Dissection of the expression signals of the spoA gene of Bacillus subtilis: glucose represses sporulation-specific expression

Viral terminal protein directs early organization of phage DNA replication at the bacterial nucleoid

The mechanism leading to protein-primed DNA replication has been studied extensively in vitro. However, little is known about the in vivo organization of the proteins involved in this fundamental process. Here we show that the terminal proteins (TPs) of phages ϕ29 and PRD1, infecting the distantly related bacteria Bacillus subtilis and Escherichia coli, respectively, associate with the host bacterial nucleoid independently of other viral-encoded proteins. Analyses of phage ϕ29 revealed that the TP N-terminal domain (residues 1-73) possesses sequence-independent DNA-binding capacity and is responsible for its nucleoid association. Importantly, we show that in the absence of the TP N-terminal domain the efficiency of ϕ29 DNA replication is severely affected. Moreover, the TP recruits the phage DNA polymerase to the bacterial nucleoid, and both proteins later are redistributed to enlarged helix-like structures in an MreB cytoskeleton-dependent way. These data disclose a key function for the TP in vivo: organizing the early viral DNA replication machinery at the cell nucleoid.

Glucose-resistant sporulation in Bacillus subtilis crsA47 mutants does not depend on promoter switching at the spo0A gene

We have found that sporulation in Bacillus subtilis crsA47 mutants does not require the sigma(H)-dependent promoter of the spo0A gene. This implies that the glucose-resistant sporulation phenotype of this strain is not related to the switch from the vegetative-stage sigma(A)-dependent promoter to the sigma(H)-dependent promoter at the spo0A gene.

Developmental gene expression in Bacillus subtilis crsA47 mutants reveals glucose-activated control of the gene for the minor sigma factor sigma(H)

The presence of excess glucose in growth media prevents normal sporulation of Bacillus subtilis. The crsA47 mutation, located in the gene for the vegetative phase sigma factor (sigma(A)) results in a glucose-resistant sporulation phenotype. As part of a study of the mechanisms whereby the mutation in sigma(A) overcomes glucose repression of sporulation, we examined the expression of genes involved in sporulation initiation in the crsA47 background. The crsA47 mutation had a significant impact on a variety of genes. Changes to stage II gene expression could be linked to alterations in the expression of the sinI and sinR genes. In addition, there was a dramatic increase in the expression of genes dependent on the minor sigma factor sigma(H). This latter change was paralleled by the pattern of spo0H gene transcription in cells with the crsA47 mutation. In vitro analysis of RNA polymerase containing sigma(A47) indicated that it did not have unusually high affinity for the spo0H gene promoter. The in vivo pattern of spo0H expression is not predicted by the known regulatory constraints on spo0H and suggests novel regulation mechanisms that are revealed in the crsA47 background.

Isolation and characterization of a sporulation initiation mutation in the Bacillus subtilis secA gene

A Bacillus subtilis secA mutant, secA12, which is blocked at an early stage of sporulation, is able to grow as well as the wild-type strain at all temperatures tested. Experiments with lacZ fusion genes showed that the induction of kinA expression, as well as the sporulation-specific transcription of the spo0A gene, was not observed in the secA12 mutant. However, transcription of the spo0H gene (coding for sigmaH, which is required for the transcription of kinA and spo0A) and accumulation of the sigmaH protein were not affected in secA12. These results suggested that mutations in secA affect a factor required for efficient transcription of kinA as well as for the activation of the phosphorelay pathway.

Expression of kinA and accumulation of sigma H at the onset of sporulation in Bacillus subtilis

Induction of the Bacillus subtilis kinA gene, which codes for a major kinase of the phosphorelay pathway, required the spo0H gene, coding for the sigma H protein, but not the genes spo0A, spo0B, and spo0F at the onset of sporulation. Also, the levels of sigma H in spo0A, spo0B, and spo0F mutants were increased at the onset of sporulation, though induction of spo0H transcription in all of these mutants was appreciably inhibited. In addition, kinA expression was almost completely eliminated in a medium supplemented with excess glucose and glutamine, even though the usual stationary-phase-associated increase in sigma H was observed under these conditions.

Effects of spo0 mutations on spo0A promoter switching at the initiation of sporulation in Bacillus subtilis

Transcriptional analyses of the Bacillus subtilis sporulation initiator gene spo0A revealed that promoter switching from the vegetative (Pv) to the sporulation-specific (Ps) promoter did not occur in the spo0A, spo0B, spo0E, spo0F, and spo0H mutants. The sof-1 mutation in spo0A restored the promoter switching in the spo0F mutant. These results strongly suggest that Spo0A plays a central role in the regulation of its own promoter switching.

