RNA polymerase from phage SP01-infected and uninfected Bacillus subtilis

Validation of Omega Subunit of RNA Polymerase as a Functional Entity

The bacterial RNA polymerase (RNAP) is a multi-subunit protein complex (α2ββ’ω σ) containing the smallest subunit, ω. Although identified early in RNAP research, its function remained ambiguous and shrouded with controversy for a considerable period. It was shown before that the protein has a structural role in maintaining the conformation of the largest subunit, β’, and its recruitment in the enzyme assembly. Despite evolutionary conservation of ω and its role in the assembly of RNAP, E. coli mutants lacking rpoZ (codes for ω) are viable due to the association of the global chaperone protein GroEL with RNAP. To get a better insight into the structure and functional role of ω during transcription, several dominant lethal mutants of ω were isolated. The mutants showed higher binding affinity compared to that of native ω to the α2ββ’ subassembly. We observed that the interaction between α2ββ’ and these lethal mutants is driven by mostly favorable enthalpy and a small but unfavorable negative entropy term. However, during the isolation of these mutants we isolated a silent mutant serendipitously, which showed a lethal phenotype. Silent mutant of a given protein is defined as a protein having the same sequence of amino acids as that of wild type but having mutation in the gene with alteration in base sequence from more frequent code to less frequent one due to codon degeneracy. Eventually, many silent mutants were generated to understand the role of rare codons at various positions in rpoZ. We observed that the dominant lethal mutants of ω having either point mutation or silent in nature are more structured in comparison to the native ω. However, the silent code’s position in the reading frame of rpoZ plays a role in the structural alteration of the translated protein. This structural alteration in ω makes it more rigid, which affects the plasticity of the interacting domain formed by ω and α2ββ’. Here, we attempted to describe how the conformational flexibility of the ω helps in maintaining the plasticity of the active site of RNA polymerase. The dominant lethal mutant of ω has a suppressor mapped near the catalytic center of the β’ subunit, and it is the same for both types of mutants.

Bacillus subtilis RNA polymerase and its modification in sporulating and phage-infected bacteria

Bacillus subtilis RNA polymerase holoenzyme consists of the subunits beta', beta, sigma, alpha, delta, and omega. In sporulating bacteria and in bacteria infected with phages SP01 and SP82, this enzyme undergoes changes in subunit composition and transcriptional specificity that could play a regulatory role in gene transcription. Sporulating bacteria may contain a specific component that inhibits the activity of the sigma subunit of polymerase probably by interfering with the binding of sigma-polypeptide to core enzyme. The hypothetical inhibitor may be metabolically unstable, since its activity is rapidly depleted from sporulating cells in the presence of chloramphenicol. Inhibition of sigma-polypeptide activity may restrict the transcription of phage DNA an infected sporulating cells. Although lacking the sigma-subunit, RNA polymerase purified from sporulating cells contains sporulation-specific subunits of 85,000 and 27,000 daltons. In SP01-infected bacteria, the sigma-subunit is replaced by phage-induced subunits. Purified enzyme containing the protein product of SP01 regulatory gene 28 directs the transcription of phage middle genes in vitro, while enzyme containing phage-induced polypeptides V and VI preferentially copies late genes. Accurate transcription of middle and late genes in vitro requires the host delta-subunit of polymerase (or high ionic strength) but not sigma-subunit. Phage PBS2 induces an entirely new multisubunit RNA polymerase that specifically transcribes PBS2 DNA in vitro. This enzyme is synthesized de novo after infection and does not arise by modification of the B. subtilis holoenzyme.

The evolving story of the omega subunit of bacterial RNA polymerase

Omega (omega) is the smallest subunit of bacterial RNA polymerase (RNAP). Although identified early in RNAP research, its function remained ambiguous and shrouded by controversy for a considerable period. It has subsequently been shown that the protein has a structural role in maintenance of the conformation of the largest subunit, beta', and recruitment of beta' to the enzyme assembly. Conservation of this function across all forms of life indicates the importance of its role. Several recent observations have suggested additional functional roles for this protein and have settled some long-standing controversies surrounding it. In this context, revisiting the omega subunit story is especially interesting; here, we review the progress of omega research since its discovery and highlight the importance of these recent observations.

