Branched pattern of regulatory interactions between late sporulation genes in Bacillus subtilis

A two-step transport pathway allows the mother cell to nurture the developing spore in Bacillus subtilis

One of the hallmarks of bacterial endospore formation is the accumulation of high concentrations of pyridine-2,6-dicarboxylic acid (dipicolinic acid or DPA) in the developing spore. This small molecule comprises 5–15% of the dry weight of dormant spores and plays a central role in resistance to both wet heat and desiccation. DPA is synthesized in the mother cell at a late stage in sporulation and must be translocated across two membranes (the inner and outer forespore membranes) that separate the mother cell and forespore. The enzymes that synthesize DPA and the proteins required to translocate it across the inner forespore membrane were identified over two decades ago but the factors that transport DPA across the outer forespore membrane have remained mysterious. Here, we report that SpoVV (formerly YlbJ) is the missing DPA transporter. SpoVV is produced in the mother cell during the morphological process of engulfment and specifically localizes in the outer forespore membrane. Sporulating cells lacking SpoVV produce spores with low levels of DPA and cells engineered to express SpoVV and the DPA synthase during vegetative growth accumulate high levels of DPA in the culture medium. SpoVV resembles concentrative nucleoside transporters and mutagenesis of residues predicted to form the substrate-binding pocket supports the idea that SpoVV has a similar structure and could therefore function similarly. These findings provide a simple two-step transport mechanism by which the mother cell nurtures the developing spore. DPA produced in the mother cell is first translocated into the intermembrane space by SpoVV and is then imported into the forespore by the SpoVA complex. This pathway is likely to be broadly conserved as DPA synthase, SpoVV, and SpoVA proteins can be found in virtually all endospore forming bacteria.

All pathogenic and non-pathogenic bacteria that differentiate into dormant endospores including Clostridium difficile, Bacillus anthracis, and Bacillus subtilis, contain very high concentrations of the small molecule dipicolinic acid (DPA). This molecule displaces water in the spore core where it plays an integral role in spore resistance and dormancy. DPA and its contribution to spore dehydration were discovered in 1953 but the molecular basis for its accumulation in the spore has remained unclear. The developing endospore resides within a mother cell that assembles protective layers around the spore and nurtures it by providing mother-cell-produced molecules. DPA is produced in the mother cell at a late stage in development and then must be translocated across two membranes into the spore core. Here, we report the discovery of the missing DPA transporter, homologs of which are present in virtually all endospore-forming bacteria. Our data provide evidence for a simple two-step transport pathway in which the mother cell nurtures the developing spore by sequentially moving DPA across the two membranes that surround it.

Role of a SpoVA protein in dipicolinic acid uptake into developing spores of Bacillus subtilis

The proteins encoded by the spoVA operon, including SpoVAD, are essential for the uptake of the 1:1 chelate of pyridine-2,6-dicarboxylic acid (DPA(2,6)) and Ca(2+) into developing spores of the bacterium Bacillus subtilis. The crystal structure of B. subtilis SpoVAD has been determined recently, and a structural homology search revealed that SpoVAD shares significant structural similarity but not sequence homology to a group of enzymes that bind to and/or act on small aromatic molecules. We find that molecular docking placed DPA(2,6) exclusively in a highly conserved potential substrate-binding pocket in SpoVAD that is similar to that in the structurally homologous enzymes. We further demonstrate that SpoVAD binds both DPA(2,6) and Ca(2+)-DPA(2,6) with a similar affinity, while exhibiting markedly weaker binding to other DPA isomers. Importantly, mutations of conserved amino acid residues in the putative DPA(2,6)-binding pocket in SpoVAD essentially abolish its DPA(2,6)-binding capacity. Moreover, replacement of the wild-type spoVAD gene in B. subtilis with any of these spoVAD gene variants effectively eliminated DPA(2,6) uptake into developing spores in sporulation, although the variant proteins were still located in the spore inner membrane. Our results provide direct evidence that SpoVA proteins, in particular SpoVAD, are directly involved in DPA(2,6) movement into developing B. subtilis spores.

Characterization of Clostridium perfringens spores that lack SpoVA proteins and dipicolinic acid