Krebs cycle function is required for activation of the Spo0A transcription factor in Bacillus subtilis

Expression of genes early during sporulation in Bacillus subtilis requires the activity of the transcription factor encoded by spo0A. The active, phosphorylated form of Spo0A is produced through the action of a multicomponent pathway, the phosphorelay. A mutant defective in the first three enzymes of the Krebs citric acid cycle was unable to express early sporulation genes, apparently because of a failure to activate the phosphorelay. Cells that produce an altered Spo0A protein that can be phosphorylated by an alternative pathway were not dependent on Krebs cycle function for early sporulation gene expression. These findings suggest that Krebs cycle enzymes transmit a signal to activate the phosphorelay and that B. subtilis monitors its metabolic potential before committing itself to spore formation.

Analysis of a suppressor mutation ssb (kinC) of sur0B20 (spo0A) mutation in Bacillus subtilis reveals that kinC encodes a histidine protein kinase

sur0B20 is a mutation that suppresses the effects of spo0B delta B or spo0F221 mutations in Bacillus subtilis, sur0B20 is an allele of the spo0A gene (Glu-14 to Val-14 conversion) and restores the sporulation of spo0B or spo0F mutants to the wild-type level. Here, we report the isolation of suppressor mutations of sur0B20 (ssb). One of these mutations, ssb-12, severely impairs the suppressor activity of sur0B20. A 2.5-kbp MboI fragment which complements the ssb-12 mutation was cloned by the prophage transformation method using phi CM as a vector. Nucleotide sequencing of the fragment revealed two open reading frames (orf1 and orf2). Gene disruption and complementation experiments showed that orf2 is the ssb gene. ssb was shown to encode a protein with a molecular weight of 48,846 (428 amino acid residues) showing strong similarity to transmitter kinases, especially KinA, of two-component regulatory systems. Therefore, ssb was renamed kinC. Deletion of kinC had no observable effect on sporulation. kinC transcription was induced at the onset of sporulation, probably from a sigma A-dependent promoter, and its expression was shut off at T3. DNase I protection experiments showed that the Spo0A protein binds to two adjoining sites in the kinC promoter region with different affinities. These results suggest that kinC expression might be regulated by Spo0A.

Temperature-sensitive sporulation caused by a mutation in the Bacillus subtilis secY gene

A thermosensitive sporulation mutant of Bacillus subtilis containing a mutation in the secY gene was isolated and characterized. No asymmetric septum specific to the sporulation was detected by electron microscopy at the nonpermissive temperature, indicating that the block occurred at a very early stage of sporulation. Furthermore, competence development in the mutant cell was affected even at the sporulation-proficient temperature. It is assumed that the SecY protein of B. subtilis has multiple roles both in the regulation of spore formation and in stationary-phase-associated phenomena.

Genetic competence in Bacillus subtilis

Genetic competence may be defined as a physiological state enabling a bacterial culture to bind and take up high-molecular-weight exogenous DNA (transformation). In Bacillus subtilis, competence develops postexponentially and only in certain media. In addition, only a minority of the cells in a competent culture become competent, and these are physiologically distinct. Thus, competence is subject to three regulatory modalities: growth stage specific, nutritionally responsive, and cell type specific. This review summarizes the present state of knowledge concerning competence in B. subtilis. The study of genes required for transformability has permitted their classification into two broad categories. Late competence genes are expressed under competence control and specify products required for the binding, uptake, and processing of transforming DNA. Regulatory genes specify products that are needed for the expression of the late genes. Several of the late competence gene products have been shown to be membrane localized, and others are predicted to be membrane associated on the basis of amino acid sequence data. Several of these predicted protein sequences show a striking resemblance to gene products that are involved in the export and/or assembly of extracellular proteins and structures in gram-negative organisms. This observation is consistent with the idea that the late products are directly involved in transport of DNA and is equally consistent with the notion that they play a morphogenetic role in the assembly of a transport apparatus. The competence regulatory apparatus constitutes an elaborate signal transduction system that senses and interprets environmental information and passes this information to the competence-specific transcriptional machinery. Many of the regulatory gene products have been identified and partially characterized, and their interactions have been studied genetically and in some cases biochemically as well. These include several histidine kinase and response regulator members of the bacterial two-component signal transduction machinery, as well as a number of known transcriptionally active proteins. Results of genetic studies are consistent with the notion that the regulatory proteins interact in a hierarchical way to make up a regulatory pathway, and it is possible to propose a provisional scheme for the organization of this pathway. It is remarkable that almost all of the regulatory gene products appear to play roles in the control of various forms of postexponential expression in addition to competence, e.g., sporulation, degradative-enzyme production, motility, and antibiotic production. This has led to the notion of a signal transduction network which transduces environmental information to determine the levels and timing of expression of the ultimate products characteristic of each of these systems.