Isolation and characterization of the Bacillus subtilis sigma 28 factor

RNA polymerase preparations isolated from vegetatively growing Bacillus subtilis cells contain the core subunits beta, beta', and alpha, together with multiple sigma factors and other core-associated polypeptides such as delta, omega 1, and omega 2. We have developed an improved, large-scale purification procedure that yields RNA polymerase fractions enriched in both the sigma 28 and delta proteins. These fractions have been used to isolate sigma 28 protein for biochemical characterization and for preparation of highly specific anti-sigma 28 antisera. The amino acid composition of purified sigma 28 protein and the amino acid sequences of tryptic peptide fragments have been determined. Anti-sigma 28 antisera specifically inhibit transcription by the purified sigma 28 -dependent RNA polymerase, yet do not affect transcription by sigma 43 -dependent RNA polymerase. Immunochemical analysis confirms that the sigma 28 protein copurifies with total RNA polymerase activity through the majority of the purification procedure and allows the steps when sigma 28 protein is lost to be identified and optimized. Immunochemical techniques have also been used to monitor the structure and abundance of the sigma 28 protein in vivo. A single form of antibody-reactive protein was detected by two-dimensional gel electrophoresis-isoelectric focusing. Its abundance corresponds to a maximal content of 220 molecules of sigma 28 per B. subtilis cell during late-logarithmic-phase growth.

The cloning and sequence of the gene encoding the omega subunit of Escherichia coli RNA polymerase

Omega is a small protein found associated with Escherichia coli RNA polymerase. The role of omega, if any, in transcription is not known. We have cloned the omega-encoding gene (rpoZ) so that we can produce large amounts of omega by over-production and to introduce mutations in its gene. We determined the N-terminal amino acid (aa) sequence of omega by aa microsequencing. Using the sequence we synthesized an eight-fold ambiguous 14-mer oligodeoxynucleotide probe and screened an E. coli genomic library using the base composition independent method of hybridization reported by Wood et al. [Proc. Natl. Acad. Sci. USA 82 (1985) 1585-1588]. With this method we isolated a clone that contained part of rpoZ which we used as a probe to isolate the complete gene. The sequence of the region containing the rpoZ gene predicts a highly charged protein of 91 aa with an Mr of 10 105. In addition, upstream from the gene is a good promoter-like sequence. We have verified by S1 mapping that in vivo transcripts originate from this promoter and possibly from a second promoter farther upstream.

Bacteriophage SPO1 DNA polymerase and the activity of viral gene 31

Bacteriophage SPO1 DNA-negative (D0) mutants were tested for the induction of viral DNA polymerase during Bacillus subtilis infection. Extracts from SPO1-infected bacteria exhibited enzymatic activity when representative mutants of seven out of the nine known D0 genes were employed. This activity was undetectable in cells infected with mutants in genes 28 and 31. The product of gene 28 (gp28) is known to be responsible for turning on SPO1 middle gene expression. Results show that nonsense mutation in gene 31 leads to the absence of a single polypeptide of 100-105 kDa and that phage DNA synthesis "in vivo" directly depends on gp31 activity. Based on these data it is proposed that SPO1 gene 31 codes for the viral DNA polymerase.

Bacteriophage SPO1 genes 33 and 34. Location and primary structure of genes encoding regulatory subunits of Bacillus subtilis RNA polymerase

Bacteriophage SPO1 gene 33 and 34 products are required for SPO1 late gene transcription. Both proteins bind to the core RNA polymerase of the Bacillus subtilis host to direct the recognition of SPO1 late gene promoters, whose sequences differ from those of SPO1 early and middle gene promoters. We have located and cloned the genes for these two regulatory proteins, and have engineered their expression in Escherichia coli by placing them under the control of the bacteriophage lambda PL promoter. Nucleotide sequence analysis indicated that genes 33 and 34 overlap by 4 base-pairs and encode highly charged, slightly basic proteins of molecular weight 11,902 and 23,677, respectively.

Transcriptional regulation of bacteriophage SPO1 protein synthesis in vivo and in vitro

There are six classes of SPO1 transcripts which are, at least partially, regulated independently of each other. Analysis of proteins made in infections by phage mutants defective in DNA synthesis, or in genes which positively control transcription, permitted each protein to be assigned to one transcription class. Most of the late proteins belong to transcription class m2l. There seem to be few, if any, phage proteins in the l class whose mRNA synthesis depends absolutely on phage DNA synthesis, UV irradiation of host cells allowed the detection of many additional early proteins. The early proteins detected in vivo were compared with proteins synthesized in vitro, using bacterial or gp28 phage-modified RNA polymerase in an Escherichia coli cell-free system. Proteins characterized in vivo as belonging to the e transcription class could be made efficiently in vitro only when transcription was performed by bacterial RNA polymerase. em proteins could be elicited through the use of either bacterial or gp28 polymerase, indicating that their genes can be transcribed in either the early or the middle mode.

