Regulation of a promoter that is utilized by minor forms of RNA polymerase holoenzyme in Bacillus subtilis

Cloning and characterization of the gene encoding inorganic pyrophosphatase of Escherichia coli K-12

Escherichia coli K-12 gene ppa encoding inorganic pyrophosphatase (PPase) was cloned and sequenced. The 5' end of the ppa mRNA was identified by primer extension mapping. A typical E. coli sigma 70 promoter was identified immediately upstream of the mRNA 5' end. The structural gene of ppa contains 528 base pairs, from which a 175-amino-acid translation product, Mr 19,572, was deduced. The deduced amino acid composition perfectly fitted with that of PPase as previously determined (P. Burton, D. C. Hall, and J. Josse, J. Biol. Chem. 245:4346-4351, 1970). Furthermore, the partial amino acid sequence (residues 1 to 108) of E. coli PPase determined by S. A. Cohen (Ph.D. thesis, University of Chicago, 1978) was the same as that deduced from the nucleotide sequence. This is the first report of the cloning of a PPase gene.

Compartment-specific transcription in Bacillus subtilis: identification of the promoter for gdh

Glucose dehydrogenase beings to accumulate in the forespore between 2 and 3 h after the onset of endospore formation in Bacillus subtilis. The promoter for the structural gene for glucose dehydrogenase (gdh) was shown to be located 800 base pairs upstream from the coding sequence by examining the effects of integrating plasmids into the gdh region of the chromosome. The location of the gdh promoter was confirmed by primer extension analysis and by the identification of two single-base substitutions in the gdh promoter that prevented its function. The results of cell fractionation experiments with a strain that contained a transcriptional fusion of the gdh promoter and lacZ indicated that the forespore-specific accumulation of glucose dehydrogenase during sporulation is probably due to forespore-specific transcription of gdh.

The promoter for a sporulation gene in the spoIVC locus of Bacillus subtilis and its use in studies of temporal and spatial control of gene expression

We have identified the transcription start site and regulatory region governing the expression of a sporulation gene in the spoIVC locus of Bacillus subtilis. Efficient expression and developmental regulation of this gene was controlled from a promoter region that extended no more than 110 base pairs upstream and no more than 4 base pairs downstream from the start site of transcription, on which basis we infer that spoIVC is regulated at the level of transcription initiation. Using a transcriptional fusion of the spoIVC gene to the lacZ gene of Escherichia coli, we found that spoIVC expression was turned on at the third to fourth hour of sporulation (at about the developmental stage [IV] that its products are required in spore formation) and that this transcription was largely restricted to the mother cell chamber of the sporangium. Mutations in many different spo genes (causing blocks at stages 0 to V) were found to influence (negatively and positively) the level of spoIVC expression. Our results distinguish the mode of spoIVC regulation from that of previously studied sporulation genes and indicate that it is representative of a new regulon of mother cell-specific gene expression.

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.

Expression of the Bacillus subtilis xyl operon is repressed at the level of transcription and is induced by xylose

Expression of xylose isomerase was repressed in Bacillus subtilis strains W23, 168, and BR151 and could be induced in the presence of xylose. The expression was also glucose repressed in strains 168 and BR151, although this effect was not observed with W23. A xyl-cat fusion gene was constructed on a multicopy plasmid, from which the xyl promoter located on a 366-base-pair (bp) DNA fragment derived from W23 directed the expression of chloramphenicol resistance. The regulation of expression was not very pronounced in this multicopy situation. The xyl promoter is a strong signal for transcription initiation. The 5' sequence of the xyl mRNA was identified by nuclease S1 mapping. The promoter consisted of the -10 sequence TAAGAT, the -35 sequence TTGAAA spaced by 17 bp, and an upstream poly(A) block with 14 As out of 17 bp. To study the regulation, a xyl-lacZ fusion gene was constructed and integrated as a single copy into the amygene of B. subtilis 168. This strain grows blue on X-Gal (5-bromo-4-chloro-3-indolyl-beta-D-galactoside) indicator plates in the presence of xylose and white in the presence of glucose. Quantitatively, the induction of beta-galactosidase by xylose was 100-fold. In the presence of xylose plus glucose, the expression of the indicator gene was repressed to 30% of the fully induced level. About 25 to 60% of the maximal lacZ expression was obtained with this strain when the 366-bp xyl DNA fragment was provided in trans on a multicopy plasmid. This result indicates that repression in the absence of xylose is mediated in trans by a soluble factor which is expressed at a low level in B. subtilis 168. The xylose effect depended on negative regulation. The estimations of mRNA amounts by dot blot analysis showed unambiguously that the induction by xylose occurs at the level of transcription. The possible molecular mechanisms are discussed with respect to the nucleotide sequence of the 366-bp xyl regulatory DNA.

