Processing of a sporulation sigma factor in Bacillus subtilis: how morphological structure could control gene expression

Establishment of cell type by compartmentalized activation of a transcription factor

Early in the process of spore formation in Bacillus subtilis a septum is formed that partitions the sporangium into daughter cells called the forespore and the mother cell. The daughter cells each have their own chromosome but follow dissimilar programs of gene expression. Differential gene expression in the forespore is now shown to be established by the compartmentalized activity of the transcription factor sigma F. The sigma F factor is produced prior to septation, but is active only in the forespore compartment of the post-septation sporangium. The sigma F factor is controlled by the products of sporulation operons spoIIA and spoIIE, which may be responsible for confining its activity to one of the daughter cells.

Sporulation operon spoIVF and the characterization of mutations that uncouple mother-cell from forespore gene expression in Bacillus subtilis

During the process of endospore formation in Bacillus subtilis the appearance of the mother-cell transcription factor sigma K by conversion from its inactive precursor pro-sigma K is coupled to events under the control of the forespore transcription factor sigma G. This intercompartmental coupling is believed to be mediated by the products of a sporulation locus called spoI V F because certain bypass-of-forespore (bof) mutations that map at the spoI V F locus relieve the dependence of pro-sigma K processing on the action of sigma G in the forespore. We now report that spoI V F is a two-cistron operon whose transcription is under the control of the sporulation transcription factor sigma E and whose products are likely to be integral membrane proteins. We show that the products of both the promoter-proximal (spoI V F A) and promoter-distal (spoI V F B) cistrons are required for spore formation at 37 degrees C, but that the spoI V F A gene product is dispensable at 30 degrees C. The bypass-of-forespore mutations are located at the extreme 3' end of the spoI V F A cistron, one such mutation causing a proline to serine substitution eight residues from the COOH terminus of SpoIVFA and another (a nonsense mutation) causing the absence of the terminal six amino acid residues of the protein. We also show that at a permissive temperature for spore formation spoI V F A null mutants exhibit a bypass-of-forespore phenotype. We hypothesize that SpoIVFA functions positively in stabilizing SpoIVFB, which we propose is thermolabile in the absence of the promoter-proximal gene product, and negatively in inhibiting the action of SpoIVFB. A model for intercompartmental coupling is presented in which SpoIVFB promotes pro-sigma K processing in response to a signal from the forespore that relieves or otherwise counteracts the inhibitory effect of SpoIVFA on SpoIVFB.

Differentiation and the establishment of cell type during sporulation in Bacillus subtilis

Differentiation in Bacillus subtilis involves the formation of specialized cell types called the mother cell and the forespore. These differ from each other and from their parent in developmental fate. Establishment of the two cell types and their subsequent differentiation is governed by the compartmentalized action of six developmental transcription factors.

Separate promoters direct expression of phoAIII, a member of the Bacillus subtilis alkaline phosphatase multigene family, during phosphate starvation and sporulation

Alkaline phosphatase (APase) expression can be induced in Bacillus subtilis by phosphate starvation or by sporulation. We have recently shown that there are multiple APase structural genes contributing to the total alkaline phosphatase expression in B. subtilis. The expression of the alkaline phosphatase III gene (phoAIII) was analysed under both phosphate-starvation induction and sporulation induction conditions. phoAII is transcribed from two promoter regions, PV and PS. The PV promoter initiated transcription 37 bp before the translation initiation codon and was used to transcribe phoAIII during phosphate-starvation induction in vegetative cells. The PS promoter initiated transcription 119 bp before the translation initiation codon and was used during sporulation induction. Genes which have previously been shown to affect total vegatative APase, pho regulon genes phoP, phoR and phoS, affected expression of phoAIII during phosphate starvation. Genes known to affect expression of total sporulation APase, i.e. spoIIA, spoIIG and spoIIE, affected phoAIII expression during sporulation induction. Our data show that one member of the APase multigene family, phoAIII, contributes to the total APase expression both during phosphate-starvation induction and sporulation induction, and that the mechanism of regulation includes two promoters, each requiring different regulatory genes.

Expression of stage II genes during sporulation in Bacillus subtilis

Two RNA polymerase sigma factors, sigma F and sigma E, are produced during the first two hours of endospore formation in Bacillus subtilis. Transcription of the structural genes for these factors is activated about one hour after the start of endospore formation. The operon encoding sigma F is transcribed by RNA polymerase containing sigma H, another secondary sigma factor, whereas the operon encoding sigma E is transcribed by RNA polymerase containing sigma A, the primary sigma factor in growing cells. Evidently, the coordinate temporal control of these transcriptional units is mediated by a factor other than the sigma factors, possibly by the DNA-binding protein encoded by spo0A. Both sigma F and sigma E activities are also regulated by mechanisms operating after transcription.

