Purification of Bacillus subtilis RNA polymerase with heparin-agarose. In vitro transcription of phi 29 DNA

Rapid preparation of 6S RNA-free B. subtilis σA-RNA polymerase and σA

The regulatory 6S-1 and 6S-2 RNAs of B. subtilis bind to the housekeeping RNA polymerase holoenzyme (σ^A-RNAP) with submicromolar affinity. We observed copurification of endogenous 6S RNAs from a published B. subtilis strain expressing a His-tagged RNAP. Such 6S RNA contaminations in σ^A-RNAP preparations reduce the fraction of enzymes that are accessible for binding to DNA promoters. In addition, this leads to background RNA synthesis by σ^A-RNAP utilizing copurified 6S RNA as template for the synthesis of short abortive transcripts termed product RNAs (pRNAs). To avoid this problem we constructed a B. subtilis strain expressing His-tagged RNAP but carrying deletions of the two 6S RNA genes. The His-tagged, 6S RNA-free σ^A-RNAP holoenzyme can be prepared with sufficient purity and activity by a single affinity step. We also report expression and separate purification of B. subtilis σ^A that can be added to the His-tagged RNAP to maximize the amount of holoenzyme and, by inference, in vitro transcription activity.

The structural basis of XRCC1-mediated DNA repair

Scaffold proteins play a central role in DNA repair by recruiting and organizing sets of enzymes required to perform multi-step repair processes. X-ray cross complementing group 1 protein (XRCC1) forms enzyme complexes optimized for single-strand break repair, but participates in other repair pathways as well. Available structural data for XRCC1 interactions is summarized and evaluated in terms of its proposed roles in DNA repair. Mutational approaches related to the abrogation of specific XRCC1 interactions are also discussed. Although substantial progress has been made in elucidating the structural basis for XRCC1 function, the molecular mechanisms of XRCC1 recruitment related to several proposed roles of the XRCC1 DNA repair complex remain undetermined.

Purification, characterization, and gene expression of all sigma factors of RNA polymerase in a cyanobacterium

The expression of RNA polymerase (RNAP) sigma factor genes and proteins was characterized as a first step toward understanding their functions in a unicellular cyanobacterium Synechocystis sp. PCC 6803, which can perform photosynthesis. All nine sigma factors (group 1, SigA; group 2, SigB to SigE; and group 3, SigF to SigI) and each RNAP core subunit (RpoA, RpoB, RpoC1 and RpoC2) were overproduced and purified from Escherichia coli cells, then polyclonal antibodies were prepared. Western blot and primer extension analyses revealed that the intracellular levels of group 1 and 2 sigma factors ranged from 0.9 fmol to 9.3 fmol per microgram of the total protein under conditions of steady-state growth, and that growth phase-dependent or constitutive transcripts were observed. Interestingly, no group 3 sigma factor proteins were detected under normal physiological conditions whereas their transcripts were robust, implying a possible regulation of translational attenuation and/or protein instability. Phylogenetic analysis also revealed that group 3 sigma factor homologues of cyanobacteria are conserved with evolutionary or functionary divergence among them. In vitro and in vivo results indicated significant evidence of high-light responsive SigD expression and its promoter recognition of the photosynthesis gene, psbA. On the other hand, autoregulated sigB transcription, a dramatically increased SigB expression upon the exposure of cells to heat-shock, and specific promoter recognition by SigB with redundancy of other sigma factors on the heat-shock hspA promoter were observed. These findings clearly indicated that SigB is a heat-shock responsive sigma factor. The unique promoter architecture and expression of the relevant sigma factor gene are also discussed herein.

The herpes simplex virus type 1 origin-binding protein. sequence-specific activation of adenosine triphosphatase activity by a double-stranded DNA containing box I

Origin-dependent replication of the herpes simplex virus type 1 genome requires the virally encoded origin-binding protein, UL9. UL9 binds specifically to the herpes simplex virus type 1 replication origin at two high affinity binding sites on the DNA, Boxes I and II. UL9 also has ATP-dependent DNA helicase and DNA-stimulated ATPase activities that are used to unwind the origin DNA. Origin-specific binding is mediated by the C-terminal domain (C-domain) of the enzyme. ATPase and helicase activities are mediated by the N-terminal domain (N-domain). Previous studies have shown that single-stranded DNA is a good coeffector for ATPase activity. We have analyzed several DNAs for their ability to stimulate the ATPase activity of UL9 and of a truncated UL9 protein (UL9/N) consisting only of the N-domain. We report here that duplex Box I DNA specifically and potently stimulates the ATPase activity of UL9 but not of UL9/N. We also find that removal of the C-domain significantly increases the ATPase activity of UL9. We have incorporated these results into a model for initiation in which the C-domain of UL9 serves to regulate the enzymatic activity of the N-domain.

