The virus-specified subunits of a modified B. subtilis RNA polymerase are determinants of DNA binding and RNA chain initiation

Genetic and physiological studies of Bacillus subtilis sigma A mutants defective in promoter melting

The Bacillus subtilis sigA gene encodes the primary sigma factor of RNA polymerase and is essential for cell growth. We have mutated conserved region 2.3 of the sigma A protein to substitute each of seven aromatic amino acids with alanine. Several of these aromatic amino acids are proposed to form a melting motif which facilitates the strand separation step of initiation. Holoenzymes containing mutant sigma factors recognize promoters, but some are defective for DNA melting in vitro. We have studied the ability of each mutant sigma factor to support cell growth by gene replacement and complementation. The two region 2.3 mutants least impaired in promoter melting in vitro (Y180A and Y184A) support cell growth in single copy, although the Y184A allele imparts a slow-growth phenotype at low temperatures. A strain expressing only the Y189A variant of the sigma A protein, known to be defective in DNA melting in vitro, grows very slowly and is altered in its pattern of protein synthesis. Only the wild-type and Y180A sigma A proteins efficiently complement a temperature-sensitive allele of sigA. Overexpression of three of the sigma A proteins defective for promoter melting in vitro (Y189A, W192A, and W193A) leads to a decrease in RNA synthesis and cell death. These results indicate that mutations which specifically impair DNA melting in vitro also impair sigma function in vivo and therefore support the hypothesis that sigma plays an essential role in both DNA melting and promoter recognition.

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.

SP01 gene 27 is required for viral late transcription

The SP01 mutant sus HA20 (gene 27) was found to be defective for synthesis of viral late RNA. It is known that gene 27 is also required for viral DNA replication. The SP01 gene 27 product resembles the T4 gene 45 product, which also has a dual role in viral DNA replication and late 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.

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.