The spoIIIA operon of Bacillus subtilis defines a new temporal class of mother-cell-specific sporulation genes under the control of the sigma E form of RNA polymerase

We have cloned and characterized a 5 kbp region of the Bacillus subtilis chromosome and show that it contains the promoter-proximal part of the spoIIIA locus. The locus consists of a polycistronic operon containing at least three genes. We show that the operon is regulated at the transcriptional level, from a promoter that is first activated about 80 minutes after the induction of sporulation, immediately after septation. Expression of spoIIIA in different spo mutant backgrounds correlates with the ability of each strain to synthesize the sporulation-specific sigma factor, sigma E. Moreover, synthesis of sigma E in vegetative cells by use of an inducible promoter causes expression of mother-cell-specific genes spoIID, spoIIIA, and spoIIID, but not the prespore-specific genes, spoIIIG and spoVA. We suggest that sigma E may be the primary determinant of mother-cell-specific gene expression and that the SpoIIID protein exerts an additional level of regulation on spoIIIA, apparently by acting as a transcriptional repressor. Since the onset of spoIIID expression occurs about 10 minutes after that of spoIIIA, spoIIIA expression is transient. Thus spoIIIA defines a third temporal class of gene controlled by the sigma E form of RNA polymerase.

Effects of mutant small, acid-soluble spore proteins from Bacillus subtilis on DNA in vivo and in vitro

alpha/beta-type small, acid-soluble spore proteins (SASP) of Bacillus subtilis bind to DNA and alter its conformation, topology, and photochemistry, and thereby spore resistance to UV light. Three mutations have been introduced into the B. subtilis sspC gene, which codes for the alpha/beta-type wild-type SASP, SspCwt. One mutation (SspCTyr) was a conservative change, as residue 29 (Leu) was changed to Tyr, an amino acid found at this position in other alpha/beta-type SASP. The other mutations changed residues conserved in all alpha/beta-type SASP. In one (SspCAla), residue 52 (Gly) was changed to Ala; in the second (SspCGln), residue 57 (Lys) was changed to Gln. The effects of the wild-type and mutant SspC on DNA properties were examined in vivo in B. subtilis spores and Escherichia coli as well as in vitro with use of purified protein. Both SspCwt and SspCTyr interacted similarly with DNA in vivo and in vitro, restoring much UV resistance to spores lacking major alpha/beta-type SASP, causing a large increase in plasmid negative supercoiling, and altering DNA UV photochemistry from cell type to spore type. In contrast, SspCAla had no detectable effect on DNA properties in vivo or in vitro, while SspCGln had effects intermediate between those of SspCAla and SspCwt. Strikingly, neither SspCAla nor SspCGln bound well to DNA in vitro. These results confirm the importance of the conserved primary sequence of alpha/beta-type SASP in the ability of these proteins to bind to spore DNA and cause spore UV resistance.

The stringent response blocks DNA replication outside the ori region in Bacillus subtilis and at the origin in Escherichia coli

When the Bacillus subtilis dnaB37 mutant, defective in initiation, is returned to permissive temperature after growth at 45 degrees C, DNA replication is synchronized. Under these conditions, we have shown previously that DNA replication is inhibited when the Stringent Response is induced by the amino acid analogue, arginine hydroxamate. We have now shown, using DNA-DNA hybridization analysis, that substantial replication of the oriC region nevertheless occurs during the Stringent Response, and that replication inhibition is therefore implemented downstream from the origin. On the left arm, replication continues for at least 190 x 10(3) base-pairs to the gnt gene and for a similar distance on the right arm to the gerD gene. When the Stringent Response is lifted, DNA replication resumed downstream from oriC on both arms, confirming that DNA replication is regulated at a post-initiation level during the Stringent Response in B. subtilis. Resumption of DNA synthesis following the lifting of the Stringent Response did not require protein or RNA synthesis or the initiation protein DnaB. We suggest, therefore, that a specific control region, involving Stringent Control sites, facilitate reversible inhibition of fork movement downstream from the origin via modifications of a replisome component during the Stringent Response. In contrast, in Escherichia coli, induction of the Stringent Response appears to block initiation of DNA replication at oriC itself. No DNA synthesis was detected in the oriC region and, upon lifting the Stringent Response, replication occurred from oriC. Post-initiation control in B. subtilis therefore results in duplication of many key genes involved in growth and sporulation. We discuss the possibility that such a control might be linked to differentiation in this organism.

Molecular cloning and characterization of two genes encoding sigma factors that direct transcription from a Bacillus thuringiensis crystal protein gene promoter