Spores of Clostridium perfringens possess high heat resistance, and when these spores germinate and return to active growth, they can cause gastrointestinal disease. Work with Bacillus subtilis has shown that the spore's dipicolinic acid (DPA) level can markedly influence both spore germination and resistance and that the proteins encoded by the spoVA operon are essential for DPA uptake by the developing spore during sporulation. We now find that proteins encoded by the spoVA operon are also essential for the uptake of Ca(2+) and DPA into the developing spore during C. perfringens sporulation. Spores of a spoVA mutant had little, if any, Ca(2+) and DPA, and their core water content was approximately twofold higher than that of wild-type spores. These DPA-less spores did not germinate spontaneously, as DPA-less B. subtilis spores do. Indeed, wild-type and spoVA C. perfringens spores germinated similarly with a mixture of l-asparagine and KCl (AK), KCl alone, or a 1:1 chelate of Ca(2+) and DPA (Ca-DPA). However, the viability of C. perfringens spoVA spores was 20-fold lower than the viability of wild-type spores. Decoated wild-type and spoVA spores exhibited little, if any, germination with AK, KCl, or exogenous Ca-DPA, and their colony-forming efficiency was 10(3)- to 10(4)-fold lower than that of intact spores. However, lysozyme treatment rescued these decoated spores. Although the levels of DNA-protective alpha/beta-type, small, acid-soluble spore proteins in spoVA spores were similar to those in wild-type spores, spoVA spores exhibited markedly lower resistance to moist heat, formaldehyde, HCl, hydrogen peroxide, nitrous acid, and UV radiation than wild-type spores did. In sum, these results suggest the following. (i) SpoVA proteins are essential for Ca-DPA uptake by developing spores during C. perfringens sporulation. (ii) SpoVA proteins and Ca-DPA release are not required for C. perfringens spore germination. (iii) A low spore core water content is essential for full resistance of C. perfringens spores to moist heat, UV radiation, and chemicals.

The products of the spoVA operon are involved in dipicolinic acid uptake into developing spores of Bacillus subtilis

Bacillus subtilis cells with mutations in the spoVA operon do not complete sporulation. However, a spoVA strain with mutations that remove all three of the spore's functional nutrient germinant receptors (termed the ger3 mutations) or the cortex lytic enzyme SleB (but not CwlJ) did complete sporulation. ger3 spoVA and sleB spoVA spores lack dipicolinic acid (DPA) and have lower core wet densities and levels of wet heat resistance than wild-type or ger3 spores. These properties of ger3 spoVA and sleB spoVA spores are identical to those of ger3 spoVF and sleB spoVF spores that lack DPA due to deletion of the spoVF operon coding for DPA synthetase. Sporulation in the presence of exogenous DPA restored DPA levels in ger3 spoVF spores to 53% of the wild-type spore levels, but there was no incorporation of exogenous DPA into ger3 spoVA spores. These data indicate that one or more products of the spoVA operon are involved in DPA transport into the developing forespore during sporulation.

Characterization of spores of Bacillus subtilis which lack dipicolinic acid

Spores of Bacillus subtilis with a mutation in spoVF cannot synthesize dipicolinic acid (DPA) and are too unstable to be purified and studied in detail. However, the spores of a strain lacking the three major germinant receptors (termed Deltager3), as well as spoVF, can be isolated, although they spontaneously germinate much more readily than Deltager3 spores. The Deltager3 spoVF spores lack DPA and have higher levels of core water than Deltager3 spores, although sporulation with DPA restores close to normal levels of DPA and core water to Deltager3 spoVF spores. The DPA-less spores have normal cortical and coat layers, as observed with an electron microscope, but their core region appears to be more hydrated than that of spores with DPA. The Deltager3 spoVF spores also contain minimal levels of the processed active form (termed P(41)) of the germination protease, GPR, a finding consistent with the known requirement for DPA and dehydration for GPR autoprocessing. However, any P(41) formed in Deltager3 spoVF spores may be at least transiently active on one of this protease's small acid-soluble spore protein (SASP) substrates, SASP-gamma. Analysis of the resistance of wild-type, Deltager3, and Deltager3 spoVF spores to various agents led to the following conclusions: (i) DPA and core water content play no role in spore resistance to dry heat, dessication, or glutaraldehyde; (ii) an elevated core water content is associated with decreased spore resistance to wet heat, hydrogen peroxide, formaldehyde, and the iodine-based disinfectant Betadine; (iii) the absence of DPA increases spore resistance to UV radiation; and (iv) wild-type spores are more resistant than Deltager3 spores to Betadine and glutaraldehyde. These results are discussed in view of current models of spore resistance and spore germination.

Binding of small, acid-soluble spore proteins to DNA plays a significant role in the resistance of Bacillus subtilis spores to hydrogen peroxide

Dormant spores of Bacillus subtilis which lack the majority of the alpha/beta-type small, acid-soluble proteins (SASP) (termed alpha- beta- spores) that coat the DNA in wild-type spores are significantly more sensitive to hydrogen peroxide than are wild-type spores. Hydrogen peroxide treatment of alpha- beta- spores causes DNA strand breaks more readily than does comparable treatment of wild-type spores, and alpha- beta- spores, but not wild-type spores, which survive hydrogen peroxide treatment have acquired a significant number of mutations. The hydrogen peroxide resistance of wild-type spores appears to be acquired in at least two incremental steps during sporulation. The first increment is acquired at about the time of alpha/beta-type SASP synthesis, and the second increment is acquired approximately 2 h later, at about the time of dipicolinic acid accumulation. During sporulation of the alpha- beta- strain, only the second increment of hydrogen peroxide resistance is acquired. In contrast, sporulation mutants which accumulate alpha/beta-type SASP but progress no further in sporulation acquire only the first increment of hydrogen peroxide resistance. These findings strongly suggest that binding of alpha/beta-type SASP to DNA provides one increment of spore hydrogen peroxide resistance. Indeed, binding of alpha/beta-type SASP to DNA in vitro provides strong protection against cleavage of DNA by hydrogen peroxide.

