Genetic aspects of bacterial endospore formation

Revised assignment for the Bacillus subtilis spo0F gene and its homology with spo0A and with two Escherichia coli genes

The nucleotide sequences of spo0F mutant genes which block the early sporulation process of Bacillus subtilis were determined. The mutation sites together with the results of complementation tests suggested that an open reading frame for a polypeptide of Mr = 14,229 is the spo0F gene. The deduced amino acid sequence shows striking homology with that of the spo0A gene. In addition, the upstream region involving the rib some binding site of the spo0F coding region is also similar to those of spo0A and spo0B. These homologies suggest that all three genes have a similar function in regulating the initiation of sporulation, and that their expression is controlled by a common mechanism. Clear homology is also seen between the spo0 gene products and the transcriptional control proteins, OmpR and Dye, of Escherichia coli suggesting that the spo0 gene products also are involved in the control of transcription.

Membrane particles from Escherichia coli and Bacillus subtilis, containing penicillin-binding proteins and enriched for chromosomal-origin DNA

Rapid-sedimenting DNA-membrane complexes were obtained from both Bacillus subtilis and Escherichia coli by a method involving gentle lysis followed by restriction enzyme digestion and sucrose gradient fractionation. These complexes were substantially enriched in chromosomal origin DNA, and in B. subtilis, the complexes were enriched in penicillin-binding proteins relative to that of the total membrane. Such complexes may represent procaryotic membrane domains which are topographically and functionally distinct.

Genetic mapping of rpoD implicates the major sigma factor of Bacillus subtilis RNA polymerase in sporulation initiation

We have mapped the chromosomal locus of rpoD, which encodes the major sigma factor of Bacillus subtilis RNA polymerase. The rpoD locus lay between aroD and lys, tightly linked to dnaE and inseparable from crsA. Marker order in this region was acf-aroD-dnaE-rpoD(crsA)-spoOG-lys. By transformation using cloned donor DNA from the rpoD region, we identified the gene immediately upstream of rpoD as dnaE, which coded for a 62,000 dalton protein essential for DNA replication. Both dnaE and rpoD were transcribed in the same direction, counterclockwise on the chromosome. The gene functions and organization in the rpoD region are thus similar to those of the E. coli sigma operon. We also used transformation to identify crsA47 as a mutation within the sigma coding region itself. The crsA alteration of sigma renders the sporulation process insensitive to glucose catabolite repression, and also restores sporulation ability to strains carrying early-blocked spoOE, spoOF, and spoOK mutations. Thus the major sigma factor and these spoO gene products directly or indirectly affect the same cellular function.

Genetic analysis of spo0A and spo0C mutants of Bacillus subtilis with a phi 105 prophage merodiploid system

An 8.0-kilobase chromosomal fragment of Bacillus subtilis which contained an intact spo0A gene was recloned onto temperate phage phi 105 from the rho 11dspo0A+-1 transducing phage. A specialized transducing phage, phi 105-dspo0A+-1, was constructed and used to transduce the spo0A12 mutant strain 1S9. A Spo+ transductant which was a single lysogen of the phi 105dspo0A+-1 transducing phage was isolated. From competent cells of this Spo+ transductant was isolated a Spo- (Spo0A) strain which was immune to phi 105. It was used to prepare a lysate of the phi 105dspo0A12 phage. Transduction of the spo0C9V recE4 strain with the phi 105dspo0A12 and phi 105dspo0A+-1 phages was carried out. The phi 105dspo0A+-1 phage gave rise to a large number of heat-resistant cells, but the phi 105dspo0A12 phage formed no heat-resistant cells. These results indicate that the spo0A12 and spo0C9V mutant genes do not complement each other in the ability to sporulate and that the spo0C9V mutation is located within the spo0A gene. Although the spo0C9V strain was completely asporogenous, the spo0C9V/spo0C9V diploid strain produced heat-resistant cells at a frequency of ca. 10(-3) in the sporulation medium. This result indicates that two copies of the spo0C9V mutant gene partially restore the ability of these cells to sporulate.

Bacillus subtilis gene involved in cell division, sporulation, and exoenzyme secretion

Bacillus subtilis strains carrying div-341 or sacU mutations, or both, have been characterized to reveal the roles of both genes in the initiation of sporulation, as well as in cell division and exoenzyme secretion. Both mutations were closely linked by transformation and caused the pleiotropic effects on sporulation and sporulation-associated events. Some sacU mutations (sacUh) resulted in hyperproduction of exoenzymes, reduced autolysis, and an ability to sporulate in the presence of excess nutrients. The div-341 mutation, on the other hand, resulted in filamentous growth at a higher temperature (45 degrees C) and showed spo0 properties at an intermediate permissive temperature (37 degrees C) in the usual sporulation medium. However, the div-341 strain sporulated better than wild-type strain at 37 degrees C in the presence of excess nutrients. Exoenzyme production and autolysis were reduced at 37 degrees C in the div-341 strain. A double mutant with sacUh32 and div-341 showed the complex phenotypes. It showed the sacUh32 property of autolysis and exoenyzme secretion. It showed the sacUh32 property of sporulation at 30 degrees C and the div-341 property at 37 degrees C. Slow growth and defective spore outgrowth of the div-341 strain at 37 degrees C were not observed in the double-mutant strain. Based on pleiotropic phenotypes and close linkages of both mutations, we discuss the relationship between the sacU and div-341 genes and their roles in sporulation, exoenzyme secretion, and cell division.