Identification and characterization of a stress-responsive promoter in the macromolecular synthesis operon of Bacillus subtilis

Bacillus subtilis DB1005 is a temperature-sensitive (Ts) sigA mutant. Induction of sigmaA has been observed exclusively in this mutant harbouring extra copies of the plasmid-borne Ts sigA gene transcriptionally controlled by the P1P2 promoters of the B. subtilis macromolecular synthesis (MMS; rpoD or sigA) operon. Investigation of the mechanisms leading to the induction has allowed us to identify a sigmaB-type promoter, P7, in the MMS operon for the first time. Therefore, at least seven promoters in total are responsible for the regulation of the B. subtilis MMS operon, including the four known sigmaA- and sigmaH-type promoters, as well as two incompletely defined promoters. The P7 promoter was activated in B. subtilis after the imposition of heat, ethanol and salt stresses, indicating that the MMS operon of B. subtilis is subjected to the control of general stress. The significant heat induction of P7 in B. subtilis DB1005 harbouring a plasmid-borne Ts sigA gene can be explained by a model of competition between sigmaA and sigmaB for core binding; very probably, the sigmaB factor binds more efficiently to core RNA polymerase under heat shock. This mechanism may provide a means for the expression of the B. subtilis MMS operon when sigmaA becomes defective in core binding.

The temperature sensitivity of Bacillus subtilis DB1005 is due to insufficient activity, rather than insufficient concentration, of the mutant delta A factor

The delta A factor of Bacillus subtilis DB1005 contains two amino acid substitutions (I198A and I202A) in the promoter-10 binding region. It has been confirmed that this delta factor is responsible for the temperature sensitivity of B. subtilis DB1005. An investigation was conducted into how the mutant delta A could cause temperature-sensitive (Ts) cell growth by analysing its structural stability, cellular concentration and transcriptional activity. The mutant delta A was unstable even at the permissive temperature of 37 degrees C (t1/2 59 min), whereas the wild-type counterpart was fairly stable under the same conditions (t1/2 > 600 min). However, neither wild-type delta A nor mutant delta A was stable at 49 degrees C (t1/2 34 min and 23 min, respectively). Analyses of the rates of delta A synthesis revealed that B. subtilis DB1005 was able to compensate for unstable delta A by elevating the level of delta A at 37 degrees C but not at 49 degrees C. Moreover, overexpression of the mutant delta A at 49 degrees C could not suppress the Ts phenotype of B. subtilis DB1005. This indicates that the temperature sensitivity of B. subtilis DB1005 is not due to insufficient delta A concentration in the cell. The greater decline of an already reduced activity of the mutant delta A at 49 degrees C suggests that the temperature sensitivity of B. subtilis DB1005 is instead the result of a very low activity of delta A; probably below a critical level necessary for cell growth.

Characterization of the primary sigma factor of Staphylococcus aureus

RNA polymerase (RNAP) isolated from Staphylococcus aureus is deficient in sigma factor and is poorly active in transcription assays. Based on amino acid sequence homology of the Bacillus subtilis vegetative sigma factor sigmaA and the predicted product of the chromosomally located plaC gene of S. aureus, it was hypothesized that plaC could encode the vegetative sigma factor. We cloned plaC under a T7 promoter and overexpressed it in Escherichia coli strain BL21(DE3)pLysE. The overproduced protein, present in inclusion bodies, was solubilized with guanidine hydrochloride, renatured, and purified by DEAE-Sephacel and Sephadex G-75 chromatography. The purified protein, designated sigmaSA, cross-reacted with the B. subtilis anti-sigmaA antibody. E. coli core RNAP, reconstituted with sigmaSA, initiated promoter-specific transcription from the S. aureus promoters hla, sea, and sec and from the E. coli promoters rpoH P1, rpoH P4, and ColE1 RNA-1, which are recognized by the E. coli sigma70. sigmaSA, when added to the purified RNAP from S. aureus, stimulated transcriptional activity of the RNAP up to 72-fold. As determined by primer extension studies, the 5'-ends of the sigmaSA-initiated mRNAs synthesized in vitro from the agr P2 and sea promoters are in general agreement with the 5'-ends of the cellular RNAs. Disruption of the plaC gene on the S. aureus chromosome was lethal. We conclude that plaC encodes the primary sigma factor in S. aureus.