Two sigma factors, sigma 35 and sigma 28, direct transcription from the Bt I and Bt II promoters of the cryIA(a) gene of Bacillus thuringiensis; this gene encodes a lepidopteran-specific crystal protoxin. These sigma factors were biochemically characterized in previous work (K. L. Brown and H. R. Whiteley, Proc. Natl. Acad. Sci. USA 85:4166-4170, 1988; K. L. Brown and H. R. Whiteley, J. Bacteriol. 172:6682-6688, 1990). In this paper, we describe the cloning of the genes encoding these two sigma factors, as well as their nucleotide and deduced amino acid sequences. The deduced amino acid sequences of the sigma 35 and sigma 28 genes show 88 and 85% identity, respectively, to the sporulation-specific sigma E and sigma K polypeptides of Bacillus subtilis. Transformation of the sigma 35 and sigma 28 genes into B. subtilis shows that the respective B. thuringiensis sigma factor genes can complement spoIIG55 (sigma E) and spoIIIC94 (sigma K) defects. Further, B. thuringiensis core polymerase reconstituted with either the sigma 35 or sigma 28 polypeptide directs transcription from B. subtilis promoters recognized by B. subtilis RNA polymerase containing sigma E and sigma K, respectively. Thus, sigma 35 and sigma 28 of B. thuringiensis appear to be functionally equivalent to sigma E and sigma K of B. subtilis. However, unlike the situation for sigma K in B. subtilis, the homologous sigma 28 gene in B. thuringiensis does not result from a late-sporulation-phase chromosomal rearrangement of two separate, partial genes.

Spo0A binds to a promoter used by sigma A RNA polymerase during sporulation in Bacillus subtilis

Examination of the effects of 56 single-base-pair substitutions in the spoIIG promoter and studies of the interaction of the spo0A product (Spo0A) with this promoter in vitro demonstrated that Spo0A acts directly to enable this promoter to be used by sigma A-associated RNA polymerase (EC 2.7.7.6). The spoIIG operon from Bacillus subtilis is transcribed during sporulation by a form o RNA polymerase containing sigma A, the primary sigma factor in vegetative cells. The spoIIG promoter is unusual in that it contains sequences that are similar to those found at the -10 and -35 regions of promoters that are used by sigma A-associated RNA polymerase, but these sigma A-like recognition sequences are separated by 22 base pairs rather than the typical 17 or 18 base pairs. We found that single-base-pair substitutions in the around the -35-like sequence, and substitutions in a region upstream from this position, around position -87, reduced promoter activity. DNase I protection and electrophoretic gel mobility shift assays were used to demonstrate that Spo0A binds specifically to these regions in vitro. Evidently, the -35-like sequence is part of a Spo0A binding site and therefore is possibly not a sigma A-recognition sequence. These results support a model in which Spo0A activates the spoIIG promoter after the onset of endospore formation.

Genetic regulation of morphogenesis in Bacillus subtilis: roles of sigma E and sigma F in prespore engulfment

Electron microscopic examination of sporulating cultures of wild-type Bacillus subtilis revealed that the morphological events previously characterized as stages II and III can be divided into four substages, namely, stages IIi, IIii, IIiii, and III. The ultrastructural phenotypes of several stage II mutant strains indicate that each of the four substages has a biochemical and genetic basis. Two of the genes needed for the transition from stage II to stage III encode transcription factors sigma E and sigma F. Their roles during spore morphogenesis have been the subject of much speculation. We now show that sigma E controls genes involved in the morphological transition from stage IIi to stage IIii and then stage IIiii, while the transition to stage III may be determined by genes controlled by sigma F. The results also indicate the existence of at least two undiscovered sporulation genes involved in B. subtilis spore morphogenesis.

A model for asymmetric septum formation during sporulation in Bacillus subtilis

Many differentiation processes in both prokaryotes and eukaryotes begin with an asymmetric division, producing 'daughter' cells that differ in size and developmental fate. This is particularly obvious in the well-studied prokaryotic life cycles of Caulobacter and Bacillus. In no system, however, is the mechanism of asymmetric division understood. Here I propose a model for the mechanism of asymmetric division during sporulation in Bacillus subtilis. The model explains both the timing and asymmetric localization of spore-septum formation. It also explains the morphological phenotypes of various asporogenous (spo) mutants.

Synthesis of a Bacillus subtilis small, acid-soluble spore protein in Escherichia coli causes cell DNA to assume some characteristics of spore DNA

Small, acid-soluble proteins (SASP) of the alpha/beta-type are associated with DNA in spores of Bacillus subtilis. Induction of synthesis of alpha/beta-type SASP in Escherichia coli resulted in rapid cessation of DNA synthesis, followed by a halt in RNA and then protein accumulation, although significant mRNA and protein synthesis continued. There was a significant loss in viability associated with SASP synthesis in E. coli: recA+ cells became extremely long filaments, whereas recA mutant cells became less filamentous. The nucleoids of cells with alpha/beta-type SASP were extremely condensed, as viewed in both light and electron microscopes, and immunoelectron microscopy showed that the alpha/beta-type SASP were associated with the cell DNA. Induction of alpha/beta-type SASP synthesis in E. coli increased the negative superhelical density of plasmid DNA by approximately 20%; UV irradiation of E. coli with alpha/beta-type SASP gave reduced yields of thymine dimers but significant amounts of the spore photoproduct. These changes in E. coli DNA topology and photochemistry due to alpha/beta-type SASP are similar to the effects of alpha/beta-type SASP on the DNA in Bacillus spores, further suggesting that alpha/beta-type SASP are a major factor determining DNA properties in bacterial spores.