Bacillus subtilis sigma factor sigma 29 is the product of the sporulation-essential gene spoIIG

Evidence is presented that the sporulation-essential locus spoIIG codes for both sigma 29 and a structurally related protein, P31. This demonstrates that at least one specific Bacillus subtilis RNA polymerase binding protein provides a critical function in endospore formation. spoIIG-specific RNA is present in B. subtilis cultures that are synthesizing P31 and sigma 29 and is absent in those that are not. A monoclonal antibody specific for an antigenic determinant on P31/sigma 29 detected crossreacting proteins (P25/P21) but not P31 or sigma 29 in a Spo- B. subtilis strain with a mutation at the spoIIG locus (spoIIG41). The appearance of P25 and P21 occurs in this mutant at a time when P31 and sigma 29 would normally appear and suggests that they are homologous proteins. Transformation of the spoIIG41 strain with plasmid DNA carrying the structural gene for spoIIG complements the Spo- phenotype and results in the synthesis of P31, sigma 29, P25, and P21 at the appropriate times during sporulation. In Escherichia coli, the cloned spoIIG sequence encoded a protein that reacted with the anti-P31/sigma 29 monoclonal antibody and had the electrophoretic mobility of authentic P31.

Cloning of sporulation gene spoIVC in Bacillus subtilis

Sporulation gene spoIVC of Bacillus subtilis was cloned by the prophage transformation method in temperate phage phi 105. The specialized transducing phage, phi 105 spoIVC-1, restored the sporulation of the asporogenous mutant of B. subtilis strain 1S47 (spoIVC133). Transformation experiments showed that the spoIVC gene resides on a 7.3 kb HindIII restriction fragment. Subsequent analysis of the 7.3 kb HindIII fragment with restriction endonuclease EcoRI showed that the spoIVC gene resides on a 3.6 kb EcoRI fragment within the 7.3 kb fragment. The 3.6 kb fragment was recloned into the unique EcoRI site of plasmid pUB110 and deletion derivatives having a deletion within the 3.6 kb insert were constructed. The plasmid carrying the entire spoIVC gene restored the sporulation of strain HU1214 (spoIVC133, recE4) at a frequency of 10(7) spores/ml, and reduced the sporulation of strain HU1018 (spo+, recE4) to 10(7) spores/ml.

Relationship between butirosin biosynthesis and sporulation in Bacillus circulans

The relationship between butirosin biosynthesis and certain biochemical characteristics related to sporulation in a strain of Bacillus circulans NRRL B-3313 was examined. The cellular content of dipicolinic acid increased while the amount of poly-beta-hydroxybutyrate decreased with changes in antibiotic productivity. Oligosporogenous mutants failed to synthesize the antibiotic and to degrade poly-beta-hydroxybutyrate. These observations suggest that spore formation may be related to antibiotic production in this strain of B. circulans.

Characterization of the spo0A locus and its deduced product

The highly pleiotropic stage 0 sporulation locus of Bacillus subtilis, spo0A, has been cloned in bacteriophage lambda, subcloned in plasmids, and sequenced. The locus was found to code for a protein of 29,691 Da. Analysis of the in vivo transcripts from this region by nuclease S1 protection experiments located the start and stop of transcription of the locus. The transcription start site was preceded by a promoter resembling sigma 37-dependent promoters. Two mutations originally assigned to a second locus, spo0C, in this region because of their weakly pleiotropic phenotypes were cloned and sequenced. The mutations were found to be different missense alterations in the same base of the 10th codon preceding the carboxyl end of the Spo0A protein. These results, along with the finding that mutations in the spo0A gene product [Hoch, J. A., Trach, K., Kawamura, F. & Saito, H. (1985) J. Bacteriol. 161, 552-555] suppress the requirement for spo0B, spo0E, and spo0F gene products in transcription from sigma 28-dependent promoters, suggest that the Spo0A protein interacts directly with the transcription machinery to effect the initiation of sporulation. The deduced amino acid sequence of the Spo0A protein was highly related to that of the OmpR regulatory protein of Escherichia coli.

Nucleotide sequences of the sporulation gene spo0A and its mutant genes of Bacillus subtilis

We have determined the nucleotide sequence of a 2375-base-pair DNA fragment, which contained the sporulation gene spo0A cloned from Bacillus subtilis. The sequence had only one long open reading frame consisting of 239 codons, which was found to correspond to the spo0A gene by comparing the nucleotide sequence of the wild-type gene with those of the mutant alleles. The calculated molecular weight of the product of the wild-type spo0A gene was 26,500. We found also a new mutation, sgi, which maps within the spo0A gene. This mutation relieves the growth inhibition of the host cells caused by a multicopy plasmid carrying the spo0A gene. The mutations spo0A12, spo0C9V, and sgi-1 were found to be an amber mutation at the 62nd codon, a missense at the 229th codon, and a frame-shift at the 223rd codon of the spo0A gene, respectively.

New Ways to Study Developmental Genes in Spore-Forming Bacteria

The regulated activation of numerous sets of genes in multiple chromosomal locations is a hallmark of cellular differentiation in both eukaryotes and prokaryotes. Certain species of bacteria that experience complex developmental cycles are especially attractive as systems in which to study the mechanisms of this kind of gene regulation because they are highly amenable to both biochemical and genetic approaches. Bacillus subtilis, which undergoes extensive cellular differentiation when it sporulates, is one such system. Many new methods are now available in this Gram-positive species for identifying, manipulating, and studying the regulation of genes involved in spore formation, including the use of transposable genetic elements that create gene fusions in vivo as an automatic consequence of insertions into genes.

Structure and organization of genes for transfer ribonucleic acid in Bacillus subtilis

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Isolation and characterization of a cis-acting mutation conferring catabolite repression resistance to alpha-amylase synthesis in Bacillus subtilis

Bacillus subtilis 168GR10 was shown to contain a mutation, gra-10, which allowed normal temporal activation of alpha-amylase synthesis in the presence of a concentration of glucose that is inhibitory to activation of amylase synthesis in the parent strain, 168. The gra-10 mutation was mapped by phage PBS-1-mediated transduction and by transformation to a site between lin-2 and aroI906, very tightly linked to amyE, the alpha-amylase structural gene. The gra-10 mutation did not pleiotropically affect catabolite repression of sporulation or of the synthesis of extracellular proteases or RNase and was unable to confer glucose-resistance to the synthesis of chloramphenicol acetyltransferase encoded by the cat-86 gene driven by the amyE promoter region (amyR1) inserted into the promoter-probe plasmid pPL603B. It therefore appears that gra-10 defines a cis-regulatory site for catabolite repression, but not for temporal activation, of amyE expression. The evidence shows that temporal activation and glucose-mediated repression of alpha-amylase synthesis in B. subtilis 168 are distinct phenomena that can be separated by mutation.

