Interaction of RNA polymerase from Escherichia coli with DNA. Influence of DNA scissions on RNA-polymerase binding and chain initiation

Redefining fundamental concepts of transcription initiation in bacteria

Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.

Transcription of adenovirus 2 DNA by human RNA polymerase II in vitro

The interaction of Adenovirus 2 DNA and human placental RNA polymerase II in vitro satisfies criteria that suggest that at least some fraction of our purified polymerase preparations corresponds to prokaryotic holoenzyme and is able to initiate transcription at "true" promoters: (1) The purified enzyme forms highly stable complexes at specific sites on Ad 2 DNA; Kass = 1--2 X 10(12) M-1. (2) Transcription of Ad 2 DNA from pre-formed complexes with human RNA polymerase II is resistant to poly I. (3) Many of the stable-binding sites correspond to Ad 2 promoters known to be active in vivo. We also present evidence consistent with a two-state (I and RS) model (Chamberlin et al. 1976; Travers 1974) for the interaction of human RNA polymerase II with Ad 2 DNA. These experiments, which are similar to those described previously in studies of wheat germ RNA polymerase II (Seidman et al. 1979), indicate that the mechanisms of transcription inhibition and promoter site selection in eukaryotic and prokaryotic systems may be very similar.

Purification of a low molecular weight non-histone chromosomal protein

A non-histone chromosomal proteins was extracted from rat liver chromatin with 0.35 M NaCl and purified more than 2758 times to near homogeneity by hydroxyapatite, gel filtration, and phosphocellulose chromatography. The final fraction was greater than 95% pure as judged by non-denaturing gel electrophoresis. The protein, designated loosely bound non-histone chromosomal protein 1, had an observed molecular weight of 15 700. This protein was demonstrated to increase the amount of RNA synthesized in a heterologous (Escherichia coli RNA polymerase) transcription system and, therefore, this activity was also used to monitor its purification. The availability of highly purified loosely bound non-histone chromosomal protein 1 will make possible an examination of its structural and/or functional role in chromatin.

The molecular topography of RNA polymerase-promoter interaction

Ultraviolet irradiation forms covalent crosslinks between E. coli RNA polymerase and the lac UV5 promoter substituted with bromouracil in the place of thymine. I have determined the polymerase subunit and the base within the promoter sequence that are joined to each other in two such crosslinks. The sigma and beta subunits of RNA polymerase, respectively, are crosslinked to the third base upstream (-3) and the second base downstream (+3) from the starting point of transcription (+1). Both bases are on the nontemplate strand of the promoter DNA. The location of the beta subunit suggests that it forms at least part of the catalytic site of the enzyme. The disposition of sigma suggests that this subunit plays a direct role in unwinding the DNA at the promoter. The sigma crosslink is close to the "Pribnow Box," which is centered about 10 bases upstream from the RNA start site, contains a striking homology between promoters and is the locus of many promoter mutations.

Studies on liver chromatin RNA from rats treated with alkylating agents

We have examined firstly some properties of rat liver chromatin RNA and nuclear sap RNA and secondly the incorporation of [3H]orotic acid into the RNA in vivo in control rats and in rats treated with the alkylating agents, N,N-dimethylnitrosamine or methyl methane sulphonate. Half or more of the nuclear RNA is associated with the chromatin and consists mainly of two species: one is labelled and probably comprises "nascent" RNA, and the other is unlabelled and of lower molecular weight. Neither species is attributable to cytoplasmic contamination. Studies with added polylysine with RNAase A and with DNAase I suggest that both species are ironically bound to protein and that the labelled species is not associated with the part of the chromatin DNA most readily degraded by DNAase I. After dimethylnitrosamine treatment, the amount of unlabelled RNA remains constant but the amount of labelled RNA increases after a low dose, and decreases after a high dose. After methyl methane sulphonate treatment, no change occurs in either species. These results can be explained by changes in extent of association of the DNA and protein within the chromatin complex.

On the initiation of mammalian RNA polymerase at single-strand breaks in DNA

Mammalian RNA polymerase B is able to initiate at single-strand breaks in the DNA template. A 3'-OH end at a nick is required for initiation whereas the 5'-end may be either -- OH or phosphate. The 3'-OH group does not function as a primer. An appreciable part of the newly synthesized RNA started at a nick remains associated with the DNA in hydrid form. Initiation of exogeneous RNA polymerase B on chromatin exhibits similar requirements.

DNA-dependent RNA polymerase C from Xenopus laevis ovaries. Ability to transcribe intact double-stranded DNA

DNA-dependent RNA polymerase C, partially purified from Xenopus laevis ovaries, has been resolved by DEAE-Sephadex chromatography in two forms, eluting at 0.2 M and 0.3 M ammonium sulfate, respectively. Both are sensitive to high concentrations of alpha-amanitin (200 mug/ml). Their ionic strength dependence and divalent cation requirements are indistinguishable. Quantitatively, RNA polymerase C represents the major form of RNA polymerase activity solubilized from the ovaries. Both RNA polymerases C are able to transcribe efficiently either high-molecular-weight Xenopus DNA or intact adenovirus DNA, as compared to nicked DNA. In contrast, RNA polymerase A has little activity on an intact DNA template. The salt dependence of the RNA polymerases C activity is different on the two kinds of template. Nicked DNA is efficiently transcribed up to a salt concentration of 100 mM ammonium sulfate. On intact DNA, optimal transcription is obtained at 40 mM ammonium sulfate and is inhibited by higher salt concentrations.