The localization of SPO1 phage resistance in the genome of Bacillus subtilis as revealed by fusion of protoplasts

We localized the gene for resistance to phage SPO1 relatively to the markers pur B 34 and ura by means of the polyethylene-glycol induced fusion of bacterial protoplasts of three-fold auxotrophic Bacillus subtilis strains S3 and S13. By this same method, the site of some auxotrophic markers was tentatively determined. The application of the protoplast fusion technique to exact genetic analysis will not be possible until the exo- and endogenous factors influencing cell wall regeneration are standardized. Fluctuations of this kind are very significant for the determination of genetic segregation.

Effects of the positively regulating product of gene 28 of the B. subtilis phage SPO1 on in vitro transcription

Some of the properties of the RNA polymerase purified from SPO1-infected Bacillus subtilis have been compared with the properties of RNA polymerase from uninfected cells (core + sigma). The two enzymes synthetize RNA from nonoverlapping regions on SPO1 DNA, and they lead to the retention of different restriction fragments of SPO1 DNA on cellulose-nitrate filters. The action of the positively regulating product of gene 28 of SPO1 (gp 28) has been analyzed. The isolated gp 28 has been shown to be unable to increase the dissociation rate of core + sigma from SPP1 DNA, while it efficiently blocks the initiation of RNA synthesis if it is added to performed complexes between core + sigma and SPP1 DNA in 0.2 M NaCl.

Template-independent poly(A) x poly(U) synthesizing activity of different forms of Bacillus subtilis RNA polymerase

Several, but not all, forms of bacillus subtilis RNA polymerase found in vegetative and sporulating cells can synthesize poly(A) x poly(U) in vitro. The vegetative delta-containing form of RNA polymerase (E delta) has little or no poly(A) x poly(U)-synthesizing activity, whereas RNA polymerase core (E) and sigma-containing core (E delta) both have significant activity. When purified vegetative delta factor was added to core, the core synthetic activity was reduced essentially to that of the vegetative enzyme E delta. When E sigma enzymes from vegetative and sporulating cells were compared for their salt sensitivity, it was found that the sporulation enzyme E sigma retained much more of its activity at 0.1 M KCl than the vegetative enzyme E sigma. Furthermore, when sporulation enzyme E delta 1 was compared with vegetative enzyme E sigma, it was found that the activity of the E sigma 1 form was much more resistant to high KCl concentrations than that of the vegetative E sigma form. These differences in enzyme activity, as affected by salt concentrations, suggest that the conformations of the sporulation E sigma and E delta 1 enzymes are different from that found in vegetative E sigma enzyme. These differences in conformation may be involved in selective gene expression during sporularion.

Novobiocin blocks the shutoff of SPO1 early transcription

Novobiocin, an inhibitor of bacterial DNA gyrase strongly impairs the development of bacteriophage SPOl. DNA replication seems to be the primary target for the antibiotic in this system, but viral-coded transcription is also affected in several aspects: (a) The level of phage transcription is diminished; (b) the shutoff of the synthesis of early RNA classes is inhibited; (c) RNAs of late class are not synthesized. This last effect is a consequence of the coupling between transcription and replication. The other two results could be taken as an indication that the appropriate secondary structure of the parental phage DNA is a requisite for the recognition of promoters. The introduction of negative turns by DNA gyrase seems to make early genes unavailable for transcription.