Synthesis of sigma 29, an RNA polymerase specificity determinant, is a developmentally regulated event in Bacillus subtilis

Using an immunological probe, we have determined that the synthesis of the Bacillus subtilis RNA polymerase promoter specificity determinant sigma 29 is a developmentally regulated event. sigma 29 is absent from vegetatively growing cells but is abundant in sporulating cells for a restricted (2-h) period during differentiation (hour 2 to hour 4 into the sporeforming process). The narrowness of this period suggests that sigma 29 is a regulatory factor that directs the transcription of a subpopulation of genes at a precise, intermediate stage of spore formation. This view predicts that sigma 29 should be dispensable for early sporulation events. We verified this prediction by an analysis of sigma 29 accumulation in mutants that are blocked at different stages of sporulation in which we show that cells can advance to at least an intermediate point in development (stage III) in the absence of detectable sigma 29. Lastly, our anti-sigma 29 antibody probe detected a second, previously unrecognized protein in Bacillus cell extracts that may be a precursor to sigma 29. This protein, P31 (molecular weight, 31,000) is synthesized earlier in sporulation than is sigma 29. It has a peptide profile that is similar to sigma 29 and is present in all Bacillus subtilis Spo- mutants that were tested and found to still be able to accumulate sigma 29.

A developmental gene product of Bacillus subtilis homologous to the sigma factor of Escherichia coli

Sporulation of Bacillus subtilis involves sequential morphological and biochemical changes and is regulated by specific genes (spo genes) estimated to occupy more than 30 loci. A mutation in any one of these genes blocks the sporulation process at the corresponding developmental stage. Despite intensive genetic studies, the nature and function of the spo gene products remain unknown. Vegetative B. subtilis RNA polymerase core enzyme may interact with several sigma factors and discriminate among different classes of promoters. During sporulation, new polypeptides are associated with the core enzyme which may have a central role in modifying its promoter recognition specificity. As a first step to understanding their function in the switch from vegetative to sporulation mode, several early sporulation genes have been cloned and analysed. Here we report the cloning and nucleotide sequence of the spoIIG gene of B. subtilis. This gene encodes a polypeptide with a predicted relative molecular mass of 27,652 which contains a 65-amino acid region highly homologous to an internal part of the Escherichia coli sigma factor.

Mutants of Aspergillus nidulans blocked at an early stage of sporulation secrete an unusual metabolite

Mutants of Aspergillus nidulans defective in conidiation (asexual sporulation) can be classified according to whether they are blocked before or after induction of conidiation. Mutants blocked before induction (preinduction mutants) appear to be unable to respond to the inducing stimulus and thus are defective in one of the earliest events in the sporulation process. Three preinduction mutants have been isolated and characterized. Each was found to exhibit the same pleiotropic phenotype: they also were defective in sexual sporulation and secreted a set of phenolic metabolites at a level much higher than did wild type or mutants blocked at later stages of conidiation. One of the metabolites has been identified as the antibiotic diorcinal (3,3'-dihydroxy-5,5'-dimethyldiphenyl ether) which is known to be involved in the synthesis of certain farnesyl phenols of unknown function. These results suggest that preinduction mutants are blocked in a phenolic metabolic pathway, one or more product of which participates in the initiation of sporulation.

Nucleotide sequence of the spo0B gene of Bacillus subtilis and regulation of its expression

The spo0B gene is one of the genes involved in initiation of sporulation of Bacillus subtilis. This gene, previously cloned into the pHV33 shuttle vector, is expressed in Escherichia coli and B. subtilis. We have determined the sequence of 1118 base pairs (bp) of the DNA insert carrying the spo0B gene. The promoter sequence of this gene shows the canonical T-A-T-A-A-T region at 10 bp from the transcriptional start (-10 region) but an unusual sequence, T-T-T-T-C-T-, in the -35 region. The nucleotide sequence shows an open reading frame encoding a 192-amino-acid polypeptide of Mr 22,542, which is close to the molecular weight of the spo0B product synthesized in E. coli minicells. To investigate the regulation of the spo0B gene under a variety of physiological conditions, we constructed an in-frame fusion between the spo0B promoter proximal region and the lacZ gene of E. coli. This hybrid gene was subsequently integrated into the B. subtilis chromosome, and the beta-galactosidase activity was measured. It was found that the spo0B gene is preferentially expressed during exponential growth; it is not induced by exhaustion of the growth medium nor repressed by glucose.

Construction of a Bacillus subtilis double mutant deficient in extracellular alkaline and neutral proteases

A mutant strain of Bacillus subtilis carrying lesions in the structural genes for extracellular neutral (nprE) and serine (aprA) proteases was constructed by the gene conversion technique. This mutant had less than 4% of the extracellular protease activity of the wild type and sporulated normally, indicating that neither of these sporulation-associated proteases is essential for development.

Cloning of the neutral protease gene of Bacillus subtilis and the use of the cloned gene to create an in vitro-derived deletion mutation

The neutral protease gene of Bacillus subtilis has been cloned, and its nucleotide sequence has been determined. The cloned gene was used to create an in vitro-derived deletion mutation, which was used to replace the wild-type copy of the gene. This deletion, in combination with a deletion of the alkaline protease gene, completely abolished protease production. The loss of the proteases had no detectable effect on growth, morphology, or sporulation.