Immobilization of heparin on polyacrylamide derivatives

Heparin was coupled via its carboxyl group with a polyacrylamide derivative containing covalently bound amino groups using the carbodiimide reaction. Heparin immobilized in this way proved to be useful as an affinity carrier for the isolation of antithrombin III and heparin-binding proteins from boar seminal plasma.

The response of a Bacillus subtilis temperature-sensitive sigA mutant to heat stress

The mutant sigA allele of Bacillus subtilis DB1005 was confirmed to be temperature sensitive (ts) and transferable among strains of B. subtilis by chromosomal transformation and gene conversion. This ts sigA allele had a pleiotropic effect on gene expression of DB1005. The induction of certain heat shock proteins in DB1005 was markedly less significant than that observed in the wild-type strain (DB2) under heat stress. In contrast, some proteins required for coping with oxidative stress and glucose starvation were induced abruptly in DB1005 but not in DB2. Heat induction of the groEL gene in vivo at both transcription and translation levels was much lower in DB1005 than in DB2. Besides, the putative sigma A-type promoter from the groESL operon of B. subtilis was able to be transcribed by the reconstituted sigma A RNA polymerase in vitro at both 37 and 49 degrees C. These results strongly suggest that the expression of the groEL gene of B. subtilis under heat stress is regulated at least in part by sigma A at the level of transcription. Our results also showed that DB1005 did not respond too differently from the wild type to ethanol stress, except after a relatively long exposure.

Isolation of DNA-dependent RNA polymerase from the thermophilic actinomycete Thermomonospora curvata

DNA-Dependent RNA polymerase (EC 2.7.7.6) was isolated from Thermomonospora curvata. The purification steps included precipitation with Polymin P, elution of the precipitate with 0.3 mol/L KCl, precipitation with ammonium sulfate, affinity chromatography on heparin-agarose and molecular filtration on Biogel A 1.5 m.

Protein expression from an Escherichia coli/Bacillus subtilis multifunctional shuttle plasmid with synthetic promoter sequences

A plasmid shuttle vector (pSP10) was designed and constructed to simplify screening of cloned DNA and to facilitate expression of the protein products. The plasmid contained the following features: (i) a selection gene, chloramphenicol acetyltransferase; (ii) an indicator gene encoding beta-galactosidase for visual identification of colonies containing DNA inserts; (iii) a cloning region immediately upstream from the indicator gene; (iv) origins of replication recognized by both Escherichia coli and Bacillus subtilis; and (v) a synthetic DNA expression control sequence, including -35 and -10 regions, ribosomal binding site, and transcriptional and translational start sites. The promoter region is a synthetic consensus sequence derived from published B. subtilis promoters. The plasmid has been shown to replicate actively in E. coli and B. subtilis and to confer chloramphenicol resistance to both hosts. DNA inserted at the cloning region inactivates the indicator gene, resulting in white colonies on 5'-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside plates. beta-Galactosidase has been expressed from pSP10 in both E. coli and B. subtilis. A comparison was made of the expression levels of beta-galactosidase from the same plasmid which had been modified to contain: (i) the synthetic control region, (ii) no promoter region, (iii) the synthetic control region cloned in the opposite orientation, or (iv) the tac promoter.

Bacillus subtilis early sporulation genes kinA, spo0F, and spo0A are transcribed by the RNA polymerase containing sigma H

The Bacillus subtilis genes kinA (spoIIJ), spo0F, and spo0A encode components of the sporulation signal transduction pathway. Recent work has suggested that these genes are transcribed by a minor form of RNA polymerase, E sigma H (sigma H is the product of spo0H, another early sporulation gene). We directly tested this hypothesis by performing in vitro transcription assays with reconstituted E sigma H and a set of plasmids containing the kinA, spo0F, and spo0A promoter regions. We were able to obtain distinct transcripts of the expected sizes with all three genes by using linearized or supercoiled templates. Furthermore, primer extension experiments indicate that the transcription start sites for the three genes in vitro and in vivo are the same. In addition, we measured steady-state levels of kinA, spo0F, and spo0A mRNAs during growth in sporulation medium; all of them were increased at or near the beginning of the stationary phase.