FtsZ in Bacillus subtilis is required for vegetative septation and for asymmetric septation during sporulation

A Bacillus subtilis strain was constructed in which the cell division gene, ftsZ, was placed under control of the isopropyl-beta-D-thiogalactoside (IPTG)-inducible spac promoter. This strain was dependent upon the presence of IPTG for cell division and colony formation indicating that ftsZ is an essential cell division gene in this organism. In sporulation medium this strain increased in mass and reached stationary phase in the presence or absence of IPTG, but only sporulated in the presence of IPTG. The expression of the sporulation genes spoIIG, spoIIA, and spoIIE occurred normally in the absence of IPTG as monitored by spo-lacZ fusions. However, expression of lacZ fusions to genes normally induced later in the developmental pathway, and that required processed pro-sigma E for expression, was inhibited. Immunoblot analysis revealed that pro-sigma E was not processed to its active form (sigma E) under these experimental conditions. Electron microscopy revealed that these FtsZ-depleted cells did not initiate asymmetric septation, suggesting that FtsZ has a common role in the initiation of both the vegetative and sporulation septa.

FtsZ and cell division

The ftsZ gene in Escherichia coli is thought to be an essential gene and to play a pivotal role in cell division. Gene disruption experiments confirmed that ftsZ is an essential gene. Examination of cellular responses to FtsZ depletion indicated that FtsZ was required for division but not for nucleoid segregation. Analysis of mutations within the ftsZ, gene, selected for resistance to the cell division inhibitor SulA, revealed that they also conferred resistance to MinCD. This raises the possibility that ftsZ is the target of these two cell division inhibitors. Analysis of the ftsZ gene from Bacillus subtilis revealed that the gene was required for both septation during vegetative growth and asymmetric septation during sporulation.

Processing of the mother-cell sigma factor, sigma K, may depend on events occurring in the forespore during Bacillus subtilis development

During sporulation of the Gram-positive bacterium Bacillus subtilis, transcription of genes encoding spore coat proteins in the mother-cell compartment of the sporangium is controlled by RNA polymerase containing the sigma subunit called sigma K. Based on comparison of the N-terminal amino acid sequence of sigma K with the nucleotide sequence of the gene encoding sigma K (sigK), the primary product of sigK was inferred to be a pro-protein (pro-sigma K) with 20 extra amino acids at the N terminus. Using antibodies generated against pro-sigma K, we have detected pro-sigma K beginning at the third hour of sporulation and sigma K beginning about 1 hr later. Even when pro-sigma K is expressed artificially during growth and throughout sporulation, sigma K appears at the normal time and expression of a sigma K-controlled gene occurs normally. These results suggest that pro-sigma K is an inactive precursor that is proteolytically processed to active sigma K in a developmentally regulated fashion. Mutations that block forespore gene expression block accumulation of sigma K but not accumulation of pro-sigma K, suggesting that pro-sigma K processing is a regulatory device that couples the programs of gene expression in the two compartments of the sporangium. We propose that this regulatory device ensures completion of forespore morphogenesis prior to the synthesis in the mother-cell of spore coat proteins that will encase the forespore.

Binding of DNA in vitro by a small, acid-soluble spore protein from Bacillus subtilis and the effect of this binding on DNA topology

The DNA within spores of Bacillus subtilis is complexed with a large amount of alpha/beta-type small, acid-soluble spore protein (SASP). Measurement of the interaction of a purified alpha/beta-type SASP with DNA in vitro by a filter binding assay showed that the binding saturated at one molecule of SASP per approximately 5 bp. SASP-DNA binding did not require a divalent cation, was optimal at pH 6.7, and was unaffected by salt up to 400 mM. Binding of SASP to relaxed plasmid DNA in the presence of topoisomerase I resulted in the introduction of 18 (for plasmid pUC19) or 36 (for plasmid pUB110) negative supertwists, a superhelical density similar to that found in several plasmids isolated from spores. The SASP-dependent introduction of negative supertwists did not require a divalent cation, was unaffected by salt, and also gave a value of one molecule of SASP per approximately 5 bp at saturation. There was at least one slow step in the binding of SASP to DNA as seen in both the filter binding and supercoiling assays.

Use of integrational plasmid excision to identify cellular localization of gene expression during sporulation in Bacillus subtilis

Sporulation in Bacillus subtilis is a simple developmental system involving the differentiation of two sister cells, the prespore and the mother cell. Many of the genes that regulate sporulation (spo genes) are thought to be expressed differentially. However, direct demonstration of differential gene expression, by fractionation of prespore and mother cell proteins, is possible only at a relatively late stage of development. H. De Lencastre and P. J. Piggot (J. Gen. Microbiol. 114:377-389, 1979) have described a genetic method for determining the cellular location of the requirement for spo gene expression. Here we describe a similar method based on the use of integrational plasmids that can insertionally inactivate any given spo gene. Loss of the integrated plasmid by homologous recombination leads to the restoration of spo gene function. If this occurs just before sporulation begins, the phenotypes of the progeny of heat-resistant spores should depend on whether the gene is required in the prespore or the mother cell. Thus, we show that for known prespore-specific genes, such as spoIIIG and spoVA, only phenotypically Spo+ progeny that have lost the integrated plasmid are produced. In contrast, for mother-cell-specific genes, such as spoIIIC and spoVJ, a substantial proportion of the progeny are asporogenous, having retained the integrated plasmid. On the basis of our results, the spoIID and spoIIIA genes, which are expressed soon after division, appear to be required only in the mother cell compartment.