Identification of the sporulation gene spoOA product of Bacillus subtilis

A 2.4-kilobase fragment of the Bacillus subtilis chromosome containing the wild-type spoOA gene derived from the phi 105dspoOA+-Bc-1 transducing phage was cloned onto plasmid pBR322 in Escherichia coli. A recombinant plasmid harboring the mutant spoOA12 allele on the 2.4-kilobase insert was also constructed from the phi 105dspoOA12-1 phage DNA and pBR322. Protein products synthesized in response to plasmid DNA in a DNA-directed cell-free system derived from E. coli were analyzed by sodium dodecyl sulfate-polyacryl-amide gel electrophoresis. A protein of approximately 27,500 daltons synthesized with the recombinant plasmid DNA harboring the wild-type spoOA gene as template was not formed with the recombinant plasmid DNA harboring the spoOA12 allele. Since the spoOA12 mutation is a nonsense mutation, we conclude that the 27.5-kilodalton protein is the product of the spoOA gene.

A novel method for the rapid cloning in Escherichia coli of Bacillus subtilis chromosomal DNA adjacent to Tn917 insertions

A rapid and general procedure has been devised for the pBR322-mediated cloning in Escherichia coli of Bacillus subtilis chromosomal DNA extending in a specified direction from any Tn917 insertion. Derivatives of Tn917 have been constructed that contain a pBR322-derived replicon, together with a chloramphenicol-resistance (Cmr) gene of Gram-positive origin (selectable in B. subtilis), inserted by ligation in two orientations into a SalI restriction site located near the center of the transposon. When linearized plasmid DNA carrying such derivatives was used to transform to Cmr B. subtilis bacteria already containing a chromosomal insertion of Tn917, the pBR322 sequences efficiently became integrated into the chromosomal copy of the transposon by homologous recombination. It was then possible to clone chromosomal sequences adjacent to either transposon insertion junction into E. coli, using a selection for ampicillin-resistance, by transforming CaCl2-treated cells with small amounts of insert-containing DNA that had been digested with various restriction enzymes and then ligated at a dilute concentration. Because pBR322 sequences may be inserted by recombination in either orientation with respect to the transposon arms, a single restriction enzyme (such as EcoRI or SphI) that has a unique recognition site in pBR322 DNA may be used to separately clone chromosomal DNA extending in either direction from the site of any transposon insertion. A family of clones generated from the region of an insertional spo mutation (spoIIH::Tn917) was used in Southern hybridization experiments to verify that cloned material isolated with this procedure accurately reflected the arrangement of sequences present in the chromosome. Strategies are discussed for taking advantage of certain properties inherent in the structure of clones generated in this way to facilitate the identification and study of promoters of insertionally mutated genes.

New mutation affecting the synthesis of some membrane proteins and sporulation in Bacillus subtilis

A new mutation, mpo, which affects the synthesis of some membrane proteins and sporulation in Bacillus subtilis was identified. The mpo mutation was tightly linked to the overproduction of membrane proteins MP32 and MP18 (molecular weights of 32,000 and 18,000, respectively) and the temperature-sensitive sporulation phenotype. Genetic analysis showed that the mpo mutation maps between the spoIIIB and lys loci.

Selective expression of a plasmid cat gene at a late stage of Bacillus subtilis sporulation

The cat-86 gene in plasmid pPL603 specifies chloramphenicol acetyltransferase (CAT) and is selectively expressed in Bacillus subtilis at a stage in sporulation in which internal spores are first observed (approximately T8). The gene is unexpressed in vegetatively growing cells. cat-86 expression and spore formation are both blocked when cells are grown in excess glucose. cat-86 expression at T8 is due to selective transcription of the gene, since cat-86 mRNA is undetectable in vegetatively growing cells but is readily demonstrated in sporulating cells. The transcription start site for cat-86 mRNA from sporulating cells is within a 203-base-pair restriction fragment designated P1, which is located upstream from the cat coding region on pPL603 . Deletion of P1 from pPL603 eliminates the sporulation -associated expression of cat-86. Host sporulation genes, whose function is absolutely required for cat-86 expression at T8, include six early sporulation, spo0 , genes and spoIIE . Therefore, pPL603 provides a novel system in which the in vivo expression of a known, plasmid-linked gene is dependent on sporulation-specific changes in B. subtilis.

Replacement of the Bacillus subtilis subtilisin structural gene with an In vitro-derived deletion mutation

The entire subtilisin structural gene from Bacillus subtilis I168 has been cloned, and its nucleotide sequence has been determined. When expressed on a high-copy-number shuttle vector, a fivefold increase in serine protease activity was observed. The DNA sequence of the gene is 80% homologous to the Bacillus amyloliquefaciens subtilisin structural gene, and the translated mature coding sequence is 85% homologous to the published protein sequence of subtilisin BPN'. The chloramphenicol resistance determinant of a plasmid integrated at the subtilisin locus was mapped by PBS1 transduction and was found to be linked to glyB (83%) and argC (60%), but not with metC or purB . The chromosomal locus containing the wild-type subtilisin allele was replaced with an in vitro-derived allele of the gene (delta apr-684) that contained a 684-base-pair deletion. The technique used for introducing the deletion is a variation of the gene replacement methods used in Saccharomyces cerevisiae and Escherichia coli. When used in B. subtilis, deletion mutants could be directly screened among the transformants. Physiological characterization of the delta apr-684 mutation revealed no discernable effect on the formation of heat-resistant endospores, but strains carrying the mutation produced only 10% of wild-type serine protease activity. A model is presented that outlines the pathway for plasmid integration and deletion formation in B. subtilis.

Expression of Bacillus megaterium and Bacillus subtilis small acid-soluble spore protein genes during stationary-phase growth of asporogenous B. subtilis mutants

The small acid-soluble spore proteins alpha and beta were not detected during stationary-phase growth of asporogenous Bacillus subtilis mutants blocked in stages 0, II, or III, but mutants blocked in stages IV or V accumulated nearly wild-type levels of these small acid-soluble spore proteins. Similar results were obtained when production of Bacillus megaterium C protein (also a small acid-soluble spore protein), as well as alpha and beta, were monitored in these mutants containing a recombinant plasmid carrying the B. megaterium C protein gene. The only exception was a spo0H mutant which synthesized a small amount of C protein, but no alpha or beta.

