mutants grow normally at low temperature (30 degrees C) but do not grow at high temperature (42 degrees C) due to the inability to synthesize sigma factor. In one mutant studied in detail (rpoD40), the rate of sigma-factor synthesis at 30 degrees C is about half that of the wild type and is decreased to 10%-15% within 1 h of incubation at 42 degrees C. The synthesis of core polymerase subunits or bulk protein is virtually unaffected at least for 2 h. The defect of the mutant in sigma synthesis and growth at high temperature can be suppressed by any of the amber suppressors tested (supD. supE or supF). RNA-polymerase holoenzymes prepared from the mutant cells carrying each of the suppressors (grown at 42 degrees C) exhibit different thermostabilities attributable to alterations in the sigma factor. The reduced sigma synthesis in the mutant is accompanied by the synthesis of polypeptide tentatively identified as 'amber fragment'. These results as well as the genetic mapping data indicate that the amber mutation (rpoD40) resides within the structural gene for the sigma factor and directly affects sigma synthesis upon inactivation of the suppressor at high temperature.

Antibodies against the subunits of E. coli RNA polymerase as probes for subunit-specific binding of DNA and other ligands

Antibodies against the isolated subunits alpha, beta, and beta' of DNA-dependent RNA polymerase from E. coli have been prepared. They have been used to compare the extent of antibody-binding, as measured by complement fixation, to the isolated subunits and to the intact enzyme, in the absence and presence of ligands, such as inhibitors, nucleotides, nucleosides, oligo- and poly-nucleotides, and DNA of different composition. In many cases the results show a subunit-specific dependence of complement fixation upon the presence of a ligand and suggest a functional topography of the interaction between the subunits alpha, beta, and beta' of RNA polymerase and defined nucleotide sequences and small ligands.

Affinity labeling of a cysteine at or near the catalytic center of Escherichia coli B DNA-dependent RNA polymerase

9-beta-D-Arabinofuranosyl-6-thiopurine was used to affinity label DNA-dependent RNA polymerase isolated from Escherichia coli B. This substrate analogue displayed competitive type inhibition which could be reversed by addition of a thiol reagent, such as dithiothreitol, while exposure to hydrogen peroxide, a mild oxidizing agent, caused an increase in both the inhibitory and enzyme binding capability of arabinofuranosyl thiopurine. Chromatographic analysis of the products obtained by pronase digestion of the 9-beta-D-arabinofuranosyl-6-[35S]thiopurine-enzyme complex suggests that disulfide bond formation occurs between the inhibitor and a cysteine residue located in or near the active center of the enzyme. In addition, polyacrylamide gel electrophoresis indicated that the arabinofuranosyl thiopurine moeity was bound to the beta' subunit of the enzyme.

Multiple effects of an RNA polymerase beta' mutation on in vitro transcription

S. tyrphimurium strain BY324 is temperature sensitive due to a mutation (rpo C32) in the gene for the RNA polymerase beta' subunit. Transcription of T7 DNA by RNA polymerase purified from this strain is temperature sensitive in vitro. The enzyme is slightly defective in template binding and RNA chain initiation, but the major defect is in RNA chain elongation. The rate of RNA chain elongation is reduced 4-5 fold relative to wild-type. RNA chain termination does not appear to be affected by the beta' mutation. While the elongation defect is suppressed by glycerol or dimethylsulfoxide, the initiation defect is not. Possible roles for the beta' subunit in enzyme function are discussed in light of these results.

Altered synthesis and stability of RNA polymerase holoenzyme subunits in mutants of Escherichia coli with mutations in the beta or beta' subunit genes

Bacteria with specific temperature sensitive lethal mutations in the gene for the beta' subunit of RNA polymerase synthesize both the beta and beta' subunits at a several fold higher rate at 42 degrees C than wild-type cells relative to total protein. Synthesis of the alpha and sigma subunits proceeds at essentially the wild-type rates under these conditions. In contrast, a mutant with a temperature sensitive lethal mutation in the beta subunit gene synthesizes beta and beta' at 42 degrees C at slightly lower rates than wild-type, while alpha and sigma synthesis is not significantly altered. In all of the mutants at 42 degrees C, newly synthesized alpha subunits are stable, while the beta, beta' and sigma subunits are rapidly degraded. The apparent uncoupling of betabeta' and alpha subunit synthesis seen in the beta' mutants at 42 degrees C might suggest that the synthesis of these subunits is at least in part controlled by different mechanisms.