The spoIIIA locus is not a major determinant of prespore-specific gene expression during sporulation in Bacillus subtilis

During sporulation in Bacillus subtilis, expression of several prespore-specific genes is strongly dependent on the spoIIIE and spoIIIG gene products. Previous reports have also indicated a requirement for the products of the spoIIIA locus. However, we have now systematically studied six different well-defined spoIIIA mutations and find that, relative to spoIIIE and spoIIIG mutations, they have only a minor effect on the expression of two different prespore-specific genes, spoVA and sspA. Moreover, we have shown that strain IS37, which has been used as a spoIIIA mutant in several previous studies, actually contains a lesion in the spo0A gene. We conclude that spoIIIA has a relatively minor or indirect role in the regulation of prespore-specific gene expression.

Cascades of sigma factors revisited

Programmed gene expression during the process of endospore formation in Bacillus subtilis is governed by the successive appearance of five developmental sigma factors. These sigma factors are encoded by genes in which mutations arrest sporulation at a defined stage. These genes are turned on sequentially and depend for their own transcription on the activity of a previously synthesized sigma factor. Superimposed on the regulation of synthesis of the sigma factors are post-transcriptional control mechanisms that couple the activation of the developmental sigma factors to the course of sporulation. Here we review evidence indicating that these developmental transcription factors comprise a regulatory cascade in the order sigma H----sigma F----sigma E----sigma G----sigma K in which the activity of each sigma factor depends on the action of the preceding sigma factor in the cascade.

Development-specific sigma-factor essential for late-stage differentiation of Myxococcus xanthus

The gene for a developmentally expressed sigma-factor, sigB, has been isolated from Myxococcus xanthus by use of the sigA gene (formerly rpoD) of the vegetative sigma-factor as a probe. The sequence of sigB has been determined, and an open reading frame of 193 amino acid residues (Mr = 21,551) was identified. The amino-terminal region of SigB contains 69 residues, of which 35 are identical (50% identity) to the region of SigA required for core RNA polymerase binding and initiation of RNA polymerization. SigB also possesses many features commonly found in other prokaryotic sigma-factors. Analysis of an M. xanthus strain carrying a sigB-lacZ fusion gene revealed that sigB is expressed from a middle to late stage of differentiation corresponding to the period from the onset of sporulation to late development. A sigB deletion mutant displayed normal mound formation and sporulation; however, production of the ops gene product in myxospores of the delta sigB strain was shown to be blocked. Myxospores from the sigB deletion strain also exhibited severe defects in stability and viability during late development. Our data indicate that sigB encodes a sigma-factor essential for the maturation of myxospores at a late stage of M. xanthus differentiation. Our results also suggest that differentiation of M. xanthus is regulated by development-specific sigma-factors.

Effects of antibiotics on synthesis and persistence of sigma E in sporulating Bacillus subtilis

A potential regulatory link between the activation of a sporulation-specific sigma factor (sigma E) and forespore septum formation was investigated by treating Bacillus subtilis with inhibitors of protein or peptidoglycan synthesis and monitoring the consequences of these treatments on sigma E activation and septation. Western blot (immunoblot) and electron microscopic analyses revealed that both the formation of sigma E and septation were inhibited to a similar degree when either rifampin or chloramphenicol was added at different times before the second hour into sporulation but that penicillin preferentially blocked septation. We interpret these results as indicating that the syntheses of the gene products for both septation and sigma E activation occur at approximately the same time in development but that synthesis of an intact septum is unlikely to be a prerequisite for the formation of sigma E. We observed that penicillin could not only block septation but, depending on the time of its addition, could also inhibit both the activation of sigma E and the synthesis of its precursor. The basis of this effect is unknown, but it is not due to an overall disruption of protein synthesis. The incorporation of [35S] methionine by the sporulating cultures was unaffected by penicillin treatment. A time course study of the effects of rifampin and chloramphenicol treatments on sigma E levels revealed that both the synthesis of sigma E and its disappearance from sporulating cultures is inhibited by these antibiotics. This suggests that ongoing macromolecular synthesis is required for the turnover of sigma E.

A forespore checkpoint for mother cell gene expression during development in B. subtilis

Gene expression in the mother cell compartment of sporulating cells of B. subtilis is partly governed by the mother cell RNA polymerase sigma factor sigma K. Paradoxically, sigma K-directed gene expression also depends on sigma G, the product of the forespore compartment regulatory gene spoIIIG, and on other forespore regulatory proteins. We now identify mutations in the genes bofA and bofB that relieve the dependence of mother cell gene expression on forespore regulatory proteins but not on sigma K. We establish that the dependence of mother cell gene expression on the forespore regulatory proteins is mediated at the level of the conversion of pro-sigma K to its mature, active form. We propose that the bofA and/or bofB proteins govern this conversion in response to a signal generated by the forespore. Activation of pro-sigma K could be a checkpoint for coordinating gene expression between the mother cell and forespore compartments of the developing sporangium.