Separation of Escherichia coli RNA polymerase sigma-70 holoenzyme from core enzyme on heparin-Sepharose columns

A method is described for the rapid purification of DNA-dependent RNA polymerase sigma-70 holoenzyme from Escherichia coli. The essential step in this protocol involves the differential elution of sigma-70 holoenzyme from core polymerase on a heparin-Sepharose column. Using a linear gradient of KCl, holoenzyme was found to elute at 0.25 M whereas core polymerase eluted at 0.35 M. From 20 g of cells, up to 1 mg of RNA polymerase holoenzyme could be isolated in two days. The preparations were greater than 95% pure with respect to protein, and saturated with the sigma subunit.

Analysis of an mRNA exhibiting anomalous translational specificity

Gene 6 mRNA of Bacillus subtilis phage phi 29 is inefficiently translated under standard in vitro conditions by Escherichia coli, while it is efficiently translated by the in vitro system derived from B. subtilis. This is a rare example of the inability of E. coli to translate mRNA translated by B. subtilis. The ionic condition in the translation systems was the key component in the differential recognition of the gene 6 message by E. coli and B. subtilis ribosomes. Its translation by E. coli ribosomes was preferentially inhibited by moderate levels of KCl, while its translation by B. subtilis ribosomes was unaffected by these concentrations of salt. This preferential inhibition with E. coli ribosomes was observed in vitro as well as in vivo. While not influencing the general phenomenon of preferential inhibition, anion-specific effects were observed in overall protein synthesis. Glutamate and acetate promoted efficient synthesis over a broad range of concentrations, whereas chloride was inhibitory at all concentrations tested.

A novel protein binds a key origin sequence to block replication of an E. coli minichromosome

A sequence of three tandem repeats of a 13-mer in the replication origin (oriC) of E. coli is the highly conserved site of opening of the duplex for initiation of DNA synthesis. A protein that binds this sequence has been discovered in E. coli and purified to homogeneity. This novel 33 kd polypeptide behaves as a dimer. Binding to the 13-mers is specific and limited to this region. At a ratio of 10-20 monomers per oriC plasmid, the binding blocks initiation by preventing the opening of the 13-mer region by dnaA protein. Once the 13-mers are opened by dnaA protein action, the 33 kd protein is without effect on the subsequent stages of replication. The specificity of binding and profound inhibitory effect suggest a regulatory role for this protein at an early stage of chromosome initiation.

In vitro transcription of the plasma protein genes of Bombyx mori

An efficient cell-free transcription system was developed from the extract of BmN cells established from an ovarian tissue of the silkworm, Bombyx mori. The cloned genes coding for major plasma proteins of B. mori including SP 1, SP 2 and 30K protein, were faithfully and efficiently transcribed in the extract prepared from BmN cells. The S1 nuclease mapping and primer extension analyses demonstrated that the transcription initiation site recognized in vitro is identical to that which functions in vivo. The transcription assay reconstituted from the fractionated BmN cell extract revealed that at least four protein factors are required for accurate transcription of the SP 1 and adenovirus major late genes. The results of in vitro transcription experiments employing a series of the 5' deleted mutant templates of the SP 1 gene indicated that partial deletion of the TATA box results in considerable loss of faithful transcript, while complete removal of the TATA-sequence totally abolishes the transcript. These observations suggest that the promoter element essential for transcription in cell-free systems is located in a region between nucleotide positions -44 and +16 of the SP 1 gene.