Differential regulation of spo0A transcription in Bacillus subtilis: glucose represses promoter switching at the initiation of sporulation

We have shown by S1 nuclease mapping with in vivo transcripts that the differential expression of a sporulation-regulatory gene, spo0A, is regulated by switching of two discrete promoters during the initiation of sporulation in Bacillus subtilis; vegetative mRNA was transcribed from an upstream promoter (Pv, vegetative promoter), and sporulation-specific mRNA was transcribed from the other promoter (Ps, sporulation-specific promoter) about 150 bp downstream of the Pv promoter. Transcription from the Pv promoter was at a low level and shut off at T0.5. On the other hand, transcription from the Ps promoter was strongly induced at T0.5 and increased until T2.5. In the presence of 2% glucose, Pv-directed transcription was not shut off and was observed even at T1.5, whereas the induction of Ps-directed transcription was completely repressed. A mutant in which the spo0A gene was transcribed only from the Ps promoter could sporulate normally in the presence of 0.1% glucose but could not sporulate at all in the presence of 2% glucose. In a catabolite-resistant sporulation mutant carrying crsA47 (sigA47), a mutation within the gene encoding sigma A, normal promoter switching from Pv to Ps was observed in the presence of 2% glucose.

The Bacillus subtilis spo0J gene: evidence for involvement in catabolite repression of sporulation

Previous observations concerning the ability of the Bacillus subtilis bacteriophages SP10 and PMB12 to suppress mutations in spo0J and to make wild-type sporulation catabolite resistant suggested that spo0J had a role in catabolite repression of sporulation. This suggestion was supported in the present report by the ability of the catabolite-resistant sporulation mutation crsF4 to suppress a Tn917 insertion mutation of the B. subtilis spo0J locus (spo0J::Tn917 omega HU261) in medium without glucose. Although crsF4 and SP10 made wild-type B. subtilis sporulation catabolite resistant, neither crsF4 nor SP10 caused a mutant with spo0J::Tn917 omega HU261 to sporulate in medium with glucose. Sequencing the spo0J locus revealed an open reading frame that was 179 codons in length. Disruption of the open reading frame resulted in a sporulation-negative (Spo-) phenotype that was similar to those of other spo0J mutations. Analysis of the deduced amino acid sequence of the spo0J locus indicated that the spo0J gene product contains an alpha-helix-turn-alpha-helix unit similar to the motif found in lambda Cro-like DNA-binding proteins.

Temporal regulation of the Bacillus subtilis early sporulation gene spo0F

The initiation of sporulation in Bacillus subtilis depends on seven genes of the spo0 class. One of these, spo0F, codes for a protein of 14,000 daltons. We studied the regulation of spo0F by using spo0F-lacZ translational fusions and also measured Spo0F protein levels by immunoassays. spo0F-lacZ and Spo0F levels increased as the cells entered the stationary phase, and this effect was repressed by glucose and glutamine. Decoyinine, which lowers GTP levels and allows sporulation in the presence of normally repressing levels of glucose, induced spo0F-lacZ expression and raised Spo0F levels. The expression of spo0F-lacZ was dependent on spo0A, -0B, -0E, -0F, and -0H genes, a spo0H deletion causing the strongest effect. In most respects, the spo0F gene was regulated in a manner similar to that of spoVG. However, the presence of an abrB mutation did not relieve the dependence of spo0F gene expression on spo0A, as it does with spoVG (P. Zuber and R. Losick, J. Bacteriol. 169:2223-2230, 1987).

Site-directed mutagenesis of a catabolite repression operator sequence in Bacillus subtilis

Catabolite repression of the Bacillus subtilis alpha-amylase gene (amyE) involves an operator sequence located just downstream of the promoter (amyR), overlapping the transcription start site. Oligonucleotide site-directed mutagenesis of this sequence identified bases required for catabolite repression. Two mutations increased both the 2-fold symmetry of the operator and the repression ratio. Although many mutations reduced the repression ratio 3- to 11-fold, some also caused a 2-fold or greater increase in amylase production. Others caused hyperproduction without affecting catabolite repression. Homologous sequences in other catabolite-repressed B. subtilis promoters suggest a common regulatory site may be involved in catabolite repression.