The subtilisin E gene of Bacillus subtilis is transcribed from a sigma 37 promoter in vivo

A cloned Bacillus subtilis gene (sprE) expressed only during the stationary growth phase is shown to encode the subtilisin E protease, an enzyme associated with sporulation. We have determined the DNA sequence of the sprE promoter region and the promoter-proximal half of the structural gene. The sprE gene codes for a putative 29-residue signal peptide and a 77-residue leader peptide preceding the mature subtilisin sequence. By plasmid integration and phage PBS1 transduction, we have mapped the sprE locus between glyB and metD on the B. subtilis chromosome, a region also containing the hyperprotease-producing hpr gene. In vitro the sprE gene is transcribed by the minor form of RNA polymerase containing a 37,000-dalton sigma factor (sigma 37). We show by S1 nuclease mapping that sprE transcription initiates at dual start sites both in vitro and in vivo and that the promoter for the downstream site has a characteristic sigma 37 recognition sequence. We propose that the physiological role of the sigma 37 RNA polymerase is to transcribe a class of genes that are catabolite repressed, that encode extracellular enzymes, or that are expressed only during the stationary phase of growth.

A temporally regulated promoter from Bacillus subtilis is transcribed only by an RNA polymerase with a 37,000 dalton sigma factor

A 1,250 base pair Bacillus subtilis chromosomal HindIII restriction fragment (S fragment) has been cloned into the B. subtilis expression-probe plasmid pGR71. The S fragment induces the expression of the pGR71 chloramphenicol resistance gene shortly after the initiation of sporulation. The transcriptional promoter responsible for the expression of this temporally regulated genetic element has been identified and mapped in vitro. This promoter is recognized exclusively by the minor B. subtilis RNA polymerase that contains the 37,000 dalton sigma factor.

Replacement and amplification of bacterial genes with sequences altered in vitro

An efficient method for the replacement of chromosomal DNA by segments altered in vitro has been developed for bacteria. The method requires (i) a recombinant plasmid with a ColE1-like replicon and (ii) a strain defective in DNA polymerase I (polA), which is unable to replicate the plasmid extrachromosomally. This method is of general use since there are a number of suitable vectors and polA strains are available in both Escherichia coli and Salmonella typhimurium, the two most widely studied bacterial species. Using the method, we have constructed two chromosomal deletions in the chemotaxis gene region of S. typhimurium. In addition, plasmid sequences integrated into the chromosome have been amplified up to 30-fold by varying the concentration of ampicillin or tetracycline in the growth medium.

Cloning of sporulation genes spo0A and spo0C of Bacillus subtilis onto rho 11 temperate bacteriophage

A HindIII fragment harboring the intact spo0C gene of Bacillus subtilis was cloned with rho 11 temperate bacteriophage as a vector. Transformation experiments with the DNA from rho 11 dspo0C+ specialized transducing phage showed that the spo0C gene resides on a 5.3-megadalton fragment generated by HindIII digestion. The 5.3-megadalton fragment also contains the intact spo0A gene, but not spoIIIA, spoIIIB, or spoIVB.

Two RNA polymerase sigma factors from Bacillus subtilis discriminate between overlapping promoters for a developmentally regulated gene

A developmentally regulated gene (spoVG) from the spore-forming bacterium Bacillus subtilis is expressed from two overlapping promoters, which direct transcription initiating from sites separated by 10 base pairs. Utilization of the upstream promoter is determined by an RNA polymerase sigma factor of molecular weight 37,000 (sigma 37). We report the isolation of a 32,000-molecular weight species of sigma factor (sigma 32), which exclusively dictates transcription initiation from the downstream promoter, and suggest a model for the way in which sigma-specific recognition sequences are intermeshed within the spoVG transcription initiation region.

Genetic transposition and insertional mutagenesis in Bacillus subtilis with Streptococcus faecalis transposon Tn917

The Streptococcus faecalis transposon Tn917 was introduced into Bacillus subtilis by transformation of competent cells with the plasmid pAM alpha 1::Tn917 and was tested for transposition activity by selection for insertions into the temperate phage SP beta. Insertions were obtained at a frequency indicating relatively efficient movement of the element, and Southern hybridization analysis of a particular insertion confirmed it to be the result of a genuine transposition event. A restriction fragment from pAM alpha 1::Tn917 containing the transposon sequences was ligated into a temperature-sensitive plasmid (pBD95), and transpositions into the B. subtilis chromosome were selected by requiring the transposon drug resistance to be maintained at temperatures nonpermissive for plasmid replication. Insertions have been recovered at many chromosomal sites, including ones that produced auxotrophy of different kinds and ones that produced various different sporulation-defective phenotypes, indicating good prospects for the use of Tn917 as a tool for insertional mutagenesis in B. subtilis.

Induction at high frequency of a unique phenotypic class of Bacillus subtilis mutants by methylxanthines

Caffeine and theophylline are mutagenic at high concentration in the B. subtilis multigene sporulation test for mutagens; caffeine is a stronger mutagen than theophylline in this test. An unusually high fraction of the mutant colonies appear to be phenotypically identical, as judged by colonial morphology and microscopic appearance of the vegetative cells. These mutants do not bring about the pH increase normally associated with sporulation of B. subtilis; such behavior is frequently associated with lack of a functional tricarboxylic acid (TCA) cycle, essential for normal sporulation of this species. Similar mutants have not been noted in the course of screening a variety of well-known mutagens, including acriflavine. Caffeine is maximally effective in inducing these mutants about 10 min after germination commences. Adenosine greatly reduces the ability of caffeine to induce these mutants.