Overproduction, purification, and characterization of Bacillus subtilis RNA polymerase sigma A factor

By use of a T7 expression system, large amounts of active Bacillus subtilis RNA polymerase sigma A factor were produced in Escherichia coli cells. This overproduced protein was found in the form of inclusion bodies and constituted 40% of the total cellular protein. Because of the ease of isolation of the inclusion bodies and the acidic properties of sigma A, the protein was purified to more than 99% purity and the yield was about 90 mg/liter of culture. Gel mobility, antigenicity, specificity of promoter recognition, and N-terminal amino acid sequence of the overproduced sigma were found to be the same as those of native sigma A. Partial proteolysis analysis of sigma A protein suggested the presence of a protease-sensitive surface region in the C-terminal part of the sigma A protein. The promoter -10 binding region of sigma A was less sensitive to proteases and was probably involved in a hydrophobic, tightly folded domain of sigma A protein.

Inhibition of transcription of cytosine-containing DNA in vitro by the alc gene product of bacteriophage T4

The alc gene product (gpalc) of bacteriophage T4 inhibits the transcription of cytosine-containing DNA in vivo. We examined its effect on transcription in vitro by comparing RNA polymerase isolated from Escherichia coli infected with either wild-type T4D+ or alc mutants. A 50 to 60% decline in RNA polymerase activity, measured on phage T7 DNA, was observed by 1 min after infection with either T4D+ or alc mutants; this did not occur when the infecting phage lacked gpalt. In the case of the T4D+ strain but not alc mutants, this was followed by a further decrease. By 5 min after infection the activity of alc mutants was 1.5 to 2.5 times greater than that of the wild type on various cytosine-containing DNA templates, whereas there was little or no difference in activity on T4 HMdC-DNA, in agreement with the in vivo specificity. Effects on transcript initiation and elongation were distinguished by using a T7 phage DNA template. Rifampin challenge, end-labeling with [gamma-32P]ATP, and selective initiation with a dinucleotide all indicate that the decreased in vitro activity of the wild-type polymerase relative to that of the alc mutants was due to inhibition of elongation, not to any difference in initiation rates. Wild-type (but not mutated) gpalc copurified with RNA polymerase on heparin agarose but not in subsequent steps. Immunoprecipitation of modified RNA polymerase also indicated that gpalc was not tightly bound to RNA polymerase intracellularly. It thus appears likely that gpalc inhibits transcript elongation on cytosine-containing DNA by interacting with actively transcribing core polymerase as a complex with the enzyme and cytosine-rich stretches of the template.

Drosophila P element transposase recognizes internal P element DNA sequences

Drosophila P transposable elements encode an 87 kd trans-acting protein, transposase, that is required to catalyze P element transposition and excision. We show here that purified transposase is a site-specific DNA binding protein. P element transposase does not interact with the terminal 31 bp inverted repeats but instead interacts specifically with an internal 10 bp consensus sequence present at both the 5' and 3' ends of P element DNA. These binding sites lie within sequences known to be important for transposition in vivo. Transposase also displays an unusually high nonspecific affinity for DNA. The transposase binding site at the 5' and overlaps sequences we show to be essential for transcription from the P element promoter in vitro, which raises the possibility that either transposase or the related 66 kd P element protein may affect P element transcription. From these and other observations, we suggest that the P element transposition reaction probably requires the binding of additional Drosophila protein factors to the terminal DNA sequences.

Identification of subunits of gonococcal RNA polymerase by immunoblot analysis: evidence for multiple sigma factors

Heparin-agarose and single-stranded DNA-cellulose chromatography were used to purify RNA polymerase 25-fold from Neisseria gonorrhoeae, and the activity of the polymerase was characterized in altered assay systems. The core subunits (beta, beta', and alpha) were tentatively identified as major proteins copurifying with polymerase activity. The identification of the core subunits was confirmed by Western (immunoblot) analysis with polyclonal antisera to Escherichia coli core RNA polymerase. Gonococcal sigma factor heterogeneity was examined by Western blot analysis with polyclonal antiserum to the major E. coli sigma factor, sigma 70, to the E. coli heat shock sigma factor, sigma 32, and with a monoclonal antiserum to Salmonella typhimurium NtrA (sigma 54). Purified RNA polymerase and whole-cell extracts from type 1, type 4, heat-shocked, and anaerobically grown gonococci were examined. Four putative gonococcal sigma factors were detected in purified RNA polymerase preparations and in whole-cell extracts from all cell types. Two of these bands appeared as a doublet, which had an estimated Mr of 80,000. A single lower-Mr band, estimated to be 40,000, was also present. All three of these bands reacted with antisera to E. coli sigma 70 and to E. coli sigma 32. A fourth gonococcal protein reacted solely with a highly specific monoclonal antibody to sigma 54 and had an Mr of 90,000. We conclude that N. gonorrhoeae may contain multiple sigma factors, which it may use to regulate gene expression.