Transcriptional regulation of a promoter in the men gene cluster of Bacillus subtilis

The control of men gene expression during growth and sporulation of Bacillus subtilis was examined at the transcriptional level. Two different approaches were used. (i) Steady-state levels of men-specific mRNA were measured directly. (ii) A men'-lacZ gene fusion was constructed. In both cases, it was observed that men promoter activity was maximal at the onset of sporulation and declined soon thereafter. These kinetics were similar to the pattern of menaquinone accumulation previously observed. Expression from the men promoter was independent of the presence of the products of the spo0A and spo0H genes and was enhanced by addition of glucose and glutamine to the culture medium. DNA sequence analysis of the promoter region revealed a potential recognition site for the principal vegetative form of RNA polymerase but not for any of the known minor polymerase forms. The functionality in vivo of the promoter sequence was confirmed by high-resolution S1 nuclease mapping of the transcript start site. An additional sequence element was identified that is shared by the sdhA, citG, and ctaA promoters and may indicate a common regulatory mechanism in the expression of these genes.

Effects on growth and sporulation of inactivation of a Bacillus subtilis gene (ctc) transcribed in vitro by minor vegetative cell RNA polymerases (E-sigma 37, E-sigma 32)

The E-sigma 37-transcribed gene ctc was inactivated by a site-specific insertion into the Bacillus subtilis chromosome. The resulting mutation inhibited sporulation by 95% at elevated temperatures (48 degrees C). If the ctc- mutation is placed in a strain that carries a mutation in the closely linked but distinct spoVC gene, ctc now affects both growth and sporulation at elevated temperatures. Growth of the ctc- spoVC285 strain was transiently inhibited when exponentially growing cultures were shifted from 37 degrees C to 48 degrees C. A similar, but less pronounced "growth lag", was also seen in a B. subtilis strain carrying only the spoVC-285 mutation. This finding suggests that both the ctc and spoVC products function in vegetatively growing B. subtilis.

Promoter determining the timing and spatial localization of transcription of a cloned Streptomyces coelicolor gene encoding a spore-associated polypeptide

Streptomyces coelicolor is a filamentous, gram-positive bacterium that exhibits a complex cycle of morphological differentiation involving the formation of an aerial mycelium of multinucleoid hyphae which undergo septation to form long chains of spores. We report the identification of two proteins of 13 and 3 kilodaltons, designated SapA and SapB, respectively, that are produced during formation of the aerial mycelium and are found in assocation with purified, mature spores. We cloned the structural gene (sapA) for one of these spore-associated proteins. Nucleotide sequence analysis suggests that the 13-kilodalton polypeptide is derived from a larger pre- or preproprotein containing a leader sequence of 37 amino acids. Nuclease protection-hybridization analysis and experiments using the Vibrio harveyi, luciferase-encoding luxAB operon as a gene tag demonstrated that expression of sapA is controlled from a promoter contained within a region of less than 110 base pairs in length, whose transcription start site is located approximately 50 base pairs upstream from the initiation codon for the sapA open reading frame. Transcription of sapA was induced at the time of appearance of the aerial mycelium, and the level of sapA transcripts was significantly reduced in certain mutants blocked in aerial mycelium (bld) and or spore (whi) formation. As further evidence of the association of sapA transcription with morphological differentiation, experiments in which we monitored sapA transcription topographically by use of a sapA-luxAB operon fusion demonstrated a close spatial correlation between colony regions undergoing aerial mycelium formation and zones of sapA-promoted light emission.