Changes in penicillin-binding proteins during sporulation of Bacillus subtilis

The penicillin-binding proteins (PBPs) of Bacillus subtilis were examined in samples collected at various times from sporulating cultures and compared with the PBPs in a presporulation sample. Large increases in vegetative PBPs 2B and 3 and the appearance of at least one new PBP (42,000 daltons) occurred at reproducible times during sporulation. In some strains a second new PBP (60,000 daltons) was also produced. By comparing the PBP activities in sporulating cells and two spo0 mutants we have classified these changes as sporulation-related events rather than the consequences of stationary-phase aging. The other vegetative PBPs (PBPs 1, 2A, 4, and 5) decreased during sporulation, but not in sufficient amount or at the appropriate time to account for the appearance of the new proteins. A possible connection between specific PBP changes and the penicillin-sensitive stages of sporulation is suggested.

Early sporulation gene spo0F: nucleotide sequence and analysis of gene product

We have determined the sequence of a 1,162-base-pair DNA fragment containing a spo0F gene which is required for an early stage of sporulation in Bacillus subtilis. The sequence has only one long open reading frame consisting of 173 codons, which has been confirmed to be the spo0F cistron by DNA-mediated transformation and in vitro transcription. In UV-irradiated "maxicells" containing pUBSF13, the plasmid that carries cloned spo0F gene, we have observed the synthesis of a 20-kilodalton polypeptide that is absent from cells carrying a vector plasmid pUB110. The molecular weight of this protein is in agreement with the calculated molecular weight of the spo0F gene product (Mr, 19,065). The putative promoter sequences of spo0F gene were 5' T-A-T-A-A-T 3' at -10 and 5' T-T-G-A-T-T 3' at -35. An octamer sequence, 5' A-A-A-G-G-A-G-G 3', situated 8 base pairs prior to the initiation codon was found to be perfectly complementary with the 3' end of 16S ribosomal RNA. This result offers additional evidence for the proposal by Rabinowitz's group that an extensive mRNA-rRNA interaction is a requirement for efficient translation by B. subtilis ribosomes.

Formation of competent Bacillus subtilis cells

The process of competent cell formation for transformation has been studied with early-stationary-phase (T1) cells of Bacillus subtilis which had been grown in an enriched Spizizen minimal medium and transferred to a second synthetic medium. Rifampin, chloramphenicol, and tunicamycin were strong inhibitors of competent cell formation, as well as vegetative growth. After formation, competent cells were no longer sensitive to the above agents. Methicillin and an inhibitor of chromosomal replication, hydroxyphenylazouracil, did not inhibit the development of competence. A D-alanine-requiring mutant strain developed competence even in the absence of D-alanine in the second medium. A T1-stage culture showed the activity of extracellular serine protease which is necessary for sporulation. Competent cell formation was completely blocked by 0.7 M ethanol, which is a specific inhibitor of early events during sporulation, including forespore septum formation. Competent cells were formed even in media which supported sporulation. The development of competence was also studied with spo0 mutants at 10 different loci. Most spo0 mutations repressed the development of competence except for spo0C, spo0G, and spo0J. These results suggest that competent cells are formed from early sporulating cells with the synthesis of cell wall materials and by factors whose genes are activated by the supply of nutrients. It is suggested that common steps are involved both in forespore septation and in competent cell formation.

Synthesis of acid-soluble spore proteins by Bacillus subtilis

The major acid-soluble spore proteins (ASSPs) of Bacillus subtilis were detected by immunoprecipitation of radioactively labeled in vitro- and in vivo-synthesized proteins. ASSP synthesis in vivo began 2 h after the initiation of sporulation (t2) and reached its maximum rate at t7. This corresponded to the time of synthesis of mRNA that stimulated the maximum rate of ASSP synthesis in vitro. Under the set of conditions used in these experiments, protease synthesis began near t0, alkaline phosphatase synthesis began at about t2, and refractile spores were first observed between t7 and t8. In vivo- and in vitro-synthesized ASSPs comigrated in sodium dodecyl sulfate-polyacrylamide gels. Their molecular weights were 4,600 (alpha and beta) and 11,000 (gamma). The average half-life of the ASSP messages was 11 min when either rifampin (10 micrograms/ml) or actinomycin D (1 microgram/ml) was used to inhibit RNA synthesis.

Molecular cloning of the spo0B sporulation locus in bacteriophage lambda

The stage 0 sporulation locus spo0B has been mapped by transformation between the pheA and spoIVF loci. Analysis of the behavior of alleles of the spo0B locus in trpE26 merodiploid strains indicates that all of the known alleles of this locus comprise a single complementation group. The spoIVF88 mutation was found to reside in a separate complementation group. The chromosomal region surrounding and including the spo0B locus was cloned in the lambda vector Charon 4A. Extensive restriction endonuclease analyses of the inserts in these phage revealed that an EcoRI fragment of DNA of 2.3 kilobases had transforming activity for spo0B mutations. Examination of the physical and genetic maps of the locus suggested that the entire spo0B locus is contained within this fragment. Subcloning of restriction endonuclease fragments of the lambda inserts and transformation analyses allowed assignment of surrounding genetic loci to specific DNA fragments.

Alcohol-resistant sporulation mutants of Bacillus subtilis

About 80% of Bacillus subtilis cells form spores when grown in nutrient broth. In medium containing various short-chain aliphatic alcohols, the frequency of sporulation was reduced to 0.5%. Mutants sporulated in the presence of alcohols at a frequency of 30 to 40%. Sporulation in the wild-type cells was sensitive to alcohol at the beginning of sporulation (stage zero). Sensitivity to alcohol in the mutants was also at stage zero, even though the sensitivity was considerably reduced. This sensitivity of sporulation to alcohol is the phenotypic expression of a genetic locus designated ssa. Mutations at this locus lead to a decreased sensitivity of sporulation to alcohol without modifying the sensitivity of growth. Genetic analysis by transduction was bacteriophage PBS1 revealed that ssa mutations are near the previously described spo0A locus. ssa mutants also differ from wild-type cells in the composition of membrane phospholipids. The relative amount of phosphatidylglycerol increased, whereas the relative amount of phosphatidylethanolamine and lysylphosphatidylglycerol decreased relative to the proportions in the wild type. The distribution of fatty acids in membrane lipids is the same as in the wild type. No differential sensitivity of phospholipid metabolism to alcohol could be detected in the mutant. This work therefore reveals that the extensive, pleiotropic changes in the membranes of ssa mutants are the phenotypic reflection of alterations at a specific gene locus.