Influence of DNA acidification on DNA premelting and template properties

Acidification of a T7 DNA sample was found to be partly irreversible as ultraviolet difference spectra measured at various sub-melting temperatures were different from those observed for a 'normal' DNA sample. This implies some subtle conformational change which is not reversed by return to neutral pH. In the same conditions, only poly(purine)-poly(pyrimidine) polymers behaved in a different manner, during premelting, according to whether they were previously acidified or not. The properties of acidified and reneutralized T7 DNA were also investigated for Escherichia coli RNA polymerase binding and transcription. An inhibition of RNA synthesis and chain initiation was observed. The results suggest that the binding of the enzyme is affected. RNA synthesized is specific but there is a decrease in the number and in the stability of the RNA-polymerase-DNA complexes.

Interaction of RNA polymerase from Escherichia coli with DNA. Analysis of T7 DNA early-promoter sites

A method was devised for directing RNA polymerase on a single promoter site on T7 DNA. Initiation complexes were formed on each of the three main promoter sites using one dinucleotide plus one nucleoside triphosphate. The ternary initiation complexes are resistant to rifampicin action, to inhibition by (rI)n at 0 degrees C and are stable at high salt concentrations. A minimum of a trinucleotide is required to form a stable ternary complex. To determine which promoter site was selected by RNA polymerase during initiation, the (rI)n-resistant RNA was digested by RNAse III to generate three characteristic initiator RNA fragments, resolved by gel electrophoresis. The three major promoter sites could be selected individually by using different primer and substrate combinations ApC plus ATP selected promoter A3, CpG plus CTP selected A2 and CpC plus ATP specified preferentially A1. A number of primer-substrate combinations specified each site at low salt concentration but the substrate requirement became very stringent at high salt concentration, suggesting that the postulated local opening of the promoter site could be more or less extensive, depending on the ionic strength. The minimum opening observed at high salt concentration corresponded to the insertion of a leader trinucleotide sequence. The promoter region melted by RNA polymerase at low salt concentration was (G plus C)-rich and corresponded to about 9 to 11 base pairs. Sequences of the melting recognition regions were tentatively inferred from the results.

Structure and transcription specificity of yeast RNA polymerase A

DNA-dependent RNA polymerase A (Nucleosidetriphosphate: RNA nucleotidyltransferase, EC 2.7.7.6) was isolated from whole yeast cells and purified to a nearly homogeneous state. The subunit structure as well as the transcription specificity of the purified enzyme were investigated. Polyacrylamide gel electrophoresis under denaturating conditions revealed that yeast polymerase A is made up of two large subunits having mol. wts of 190 000 and 135 000, and five smaller subunits with mol. wts of 54 000, 44 000, 35 000, 25 000 and 16 000, respectively. The molar ratios of all these polypeptides were found to be about unity. The transcription specificity of yeast polymerase A was tested using homologous nuclear DNA as a template. The in vitro synthesized RNA was characterized by determining its degree of self-complementarity and its ability to compete with purified ribosomal RNA in hybridization experiments. It was found that yeast polymerase A is capable of a highly selective transcription in vitro of the rRNA cistrons, provided DNA of high integrity is used as a template.

Difference in the action of ethyl and methyl methane sulfonates on DNA template activity for RNA synthesis in vitro

RNA produced in vitro from alkylated T7 DNA has been characterized by polyacrylamide gel electrophoresis. Methylation of T7 DNA by methyl methane sulfonate reduces RNA chain length. In contrast, ethylation of T7 DNA by ethyl methane sulfonate, while reducing RNA synthesis to the same extent, does not alter chain length.

DNA-dependent RNA polymerase from Pseudomonas BAL-31. II. Transcription of the allomorphic forms of bacteriophage PM2 DNA

Transcription of the supercoiled form (I) and the relaxed circular form (II) of bacteriophage PM2 DNA was studied utilizing the DNA-dependent RNA polymerase from its host, Pseudomonas BAL-31. Transcription of both templates is continuous for up to 2 hr, but proceeds at a two-fold higher rate on I than on II. This difference is mainly due to a 2.2-fold higher rate of chain initiation on I. When rifampicin (Rif) is added ater 10 min of synthesis, (1) transcription of II ceases by 30 min with a maximum product length of 7000 nucleotides (number average) being produced; (2) transcription of I continues with little rate reduction and with the product reaching 16,000 nucleotides (number average) by 2 hr. Sucrose gradient analysis shows that the product of II achieves maximum size 20 min after Rif addition and sediments in three peaks of 24, 33, and 39 S (approximately one-third, two-thirds, and one genome lengths). The product of I has a heterogeneous distribution and grows continuously with a large fraction reacting greater than 3 genome lengths by 90 min. The same differences in synthesis kinetics, Rif inhibition, and product size distribution are observed when I and II are transcribed by Escherichia coli RNA polymerase. These experiments show that (i) PM2 form I DNA is transcribed mainly by a process of continuous chain elongation, with little chain termination occurring; (ii) PM2 form II is transcribed by a process of continuous chain initiation, elongation, and termination of yield discrete products. Thus, the tertiary structure of circular DNA influences chain termination by RNA polymerase.

Template specificity of transcription during sporulation of Bacillus subtilis

Partially purified extracts from sporulating Bacillussubtilis cultures transcribed different natural DNAs with different efficiencies. This template specificity results in an increased or a decreased synthetic activity with respect to extracts from vegetative cells, depending on the template used. With SPP1 DNA a decrease in activity occurs, whereas with T7 DNA an increased activity was observed, which is due to a higher efficiency of initiation. This is not an intrinsic property of RNA polymerase, but is due to some fraction(s) which can be separated from the enzyme. Together with invivo experiments on transcription and SPP1 phage production during sporulation, these results suggest a possible role of promoter recognition in sporulation.