Suppression of ctc promoter mutations in Bacillus subtilis

Transcription from the Bacillus subtilis ctc promoter is induced as cells enter stationary phase under conditions in which the enzymes of the tricarboxylic acid cycle are repressed. This transcription requires the presence of a secondary form of RNA polymerase, E sigma B, that is found in exponentially growing cells and in early-stationary-phase cells. Starting with a defective ctc promoter that had either a base substitution at position -15 or a base substitution at position -36, we were able to identify four independent second-site mutations within these mutated promoters that suppressed the effect of the original mutations and thereby restored function to the ctc promoter. Three of these mutated promoters had an additional base substitution(s) at positions -5, -9, or both -5 and -9 that enhanced their utilization in vivo by E sigma B, whereas one of the promoters had a single-base-pair deletion in the -15 region that placed it under a completely different form of regulation than that of the wild-type ctc promoter. In addition to mutations in the ctc promoter region, we also isolated three classes of mutants that exhibited increased ctc expression. The effects of the mutations in these strains were not allele specific, since they increased expression from both mutant and wild-type ctc promoters. One class of mutants which affected expression from the ctc promoter carried mutations that blocked the activity of the tricarboxylic acid cycle. A second class of mutations mapped near cysA and was unable to sporulate. Three-factor transformation crosses and complementation analysis indicated that one of these mutations was an allele of spo0H. The third class of mutations is closely linked to dal and may define a regulatory gene for sigB, the sigma B structural gene.

Genetic studies of a secondary RNA polymerase sigma factor in Bacillus subtilis

sigma B (sigma 37) is a secondary species of RNA polymerase sigma factor found in the gram-positive bacterium Bacillus subtilis. To study the function of sigma B genetically, we sought mutations that block the expression of a gene (ctc) known to be transcribed by sigma B-containing RNA polymerase in vitro. One such mutation, called crl, was found to map in or near the structural gene (sigB) for sigma B. To determine directly whether mutations in sigB would prevent transcription of ctc, we replaced sigB in the B. subtilis chromosome with insertion and deletion mutations that disrupted the sigma B coding sequence. Like crl, these in vitro-constructed mutations blocked expression of ctc, but had little or no effect on viability, sporulation, expression of the sporulation gene spoVG, or production of sporulation-associated alkaline protease. Using fusions of ctc to the reporter genes xylE and lacZ, we also identified mutations that enhanced ctc expression. One such mutation, called socB, was found to be located in an open reading frame immediately downstream of sigB.

Organization and regulation of an operon that encodes a sporulation-essential sigma factor in Bacillus subtilis

Deletion of sigE, the structural gene for the sporulation-induced RNA polymerase sigma factor, sigma E, prevented endospore formation by Bacillus subtilis. The effects of integration of plasmids into the sigE region of the chromosome and the use of complementation analyses demonstrated that sigE is part of an operon that includes a promoter-proximal gene, spoIIGA, that is essential for sporulation. Gene fusions to the promoter of this operon, spoIIG, demonstrated that transcription from this promoter is induced at the beginning of sporulation and is dependent on several spoO genes.