Extracellular exonuclease as a stage 0 biochemical marker in Bacillus subtilis sporulation

Calcium-dependent exonuclease activity was produced by sporulating cells of Bacillus subtilis 168. Nuclease activity was released into the culture medium at approximately the same time as sporulation proteases, and production of these enzymes was tied to DNA replication. Results suggest that nuclease production is a function of the spo0H locus.

[Physiological and cell biological characterization of the protease producer Thermoactinomyces vulgaris during prolonged culture in a stirred fermenter]

The physiological behaviour of Thermoactinomyces vulgaris - producing a thermostable serine-protease - was analyzed during fermentation. During 38 h the consumption of nutrients and oxygen as well as the rates of macromolecular and protease synthesis were measured. The morphological and ultrastructural changes of the mycelia were also studied. The mycelia grew exponentially for about 5 hours. After a short lag and a second slower growth phase, growth continued about linearly until the end, as was indicated by a constant rate of incorporation of labelled thymidine. However, at the same time a changing portion of hyphae - up to 45% - underwent lysis. According to the changing ratio of growing and lysing material, regarding the physiological activity of the culture the fermentation process could be divided into 4 periods. The formation of the protease started at the transition to the slow growth phase and continued linearly. The ability to produce the protease was attributed to a mycelium being formed after the shift down caused by limitation of supply of utilizable nitrogen compounds. The end of protease production 10 h later was correlated to a drastic decrease of the respiratory activity of the mycelia, probably caused by exhaustion of easily utilizable carbohydrates.

Macrolide and aminoglycoside antibiotic resistance mutations in the bacillus subtilis ribosome resulting in temperature-sensitive sporulation

Mutants of Bacillus subtilis resistant to various macrolide antibiotics have been isolated and characterized with respect to their sporulation phenotype and the electrophoretic mobility of their ribosomal proteins (r-proteins). Two types of major alterations of r-protein L17, one probably due to a small deletion, are found among mutants exhibiting high-level macrolide resistance. These mutants are all temperature-sensitive for sporulation (Spots). Low-level resistance to some macrolides is found to be associated with minor alterations in r-protein L17. These mutations do not cause a defective sporulation phenotype. All of the macrolide resistance mutations map at the same locus within the Str-Spc region of the B. subtilis chromosome. Hence, changes in a single ribosomal protein can result in different sporulation phenotypes. Mutants resistant to the aminoglycoside antibiotics neomycin and kanamycin have been isolated. Approximately 5% of these are Spots. Representative mutations, neo162 and kan25, cause concomitant drug resistance and sporulation temperature-sensitivity and map a single-site lesions in the Str-Spc region of the chromosome. Strains bearing neo162 or kan25 are equally cross-resistant to streptomycin or spectinomycin. These mutations define a new B. subtilis drug resistance locus at which mutation can cause defective sporulation.

Identification of a new developmental locus in Bacillus subtilis by construction of a deletion mutation in a cloned gene under sporulation control

We removed by recombinant deoxyribonucleic acid (DNA) techniques a small DNA segment from within a cloned gene (the 0.4 kb gene) in which transcription in under sporulation control in Bacillus subtilis. These deletion mutation was introduced into the B. subtilis chromosome by transformation with cloned DNA. Competent cells bearing a mutation (tms-26) that is closely linked to the 0.4 kb gene were transformed with linearized plasmid DNA containing the truncated 0.4 kb gene and the wild-type allele of the tms locus. Selection for Tms+ transformants yielded oligosporogenous mutants of unusually dark-brown colony pigmentation. This phenotype was caused by a mutation which mapped at or very near the site of the 0.4 kg gene deletion, whose presence and position in chromosomal DNA was confirmed by Southern hybridization analysis. Phase-contrast microscopy and electron microscopy showed that the mutation, which we designated as spoVG, impaired sporulation at about the fifth stage; bacteria harboring the spoVG mutation proceeded normally through stage IV of development but frequently lysed thereafter, apparently as a result of disintegration of an immature spore cortex. This identifies the 0.4 kb gene (or DNA in its immediate vicinity) as a new sporulation locus and shows that its product functions at a late stage in development.

Regulation of polypeptide synthesis during Caulobacter development: two-dimensional gel analysis

The gram-negative bacterium Caulobacter crescentus progresses through three distinct morphological transitions, including both motile and nonmotile cell types, during its cell cycle. Assessment of the extent of regulation of polypeptide synthesis during these transitions was carried out with two-dimensional gel electrophoresis of whole-cell extracts. Synchronous cells were pulse-labeled with 14C-amino acids for 10-min intervals throughout the entire 2-h cell cycle. The radioactively labeled polypeptides were analyzed by two-dimensional polyacrylamide gel electrophoresis. Autoradiograms resulting from fluorography of the second dimension provided the detection of approximately 1,000 unique spots. The 600 predominant polypeptide spots, representing approximately 40% of the coding capacity of Caulobacter deoxyribonucleic acid, were analyzed for major changes in their synthetic rates. Quantitation by densitometric scanning of individual polypeptide spots represented on the sequential fluorograms demonstrated significant changes in the temporal synthesis of 6% of the polypeptides. Extracts from asynchronous cells were fractionated to obtain total-membrane and deoxyribonucleic acid-binding polypeptide fractions. Subsequent electrophoresis of these cellular fractions revealed approximately 100 membrane polypeptides and 25 deoxyribonucleic acid-binding polypeptides. Eight of the regulated polypeptides were identified as membrane or deoxyribonucleic acid-binding proteins. The regulated polypeptides can be grouped into three main categories based on their interval of synthesis. The three categories are in direct correlation with the three distinct cell cycle stages. This analysis has also revealed a unique transition period in the cell cycle in which a significant proportion of gene expression is regulated.