Purification and DNA-binding properties of RNA polymerase from Bacillus subtilis

Four RNA-polymerizing activities having different subunit composition can be purified from uninfected and from SPO1-infected Bacillus subtilis. Lysozyme and sodium deoxycholate are used for lysing the cells. Polymin P is used for precipitating nucleic acids and DEAE-cellulose chromatography allows separation of enzymatic activity from the residual Polymin P. After these common steps, one can purify core + sigma + delta by chromatography on single-stranded DNA-agarose followed by gel filtration while pure core + sigma can be obtained by chromatography on double-stranded DNA cellulose. Core + delta is obtained by high-salt sucrose/glycerol gradient centrifugation. The host enzyme modified by the product of gene 28 of phage SPO1 can be purified from SPO1 infected cells by chromatography on DNA cellulose (or CNA agarose) followed by chromatography on phosphocellulose. The pH and salt dependance of the initial rate of RNA synthesis of core + sigma has been investigated using SPO1 and SPP1 DNA as templates. The optimum pH for the initial rate of transcription is 8.2 at 30 degrees C in 50 mM N,N-bis(2-hydroxyethyl)glycine buffer, and the optimum Na+ concentration is between 0.1 and 0.15 M. The kinetics of formation and of dissociation of non-filterable complexes between SPP1 DNA and core + sigma have been analyzed at different cationic concentrations. The value of the rate constant of dissociation in 0.1 M NaCl at 30 degrees C is kd = 2.16 x 10(-4) S-1. The value of the rate constant of association, under the same conditions, is ka = 5.5 x 10(8) M-1 S-1; this value is compatible with a diffusion-controlled reaction for promoter selection.

The nature of transcription selectivity of bacteriophage SPO1-modified RNA polymerase

Escherichia coli and Bacillus subtilis RNA polymerase have almost identical transcription specificities on bacteriophage SPO1 DNA when assayed in a coupled transcription-translation cell free system. SPO1-modified B. subtilis RNA polymerase has altered transcription specificity. It is shown that rifampicin-inhibited E. coli RNA polymerase can completely block transcription of SPO1 DNA by rifampicin resistant B. subtilis enzyme, whereas it has no effect on transcription by SPO1-modified B. subtilis RNA polymerase. We conclude that the new transcription by SPO1-modified RNA polymerase results from newly recognized promoters, rather than by elongation of transcripts which could also be made by B. subtilis vegetative RNA polymerase.

Utilization of promoter and terminator sites on bacteriophage T7 DNA by RNA polymerases from a variety of bacterial orders

The transcriptional properties of bacterial RNA polymerases purified from seven different species and representing a variety of bacterial orders have been studied using the well characterized DNA from phage T7 as template. The subunit composition of the different preparations suggests that each RNA polymerase holoenzyme has a promoter structure (betabeta'alpha2sigma) similar to that of the well studied E. coli and B. subtilis enzymes. Each enzyme utilizes DNA from bacteriophage T7 as an effective template for RNA synthesis, although all preparations contain a substantial fraction of inactive enzyme. Electrophoretic analysis of the RNA products made with the different RNA polymerases in vitro using T7 DNA (deletion mutant deltaD111) as template reveals that with minor exceptions, all of the heterologous RNA polymerases utilize the same collection of promoter sites on T7 used by the E. coli host enzyme, and only those promoter sites. The T7 early terminator is also efficiently utilized by each enzyme. Since the different bacterial species from which the RNA polymerases were derived are genetically quite distant, it appears that there is a structural element in the promoter which governs its recognition and which is universally recognized among RNA polymerases of different bacterial species. While the different bacterial RNA polymerases generally utilize the same set of T7 promoter sites, the efficiency of utilization of the different promoters varies considerably for different RNA polymerases and for different reaction conditions with the same RNA polymerase. Hence although the several T7 promoter sites share the ability to be recognized by bacterial RNA polymerases, each shows a unique pattern of utilization and therefore must possess a unique element of promoter structure as well. It has previously been shown (Stahl and Chamberlin, 1977) that T7 promoters A1, C, D and E interact differently with E. coli RNA polymerase as judged by the properties of complexes formed between each promoter and the latter enzyme. Since competition takes place among different promoter sites on a template and since these sites can differ functionally, small changes in reaction conditions or in the structure of the RNA polymerase can lead to significant changes in the rate of utilization of different promoter sites even when these promoter sites share common elements. Because the T7 promoters and terminator are utilized efficiently by such a wide range of RNA polymerases and because each of the several T7 promoters possesses unique properties which govern its utilization by RNA polymerase, analysis of the transcripts formed on a T7 DNA template provides a simple and rapid procedure for detecting and analyzing alterations in bacterial RNA polymerases which affect promoter or terminator recognition or utilization.