Surface-induced swarmer cell differentiation of Vibrio parahaemolyticus

Vibrio parahaemolyticus distinguishes between life in a liquid environment and life on a surface. Growth on a surface induces differentiation from a swimmer cell to a swarmer cell type. Each cell type is adapted for locomotion under different circumstances. Swimmer cells synthesize a single polar flagellum (Fla) for movement in a liquid medium, and swarmer cells produce an additional distinct flagellar system, the lateral flagella (Laf), for movement across a solid substratum, called swarming. Recognition of surfaces is necessary for swarmer cell differentiation and involves detection of physical signals peculiar to that circumstance and subsequent transduction of information to affect expression of swarmer cell genes (laf). The polar flagellum functions as a tactile sensor controlling swarmer cell differentiation by sensing forces that restrict its movement. Surface recognition also involves a second signal, i.e. nutritional limitation for iron. Studying surface-induced differentiation could reveal a novel mechanism of gene control and lead to an understanding of the processes of surface colonization by pathogens and other bacteria.

Cascade regulation of spore coat gene expression in Bacillus subtilis

Endospores of the Gram-positive bacterium Bacillus subtilis are encased in a tough protein shell known as the coat. The coat is composed of a dozen or more different structural proteins. We report the identification of and studies on the regulation of promoters governing the expression of coat protein (cot) genes designated B to E encoding polypeptides of 59, 12, 11 and 24 kDa, respectively. We show that transcription of genes B, C and D is governed by single promoters and that transcription of gene E is governed by tandem promoters designated P1 and P2. In extension of recent work on the transcription of cot gene A and the mother-cell regulatory genes gerE, sigK and spoIIID, we show that genes involved in coat formation are turned on in a regulatory cascade of at least four co-ordinately controlled gene sets. The cascade consists of: cotE as transcribed from its P1 promoter and spoIIID, which are turned on during hours three to four of sporulation; cotE as transcribed from its P2 promoter and sigK, which are turned on during hour five by the appearance of the product (a small DNA-binding protein) of spoIIID; cotA, cotD and gerE, which are turned on during hours five to six by the appearance of the product (sigma factor sigma K) of sigK; and cotB and cotC, which are turned on during hour seven by the appearance of the product (an inferred DNA-binding protein) of gerE. The cascade is hierarchical in that the first three gene sets each contain the regulatory gene that turns on the expression of the next gene set in the pathway. We also show that the level of expression of a member (cotC) of the terminal class of gene expression is strongly influenced by medium and that this effect directly or indirectly depends on the product of sporulation gene spoIV A.

Differential gene expression during sporulation in Bacillus subtilis: structure and regulation of the spoIIID gene

The gene spoIIID, which is essential for spore formation in Bacillus subtilis, was cloned and sequenced. It consists of one open reading frame which would encode a 93-amino-acid protein with a classic helix-turn-helix motif, characteristic of sequence-specific DNA-binding proteins. SpoIIID protein is a previously identified transcription factor, capable of altering the specificity of RNA polymerase containing sigma K in vitro (Kroos et al., 1989). The spoIIID83 mutation (by which the locus was originally identified), was sequenced and found to be a single base substitution in the ribosome binding site upstream of the spoIIID open reading frame. A transcriptional fusion to lacZ was constructed and used to examine the regulation of spoIIID. Expression of spoIIID occurred only during sporulation, beginning 1.5 to 2 hours after the initiation of sporulation. The dependence of spoIIID expression on other spo loci suggests that it is mother-cell-specific, and that it is transcribed by sigma E-containing RNA polymerase.

The spoIIJ gene, which regulates early developmental steps in Bacillus subtilis, belongs to a class of environmentally responsive genes

The Bacillus subtilis spoIIJ locus is defined by a Tn917 insertion which leads to an oligosporogenous phenotype. Here we show that this mutation severely decreases transcription of spoIIA, spoIIE, and spoIIG, three operons involved in asymmetric septation, the earliest morphological event of sporulation. A 14.3-kilobase region overlapping the site of the spoIIJ::Tn917 insertion was cloned and the exact location of the spoIIJ gene was defined with various integrative plasmids carrying subfragments of that region. DNA sequencing established that spoIIJ is a monocistronic locus encoding a 606-amino-acid polypeptide which contains a canonical "transmitter" domain, indicating that spoIIJ is a new member of the "sensor" class of signal-transducing systems in bacteria. Thus, spoIIj, which is transcribed during vegetative growth, presumably under the control of sigma H, encodes a protein that could interact with major regulators of early sporulation stages, such as SpoOA and/or SpoOF.