A cloned gene that is turned on at an intermediate stage of spore formation in Bacillus subtilis

Cells of Bacillus subtilis synthesize a relatively long-lived ribonucleic acid (RNA) of about 300 bases during the course of spore formation. This transcript does not appear until an intermediate stage (III or IV) of development but is the predominant sporulation-specific transcript among RNAs of discrete size in late (stages IV to VI) developing cells. Appearance of the 300-base RNA is under sporulation control as this transcript could not be detected in cells of an early-blocked sporulation mutant (Spo0A). We have located the coding sequence for the 300-base RNA within a cloned chromosomal segment from the purA-cysA region that was previously shown to contain a cluster of genes that are actively transcribed during sporulation. The coding sequence for the 300-base RNA (designated as the 0.3 kb gene) mapped between a gene (veg) that was actively transcribed during growth and development and a gene (0.4 kb) that was turned on at the onset of sporulation. Although clustered within a small segment of the chromosome, the veg, 0.3 kb, and 0.4 kb transcription units exhibited, therefore, distinct patterns of temporally programmed gene expression. Models for the activation of the 0.3 kb gene at an intermediate stage of development are discussed.

Cloning of an early sporulation gene in Bacillus subtilis

A 0.8-megadalton BglII restriction fragment of Bacillus licheniformis cloned into the BglII site of plasmid pBD64 can complement spo0H mutations of Bacillus subtilis. The clone was isolated by selecting for the Spo+ phenotype and antibiotic resistance, using the helper system described by Gryczan et al. (Mol. Gen. Genet. 177:459-467, 1980). The insert is functional in both orientations and thus presumably has its own promoter. A deletion generated within the 0.8-megadalton insert by HindIII restriction and subsequent religation eliminates the ability of the cloned fragment to complement spo0H mutations. The cloned B. licheniformis deoxyribonucleic acid segment specifies the synthesis, in minicells, of a polypeptide of approximately 27,000 daltons. This protein is observed with both orientations, but not when the HindIII deletion is present in the cloned B. licheniformis chromosomal fragment. We have also demonstrated that ribonucleic acid complementary to the cloned B. licheniformis sporulation gene is transcribed in B. licheniformis both during vegetative growth and sporulation.

Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome

We describe a model system for studying developmentally regulated transcription during spore formation in Bacillus subtilis. This model system is a cloned cluster of genes known as 0.4 kb, ctc, and veg from the purA-cysA region of the B. subtilis chromosome. Each gene exhibited a distinct pattern of transcription in cells growing in glucose medium and in cells deprived of nutrients in sporulation medium. The 0.4 kb gene was transcribed at a low level in growing cells but was actively transcribed during nutrient deprivation in sporulation medium. This ribonucleic acid (RNA) synthesis was dependent upon the products of five B. subtilis genes that are involved in the initiation of spore formation:spo0A, spo0A, spo0E, spo0F, and spo0H. A mutation in any one of these regulatory genes severely restricted transcription of the 0.4 kb sequence. Transcription of the ctc gene was also turned on by nutrient deprivation, but this RNA synthesis was not impaired in spo0 mutants. Although not under spo0 control, the ctc gene probably corresponds to a locus, spoVC, whose product is required at a late stage of sporulation. Finally, the veg gene was actively transcribed both in growing cells and in nutrient-deprived cells. Like ctc RNA synthesis, transcription of the veg gene was not dependent upon the spo0 gene products. We propose that the spo0A, spo0B, spo0E, spo0F, and spo0H gene products are components of a pathway(s) that senses nutrient deprivation in B. subtilis and translates this environmental signal into the transcriptional activation of a subset of developmental genes.

Cloning of sporulation gene spoOB of Bacillus subtilis and its genetic and biochemical analysis

A specialized transducing phage carrying a sporulation gene (spoOB) was constructed from Bacillus subtilis temperate phage rho 11 by in vitro and in vivo recombinations. Transformation experiments showed that the spoOB gene resides on a 1.4-megadalton fragment generated by EcoRI endonuclease treatment of the phage deoxyribonucleic acid (DNA). Mutants of this phage which lost transducing activity were isolated and used for genetic complementation tests and the analysis of protein(s) coded by the 1.4-megadalton fragment. The spoOB locus was shown to be composed of one cistron. Sodium dodecyl sulfate-polyacrylamide gel analysis of proteins synthesized in ultraviolet-irradiated cells infected with these phages showed that the 1.4-megadalton fragment codes at least one protein, of molecular weight 39,000, which is synthesized in both vegetative and sporulating cells. A cleavage map of the phage DNA was constructed by use of restriction endonucleases, EcoRI, BamHI, and SalI, and the site of integration of the 1.4-megadalton fragment was determined. Expression and function of the spoOB gene are discussed.

Analysis of Bacillus subtilis sporulation with spore-converting bacteriophage PMB12

Previous observations concerning the ability of the spore-converting bacteriophage PMB12 to cause sporulation in certain sporulation-deficient mutants of Bacillus subtilis 168 were extended to include a spoOK mutant and a mutant temperature sensitive for sporulation due to a ribosomal mutation. Mutants of PMB12 that were unable to induce sporulation in the spoOK mutant were isolated to determine whether PMB12-encoded products had to affect the sporulation-specific functions of both the transcription and the translation systems of B. subtilis to induce sporulation. A complementation assay for spore conversion was used to assign the spore conversion-negative PMB12 mutants to four groups. One group of mutants repressed the ability of wild-type PMB12 to induce sporulation. None of the spore conversion-negative PMB12 mutants could induce significant levels of sporulation in B. subtilis mutants that were temperature sensitive for sporulation due to mutations in the beta subunit of ribonucleic acid polymerase or the 30S ribosomal subunit. Our data suggest that PMB12 may have at least three genes for spore conversion. The products of these genes apparently interact with a host cell pathway that is expressed during the earliest stage of sporulation and is not dependent for expression upon sporulation-specific functions of the host cell's transcription and translation systems.