RNA polymerase mutant with altered sigma factor in Escherichia coli

A structural gene for sigma factor (rpoD) of DNA-dependent RNA polymerase (RNA nucleotidyltransferase; nucleoside-triphosphate: RNA nucleotidyltransferase, E.C. 2.7.7.6) was mapped precisely by a set of F' factors including those already published (Proc. Natl. Acad. Sci. USA. 74, 1831-1835 (1977)). Based on the result that rpoD is located at the dnaG-uxaAC region, a number of mutants containing a temperature-sensitive mutation at or near the uxaA gene were isolated by localized mutagenesis. One of these mutants was found to produce RNA polymerase altered in both thermostability and optimum salt concentration as a result of structural alteration of sigma factor. This mutation, U303, maps at 66 min on the genetic map of E. coli, near the dnaG locus, and affects normal growth of cells.

Delta factor can displace sigma factor from Bacillus subtilis RNA polymerase holoenzyme and regulate its initiation activity

A protein with a molecular weight of 21,000 daltons is found associated with a fraction of Bacillus subtilis RNA polymerase core. This protein (delta) does not react with antibody made against sigma factor and has a peptide map which is significantly different from sigma factor. At ratios of 2:1 to 4:1 (delta:holoenzyme) the delta displaces sigma factor completely from the core and associates in a 1:1 ratio with core to form delta-core. Under the same incubation conditions sigma factor at a ratio of 10:1 (sigma factor:delta-core) does not displace delta from the delta-core. The delta-core has much less activity as compared to holoenzyme on various DNA templates. However, sigma factor does stimulate the activity of delta-core enzyme under conditions of RNA synthesis. These observations and the results of others suggest that delta-core enzyme binds initially to specific DNA sites followed by delta release from the core-DNA complex and that the sigma factor binds to the core-DNA complex to initiate RNA synthesis. Thus both delta and sigma factors are required in a sequential fashion for specific transcription to occur in B subtilis.

Purification of a positive regulatory subunit from phage SP01-modified RNA polymerase

A phage-induced subunit has been purified from phage SP01-modified Bacillus subtilis RNA polymerase. This subunit binds in vitro to RNA polymerase core from uninfected B. subtilis thereby template-selective transcription and asymmetric synthesis of SP01 middle RNA.

Purification and comparative properties of the delta and sigma subunits of RNA polymerase from Bacillus subtilis

Bacillus subtilis delta protein is a 21 500-Mr polypeptide that can be isolated in association with RNA polymerase holoenzyme from uninfected bacteria and with modified forms of RNA polymerase from cells infected with phage SP01 [Pero, J., Nelson, J. and Fox, T. (1975) Proc. Natl Acad. Sci. U.S.A. 72,1589]. Although no function has been assigned to delta protein in uninfected cells, this host polypeptide enhances the specificity of transcription by phage-modified forms of RNA polymerase that contain SP01-coded regulatory subunits. This report describes the purification of delta and sigma proteins from uninfected B. subtilis and examines the comparative effects of these polypeptides on transcription by core RNA polymerase. Purified sigma polypeptide was found to stimulate the transcription of phage DNA while having little effect on RNA synthesis with the synthetic DNA poly(dA-dT) as template. In contrast, purified delta protein markedly depressed the transcription of poly(dA-dT) while having little effect on enzyme activity with phage DNA as template. The inhibitory effect of delta protein on poly (dA-dT) transcription was strongly dependent on the presence of KC1 in the RNA synthesis reaction mixture.

Two polypeptides associated with the ribonucleic acid polymerase core of Bacillus subtilis during sporulation

The ribonucleic acid (RNA) polymerase from log-phase and sporulating cells of Bacillus subtilis was analyzed to determine whether any structural changes occurred during sporulation. The elution pattern of RNA polymerase from a deoxyribonucleic acid (DNA)-cellulose column revealed that sporulating cells at stages III and IV contained a new RNA polymerase fraction in addition to the vegetative holoenzyme (alpha2betabeta'sigma). Stage III cells contained the vegetative holoenzyme and a new enzyme with the composition alpha2betabeta'delta1; the molecular weight of delta1 was 28,000. Stage IV cells contained the vegetative holoenzyme, the delta1-containing enzyme, and another enzyme with the composition alpha2betabeta'delta2. The delta2 factor had a molecular weight of around 20,000. The delta-containing enzymes have a higher affinity for the DNA-cellulose column and a higher specific activity on various templates than vegetative holoenzyme. The simultaneous appearance of these enzymes with vegetative holoenzymes in sporulating cells is consistent with the data found previously with DNA-RNA hybridization studies, which showed that sporulating cells contained both vegetative and sporulation messenger RNAs.