Temporal and spatial control of the mother-cell regulatory gene spoIIID of Bacillus subtilis

Gene expression during endospore formation in Bacillus subtilis is compartmentalized between the mother-cell and forespore chambers of the sporangium, which follow separate pathways of cellular differentiation. The earliest acting regulatory gene so far identified in the mother-cell line of gene expression is spoIIID, whose product is required for the transcription of the composite gene (sigK) encoding the mother-cell RNA polymerase sigma-factor sigma K and for the chromosomal rearrangement that gives rise to the composite gene. Here we report the nucleotide sequence of spoIIID and studies on the temporal, spatial, and genetic control of its expression during sporulation. We show that the deduced spoIIID gene product, a 93-residue-long polypeptide, is a previously identified transcription factor that is known to activate the promoter for the sigK gene in vitro. Expression of spoIIID is largely confined to the mother-cell chamber of the sporangium and is turned on at, or shortly before, the time (hour 3 of sporulation) that the mother-cell chromosome is rearranged and transcription of the sigK gene commences. This gene expression depends strongly on the sporulation sigma-factor sigma E and partially on the spoIIID gene product, itself. We conclude that the timing and compartmentalization of the rearrangement and transcription of the sigK gene and, hence, of subsequent gene activation in the mother cell, are, in part, direct consequences of the temporal and spatial control of spoIIID gene expression.

Timing of spoII gene expression relative to septum formation during sporulation of Bacillus subtilis

spoII mutants formed heat-resistant spores when transformed with spo+ DNa near the start of sporulation. Many of the spores formed remained genetically spoII. It is deduced from this result and previous epistasis experiments that the spoII loci are transcribed before the spore septum is formed.

Influence of spo mutations on sigma E synthesis in Bacillus subtilis

Bacillus subtilis mutants blocked at the same stage of development (stage II) as strains with mutations in the structural gene for sigma E (sigE[spoIIGB]) were analyzed immunologically for sigma E and its precursor protein, P31. Mutations at spoIIL, spoIIN, and spoIIJ loci but not at the spoIIM locus significantly reduced P31 formation. Mutations at the spoIIAA, spoIIAC, spoIIEA, spoIIEB, and spoIIEC loci did not affect P31 synthesis but blocked its processing into sigma E. These results demonstrate a requirement for at least eight stage II gene products in the developmental pathway which leads to sigma E and brings to 11 the number of stage II genes (including spoIIGA, spoIIGB, and spoIIF) now known to be needed for sigma E formation.

Identification of Bacillus subtilis genes expressed early during sporulation

Labelled cDNA transcribed in vitro from early-sporulation RNA was enriched for sporulation-specific sequences by subtractive hybridization to an excess of vegetative RNA and used to probe libraries of Bacillus subtilis chromosomal DNA. From the initial collection of clones that coded for RNAs transcribed preferentially during sporulation, several were subcloned and studied in more detail. It was found that two clones contained sequences (dciA and dciB) that had an undetectable level of transcription during vegetative growth but had transcripts that started to appear no later than eight minutes after induction of sporulation. A third DNA segment (dciC) was expressed at a low level in vegetative cells and increased within four minutes after induction of sporulation. The effects of spoO mutations, i.e. mutations that prevent cells from reaching stage I of the sporulation process, were tested. Induction of the dciA and dciB transcripts was significantly reduced in strains carrying mutations in the spoOA and spoOH genes but not in a spoOB mutant strain. In addition, a product of the abrB locus, a locus in which mutations are known to partially overcome the pleiotropic effect of spoOA and spoOB mutations, seemed to be required for dciA and dciB expression.

Differential gene expression during sporulation in Bacillus subtilis: regulation of the spoVJ gene

The process of spore formation in the Gram-positive bacterium Bacillus subtilis is a simple developmental system controlled by 50 or more genes. The complex pattern of regulatory interactions between these genes is beginning to be elucidated. spoVJ is a poorly characterized locus in which mutations affect spore development at a relatively late stage (Stage V). We have now cloned and physically characterized the spoVJ locus, and analysed its expression by lacZ fusion. Expression of spoVJ is temporally delayed until about two hours after the initiation of sporulation. Its expression is also spatially restricted to the mother cell compartment; as such, it represents the earliest known mother-cell-specific event. Control of spoVJ transcription is complex: expression is dependent upon the products of all of the spoO genes and on some of the spoII genes but it is independent of all later genes except spoIIID. As spoIIID mutations do not affect prespore development, this gene must be an important early determinant of mother-cell-specific gene expression.

Promoter specificity of sigma G-containing RNA polymerase from sporulating cells of Bacillus subtilis: identification of a group of forespore-specific promoters

During sporulation in Bacillus subtilis, expression of the genes sspA, sspB, sspC, sspD, and sspE, which encode a family of small, acid-soluble spore proteins, as well as of the spoVA and gdh operons is transcriptionally activated at stage III of sporulation only in the forespore compartment. Transcription of these genes is mediated by RNA polymerase containing sigma G (E sigma G), the product of the sigG gene, which is itself expressed at stage III in the developing forespore. We have determined the 5' ends of transcripts generated both in vivo and in vitro by the action of E sigma G on various genes of B. subtilis and other bacilli. The 5' ends of the in vivo and in vitro mRNAs were found to coincide and were therefore considered to define the transcription initiation sites for the genes examined. We identified highly homologous DNA sequences centered at 35 and 10 base pairs preceding the transcriptional start sites of the genes examined. Consequently, we propose that these sequences define a class of promoters recognized only by E sigma G which allow transcription of genes expressed uniquely at stage III in the developing forespore.