Bacillus subtilis subtilisin gene (aprE) is expressed from a sigma A (sigma 43) promoter in vitro and in vivo

In vitro studies demonstrated that the Bacillus subtilis subtilisin gene (aprE) could be transcribed by RNA polymerase holoenzyme reconstituted from core and sigma A factor obtained from vegetative cells. Upstream deletions (from -45) reduced the amount of transcription from the promoter. A deletion downstream of the promoter that overlapped a putative downstream minor promoter did not affect transcription from the sigma A promoter, which indicated that the putative downstream promoter is not utilized in vivo. S1 nuclease mapping studies showed that there was a low level of transcription from the subtilisin promoter during the growth phase and that the site of transcription initiation was the same during log and stationary phases. We conclude from these findings that there is only one promoter for the subtilisin gene and that it can be transcribed by the sigma A form of RNA polymerase in vitro.

Purification, immunoassay, and tissue distribution of rat C1-tetrahydrofolate synthase

C1-tetrahydrofolate synthase (C1-THF synthase), a eukaryotic trifunctional enzyme, catalyzes three sequential folate-mediated one-carbon interconversions. These three reactions supply the activated one-carbon units required in the metabolism of purines, thymidylate, and several amino acids. In order to study the regulation of C1-THF synthase expression in mammals, we have purified the enzyme to homogeneity from rat liver, raised polyclonal antisera to it in rabbits, and developed a sensitive solid-phase immunoassay for the enzyme. The enzyme was purified approximately 600-fold to a specific activity of 24.6 U/mg protein based on 10-formyl-THF synthetase activity. Western blot analysis indicated that the antisera is specific for one protein in crude liver extracts which comigrates with purified C1-THF synthase. Using the solid-phase immunoassay, as little as 200 pg of immunoreacting protein can be detected in tissue homogenates. Several rat tissues were examined for the three C1-THF synthase enzymatic activities and immunoreactive protein. The results indicated that the level of C1-THF synthase is regulated in a tissue-specific manner. Enzyme assays revealed that certain tissues differ by more than 100-fold in enzyme activity, with liver and kidney containing the highest levels, and lung and muscle the lowest. However, immunoassay of these same tissues indicated only a 10-fold difference in C1-THF synthase concentration. This apparent masking of enzyme activity was observed in all tissues, but to varying degrees. These results emphasize the advantages of an immunoassay in studying the regulation of C1-THF synthase.

Identification of a new sigma-factor involved in compartmentalized gene expression during sporulation of Bacillus subtilis

During sporulation of Bacillus subtilis, two identical genomes segregate in two compartments, the forespore and mother cell. These genomes are expressed differentially, with some genes such as sspE turned on only in the forespore. In vitro transcription of sspE was obtained only with RNA polymerase extracted from sporulating cells. Fractionation of factors associated with this enzyme and reconstitution with core RNA polymerase from vegetative cells generated an enzyme accurately transcribing sspE in vitro and led to purification of a polypeptide with the amino-terminal sequence of the spoIIIG product. Inactivation of spoIIIG abolished expression of sspE and five other forespore-specific genes, whereas synthesis of the spoIIIG product in vegetative cells rapidly turned these genes on. Therefore, spoIIIG encodes a sigma-factor, sigma G, which controls the expression of multiple genes in the forespore compartment.

Functional cooperativity between transcription factors UBF1 and SL1 mediates human ribosomal RNA synthesis

The human ribosomal RNA promoter contains two distinct control elements (UCE and core) both of which are recognized by the sequence-specific DNA binding protein UBF1, which has now been purified to apparent homogeneity. The purified factor activates RNA polymerase I (RNA pol I) transcription through direct interactions with either control element. A second RNA pol I transcription factor, designated SL1, participates in the promoter recognition process and is required to reconstitute transcription in vitro. Although SL1 alone has no sequence-specific DNA binding activity, deoxyribonuclease I footprinting experiments reveal that a cooperative interaction between UBF1 and SL1 leads to the formation of a new protein-DNA complex at the UCE and core elements. In vitro transcription experiments indicate that formation of the UBF1-SL1 complex is vital for transcriptional activation by UBF1. Thus, protein-protein interactions between UBF1 and SL1 are required for targeting of SL1 to cis-control sequences of the promoter.