Conversion of Escherichia coli RNA polymerase to a template independent enzyme

Preparations of RNA polymerase (E.C.2.7.7.6) from uninfected Escherichia coli, T4 infected Escherichia coli, and Acinetobacter calcoaceticus when centrifuged in sucrose gradients in the absence of magnesium ions gave rise to five peaks, all of which were able to form polymers from ribonucleoside 5'-triphosphates in the absence of template or primer. All of the peaks obtained from the Escherichia coli enzyme appeared to contain the subunit alpha and beta and, in addition, polypeptides which appeared to be derived from the subunit beta.

On the kinetics of the rifampicin-RNA-polymerase complex. Differences between crude and purified enzyme fractions

The antibiotic rifampicin forms a very tight complex with DNA-dependent RNA polymerase of Escherichia coli. The rate constants of association and dissociation of this complex have been measured and found to be dependent on the purity of the enzyme. Thus a crude RNA polymerase (fraction-3 enzyme) has rate constants different from those of an enzyme further purified by DEAE-cellulose chromatography (fraction-4 enzyme). The complex produced by the antibiotic and the fraction-3 enzyme is about ten times more stable and is formed about ten times more slowly than the complex with fraction-4 enzyme. It has been shown that the RNA present in the crude enzyme and removed by chromatography on DEAE-cellulose is the cause of the change in the kinetics of the complex. tRNA of rat liver and crude rat liver RNA added to purified RNA polymerase have a similar effect. Mg2+, which has no intrinsic influence, augments the effect of the nucleic acids, whereas monovalent cations do not. Since nucleic acids increase the stability of the complex, but at the same time decrease the rat of its formation, the equilibrium constant, Keq, remains almost the same. The possible effects of nucleic acids on the rifampicin binding site are discussed.

Peptide analysis of RNA polymerase alpha subunit from Escherichia coli: comparison of free with assembled form

The analysis of tryptic peptides was performed on the unassembled as well as assembled form f alpha subunit of the DNA-dependent RNA polymerase from Escherichia coli. The peptide profiles obtained by Dowex 50 column chromatography of the unassembled alpha subunit prepared from cells, either pulse-labeled or continuously labeled with radioactive lysine or arginine, were essentially identical with those of the alpha subunit from intact RNA polymerase. The results suggest that newly synthesized free alpha subunit is assembled into the polymerase structure without any remarkable modifications. The number of lysine- and arginine-containing peaks were close to the values expected from the amino acid composition of alpha subunit assuming that the two alpha subunits in RNA polymerase core enzyme have identical primary structure.

The reconstitution of Anacystis nidulans DNA-dependent RNA polymerase from its isolated subunits

The DNA-dependent RNA polymerase of the blud-green alga Anacystis nidulans was reconstituted from its isolated subunits in the absence of urea. Applying this technique the kinetics and the subunit requirements of the reconstitution process were analyzed. The results reveal differences with respect to the reconstitution of Escherichia coli polymerase. Reconstitution proceeds much more slowly in the case of the A. nidulans enzyme. Reconstitution here is absolutely dependent on the presence of the subunit sigma. On the other hand, the largest of the subunits of Mr=190000 can be fully substituted by a specific degradation product of this subunit of Mr=175000. Heterologous reconstitution between subunits of E. coli and A. nidulans polymerase does not result in active enzyme hybrids, showing a divergent evolution of the structure of this enzyme in these procaryotic organisms.

Digestion with matrix-bound proteases as a possible probe for the topography of the DNA-dependent RNA polymerase from Escherichia coli

DNA-dependent RNA polymerase lacking subunit sigma was digested with matrix-bound chymotrypsin or trypsin in the presence of 0.4 M NaCl in the monomeric form or at low ionic strength in the oligomeric form. Sigma-containing polymerase was digested in the same way. The course of proteolysis was followed by polyacrylamide gel electrophoresis after dissociation of the enzyme with detergent into subunits and the fragments produced by the hydrolysis. The following results were obtained. (a) The large subunits beta and beta' are cleaved with a much higher rate in the monomeric than in the oligomeric polymerase. (b) Both large subunits are hydrolysed with the same rate. (c) Subunit alpha is hydrolysed almost with the same rate in the monomeric and oligomeric form of polymerase. (d) The same was found for subunit sigma. (e) These effects were independent of the substrate specificity of the protease used. (f) Subunit sigma is much more susceptible to chymotrypsin than to trypsin. (g) Subunit sigma protects the large subunits beta and beta' against tryptic cleavage. These results can be explained in terms of a tentative model for the topography of the protomer-protomer interactions in RNA polymerase. According to this model subunits beta and beta' contain two sites for isologous interactions of protomers. One site can be blocked by attachment of subunit sigma. Subunits alpha and sigma do not participate directly in the association.