The sigma E subunit of Bacillus subtilis RNA polymerase is present in both forespore and mother cell compartments

Bacillus subtilis cells harvested 3.5 h after the onset of sporulation (t3.5) were fractionated into extracts enriched in either mother cell or forespore components and were analyzed immunologically for sigma E and its precursor protein, P31. We determined by Western blot (immunoblot) analysis that equivalent amounts of P31 and sigma E were present in both mother cell and forespore extracts. This result implies that, although sigma E is not synthesized until a stage in development when the cell is partitioned into progenitor forespore and mother cell compartments, it probably directs the transcription of genes that are expressed in both of these structures.

The essential nature of teichoic acids in Bacillus subtilis as revealed by insertional mutagenesis

A 30 kb DNA segment from the region of the Bacillus subtilis strain 168 chromosome which contains most, if not all, loci specifically involved in teichoic acid biosynthesis, has been cloned. A restriction map was established to which genetic markers were assigned. Four loci, tagA, tagB, gtaA and gtaD, are located on a DNA segment of about 7 kb, whereas the gtaB locus lies some 10 kb distant. The tagA and tagB loci are apparently transcribed independently. Insertional mutagenesis, using integrational plasmids carrying relevant fragments from the tag region, provides strong evidence that biosynthesis of polyglycerol phosphate [poly(groP)], so far largely considered as a dispensable polymer, is in fact essential for growth.

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.

Tandem genes encoding sigma-factors for consecutive steps of development in Bacillus subtilis

During sporulation, Bacillus subtilis undergoes successive morphological changes that can be arrested at various stages by mutations in many genes. One of these, spoIIGB, encodes a transcriptional factor, sigma E, which is necessary to proceed beyond stage II and to differentiate the cell in two compartments, the forespore and the mother cell. Mutations were introduced in an open reading frame located immediately downstream of spoIIGB. They block sporulation at stage III and define a new gene, spoIIIG, encoding a 260-amino-acid polypeptide highly similar to bacterial sigma-factors. A promoter was identified in the spoIIGB-spoIIIG interval by transcriptional fusion to lacZ. It is turned on 1 hr after the start of sigma E synthesis and is specifically activated in the forespore. The tandemly arranged spoIIGB and spoIIIG genes appear to encode homologous proteins that modulate transcription in a sequential fashion during sporulation.

Switch protein alters specificity of RNA polymerase containing a compartment-specific sigma factor

During sporulation in Bacillus subtilis, expression of developmental genes spoIVCB and cotD is induced in the mother cell compartment of the sporangium at morphological stages IV and V, respectively. A 27-kilodalton RNA polymerase sigma factor called sigma K (or sigma 27) has been found that causes weak transcription of spoIVCB and strong transcription of cotD. A 14-kD protein was also discovered that changes the specificity of sigma K-containing RNA polymerase, greatly stimulating spoIVCB transcription and markedly repressing cotD transcription. Both sigma K and the 14-kD protein are products of genes known to be required for expression of specific genes in the mother cell. Thus, sigma K directs gene expression in the mother cell and it is proposed that inactivation or sequestering of the 14-kD protein switches the temporal pattern of gene expression during the transition from stages IV to V of development.

Characteristics of an RNA polymerase population isolated from Bacillus subtilis late in sporulation

The sigma-factor composition of Bacillus subtilis RNA polymerase alters during endospore formation. The best-documented change is the appearance of a major sporulation-specific sigma factor (sigma epsilon), which is an RNA polymerase subunit readily detected at 2 to 4 h into the 8-h sporulation process. To determine the nature of the RNA polymerase in differentiating cells after the period of sigma epsilon abundance, we isolated RNA polymerase from cells that were harvested at 6 h after the onset of sporulation. Highly purified fractions of RNA polymerase from these cells contained at least six proteins which cosedimented with core RNA polymerase (beta beta' alpha 2) during glycerol gradient centrifugation. Most of these proteins were in the size range of 20,000 to 29,000 daltons, although one 90,000-dalton protein was also evident. None of the putative RNA polymerase subunits were present in quantities similar to that observed for sigma epsilon during its period of prominence in the cell but instead resembled the minor vegetative-cell sigma factors in abundance. In vitro transcriptions using cloned B. subtilis DNAs as templates revealed at least two novel transcriptional activities in the enzyme that was isolated from cells at 6 h after the onset of sporulation but absent in an RNA polymerase preparation extracted from cells at 4 h after the onset of sporulation. One of these activities was reconstituted by the addition of a 25,000 to 27,000-dalton protein fraction to core RNA polymerase.