Gene encoding sigma E is transcribed from a sigma A-like promoter in Bacillus subtilis

Bacillus subtilis produces several RNA polymerase sigma factors. At least two of these factors are essential for endospore formation, sigma H, which is present in vegetative cells, and sigma E, which is produced exclusively after the start of endospore formation. The structural gene that encodes sigma E is part of the spoIIG operon, which is transcribed after the onset of sporulation. We have determined the starting point of transcription and the nucleotide sequence of the spoIIG promoter. This promoter contains sequences that are similar to those found at the -10 and -35 regions of promoters that are used by E sigma A, the primary form of RNA polymerase in vegetative cells. The unusual feature of this promoter is that these putative sigma A contact sites are separated by 22 base pairs, rather than the typical 17 or 18 base pairs. Single-base substitutions in the -10-like sequence reduced utilization of the spoIIG promoter in vivo. Furthermore, E sigma A, but not E sigma H and other secondary forms of RNA polymerase, accurately initiated transcription from the spoIIG promoter in an in vitro assay; therefore, we suggest that E sigma A transcribes the spoIIG operon in vivo. A base substitution in the -35-like sequence caused constitutive transcription from the promoter in vegetative cells; therefore, regulation of this sporulation-specific transcription may involve a novel mechanism.

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.

An improved method for the purification of DNA-dependent RNA polymerase from Escherichia coli

DNA-dependent RNA polymerase from Escherichia coli was purified further by elution through heparin-Sepharose CL-6B column after the enzyme was obtained, partially purified, using Burgess and Jendrisak's method [(1975)Biochemistry 14, 4634] The total yield of the pure protein was 10 mg from 50 g of E.coli cells. The method was found to be very reproducible and convenient. The enzyme preparation had 60% active molecules and the elongation rate of RNA synthesis by this enzyme was measured to be 11 bases/s over delta D111 T7 DNA.

Effect of the delta subunit of Bacillus subtilis RNA polymerase on initiation of RNA synthesis at two bacteriophage phi 29 promoters

Initiation of RNA synthesis by Bacillus subtilis RNA polymerase (sigma-43) has been examined at two early promoters of phage phi 29: the A2 promoter, which is a weak promoter, and the G2 promoter, which is a strong promoter. The delta subunit of the polymerase inhibits the rate of initiation at A2, but not G2. In addition, formation of stable complexes by the polymerase at A2, but not at G2, requires the presence of the first two nucleotides of the A2 transcript.

A 100-kD HeLa cell octamer binding protein (OBP100) interacts differently with two separate octamer-related sequences within the SV40 enhancer

Numerous eukaryotic upstream promoter and enhancer regions contain a functional octamer sequence ATGCAAAT. We have examined the interactions between an octamer binding protein isolated from HeLa cells and the SV40 and immunoglobulin heavy-chain (IgH) gene enhancers. A partially purified octamer binding activity forms a single complex with the IgH enhancer octamer in a gel retardation assay, but two complexes with a SV40 enhancer fragment containing a single 72-bp element. By using point mutants and both dimethyl sulfate and diethyl pyrocarbonate modification interference assays, we show that the SV40 complexes result from binding of a factor to the octamer-related sequence ATGCAAAG (Octa1) and to an adjacent previously unidentified octamer-related sequence ATGCATCT (Octa2). The base-specific interactions with Octa1 and Octa2 differ; chemical modifications over a 10-bp sequence TATGCAAAGC affect Octa1 binding whereas Octa2 binding is affected by modifications spanning a 13-bp sequence ATGCATCTCAATT in which the octamer-like sequence is not centered. The octamer binding activity has been purified extensively by a DNA affinity precipitation procedure and SDS-polyacrylamide gel electrophoresis. The purified protein, OBP100, has an apparent molecular weight of 100 kD and binds both SV40 Octa1 and Octa2, as well as the IgH enhancer. The distinct interactions of OBP100 with the differently sized Octa1 and Octa2 binding sites suggest remarkably flexible sequence recognition between OBP100 and its binding sites.