Relationship between aconitase gene expression and sporulation in Bacillus subtilis

The citB of Bacillus subtilis codes for aconitase (D. W. Dingman and A. L. Sonenshein, J. Bacteriol. 169:3060-3065). By direct measurements of citB mRNA levels and by measurements of beta-galactosidase activity in a strain carrying a citB-lacZ fusion, we have examined the expression of citB during growth and sporulation. When cells were grown in nutrient broth sporulation medium, citB mRNA appeared in mid- to late-exponential phase and disappeared by the second hour of sporulation. This timing corresponded closely to the kinetics of appearance of aconitase enzyme activity. Decoyinine, a compound that induces sporulation in a defined medium, caused a rapid simultaneous increase in aconitase activity and citB transcription. After decoyinine addition, the rate of increase in aconitase activity in a 2-ketoglutarate dehydrogenase (citK) mutant and in a citrate synthase (citA) mutant was significantly less than in an isogenic wild-type strain. This is apparently due to a failure to deplete 2-ketoglutarate and accumulate citrate. These metabolites might act as negative and positive effectors of citB expression, respectively. Mutations known to block sporulation at an early stage (spo0H and spo0B) had no appreciable effect on citB expression or aconitase activity. These results suggest that appearance of aconitase is stimulated by conditions that induce sporulation but is independent of certain gene products thought to act at an early stage of sporulation.

Expression of competence genes in Bacillus subtilis

A set of competence (com) mutants of Bacillus subtilis was constructed by using Tn917lacZ as a mutagen. In about half of the mutants, the promoterless lacZ element on the transposon was placed under control of putative com promoters. Expression of the mutant com genes was studied by using the beta-galactosidase tag. Two of the mutant genes (those represented by com-124 and com-138) were expressed early in the growth cycle in all of the media tested and were not dependent on the spo0A or spo0H product for expression. The remaining mutants, which represented a minimum of four additional genes, expressed beta-galactosidase in stationary phase during the period in which competence developed. We conclude that expression of com genes is probably regulated transcriptionally and in a growth stage-specific manner. Expression of these genes was also dependent on growth in competence medium and, like competence development, required the presence of glucose and was dependent on the spo0H products. The dependence on the spo0A gene product was partially bypassed by the abrB703 mutation. These effects were qualitatively equivalent to those on competence development. The latter was dependent on spo0A and spo0H, and the spo0A dependency was partially suppressed by abrB703. Several of the mutants were still capable of resolution into light and heavy buoyant density cell fractions when grown in competence medium. All of these expressed beta-galactosidase to a greater extent in the light fraction, showing that expression of these com genes was cell type specific. Development of competence was not markedly affected by mutations in spo0B, spo0E, spo0F, spo0J, or sigB, the structural gene of sigma 37.

Identification of the promoter for a peptide antibiotic biosynthesis gene from Bacillus brevis and its regulation in Bacillus subtilis

Tyrocidine is a cyclic decapeptide antibiotic which is produced and secreted by stationary-phase cells of the sporeforming bacterium Bacillus brevis. We identified the promoter for the B. brevis structural gene (tycA) for tyrocidine synthetase I, the enzyme catalyzing the first step in tyrocidine biosynthesis, and studied its regulation in cells of B. brevis and Bacillus subtilis. Transcription from the tycA promoter was induced at the end of the exponential phase of the growth cycle in B. brevis cells growing in sporulation medium. To study the regulation of tycA in B. subtilis, we constructed a derivative of the B. subtilis bacteriophage SP beta containing a transcriptional fusion of the tycA promoter to the lacZ gene of Escherichia coli and introduced the tycA-lacZ operon fusion by means of specialized transduction into sporulation mutants known to be blocked in sporulation-associated antibiotic production. Our principal finding was that tycA-directed lacZ expression was impaired in the stage-0 mutants with mutations spo0A, spo0B, and spo0E but not in spo0C, spo0F, spo0H, or spo+ bacteria. The dependence on the spo0A gene product could be entirely bypassed by an abrB suppressor mutation, which caused tycA-lacZ to be transcribed constitutively at all stages of growth. A simple model is proposed for the mechanism of tycA induction based on the Spo0A-dependent inactivation of Ab-B protein, which is proposed to be a negative regulator of tycA transcription.