A sporulation gene in Coxiella burnetii?

During a search for conserved target sequences on the genome of Coxiella burnetii for a diagnostic PCR a NotI/EcoRV DNA fragment was cloned and sequenced from the isolate "Nine Mile", Phase I (sequence data are registered under accession number X70045 in data bases EMBL, GENEBANK and DDBJ). On this fragment we have found a sequence of 1741 base pairs which showed an exceptionally high homology (60% on the nucleic acid level and 49.6% on the amino acid level) to the sporulation gene "spoIIIE" of the gram-positive bacterium Bacillus subtilis. This is first evidence of the molecular basis for formation of spores in Coxiella burnetii which has been postulated in the literature by electron microscopic investigations.

Proteolytic processing of the protease which initiates degradation of small, acid-soluble proteins during germination of Bacillus subtilis spores

Degradation of small, acid-soluble spore proteins during germination of Bacillus subtilis spores is initiated by a sequence-specific protease called GPR. Western blot (immunoblot) analysis of either Bacillus megaterium or B. subtilis GPR expressed in B. subtilis showed that GPR is synthesized at about the third hour of sporulation in a precursor form and is processed to an approximately 2- to 5-kDa-smaller species 2 to 3 h later, at or slightly before the time of accumulation of dipicolinic acid by the forespore. This was found with both normal levels of expression of B. subtilis and B. megaterium GPR in B. subtilis, as well as when either protein was overexpressed up to 100-fold. The sporulation-specific processing of GPR was blocked in all spoIII, -IV, and -V mutants tested (none of which accumulated dipicolinic acid), but not in a spoVI mutant which accumulated dipicolinic acid. The amino-terminal sequences of the B. megaterium and B. subtilis GPR initially synthesized in sporulation were identical to those predicted from the coding genes' sequences. However, the processed form generated in sporulation lacked 15 (B. megaterium) or 16 (B. subtilis) amino-terminal residues. The amino acid sequence surrounding this proteolytic cleavage site was very homologous to the consensus sequence recognized and cleaved by GPR in its small, acid-soluble spore protein substrates. This observation, plus the efficient processing of overproduced GPR during sporulation, suggests that the GPR precursor may autoproteolyze itself during sporulation. During spore germination, the GPR from either species expressed in B. subtilis was further processed by removal of one additional amino-terminal amino acid (leucine), generating the mature protease which acts during spore germination.

Bacillus subtilis sporulation: regulation of gene expression and control of morphogenesis

Bacillus subtilis sporulation is an adaptive response to nutritional stress and involves the differential development of two cells. In the last 10 years or so, virtually all of the regulatory genes controlling sporulation, and many genes directing the structural and morphological changes that accompany sporulation, have been cloned and characterized. This review describes our current knowledge of the program of gene expression during sporulation and summarizes what is known about the functions of the genes that determine the specialized biochemical and morphological properties of sporulating cells. Most steps in the genetic program are controlled by transcription factors that have been characterized in vitro. Two sporulation-specific sigma factors, sigma E and sigma F, appear to segregate at septation, effectively determining the differential development of the mother cell and prespore. Later, each sigma is replaced by a second cell-specific sigma factor, sigma K in the mother cell and sigma G in the prespore. The synthesis of each sigma factor is tightly regulated at both the transcriptional and posttranslational levels. Usually this regulation involves an intercellular interaction that coordinates the developmental programmes of the two cells. At least two other transcription factors fine tune the timing and levels of expression of genes in the sigma E and sigma K regulons. The controlled synthesis of the sigma factors and other transcription factors leads to a spatially and temporally ordered program of gene expression. The gene products made during each successive stage of sporulation help to bring about a sequence of gross morphological changes and biochemical adaptations. The formation of the asymmetric spore septum, engulfment of the prespore by the mother cell, and formation of the spore core, cortex, and coat are described. The importance of these structures in the development of the resistance, dormancy, and germination properties of the spore is assessed.

Dipicolinic Acid Greatly Enhances Production of Spore Photoproduct in Bacterial Spores upon UV Irradiation

Formation of the spore photoproduct (SP) (5-thyminyl-5,6-dihydrothymine) in DNA of dormant spores of Bacillus subtilis upon UV irradiation is due to binding of α/β-type small, acid-soluble proteins (SASP). However, the yield of SP as a function of UV fluence is ∼15-fold higher in spores than in an α/β-type-SASP-DNA complex in vitro. The yield of SP as a function of UV fluence in forespore DNA from mutants which make α/β-type SASP but not dipicolinic acid (DPA) was 10 to 20 times lower than that in dormant spores. Furthermore, the yield of SP as a function of UV fluence in an α/β-type-SASP-DNA complex in vitro was increased sixfold by DPA. These data provide further support for the idea that the high DPA level in dormant spores increases the yield of SP as a function of UV fluence and thereby sensitizes spores to UV.

Sequential activation of dual promoters by different sigma factors maintains spoVJ expression during successive developmental stages of Bacillus subtilis

The spoVJ gene of Bacillus subtilis encodes a 36 kDa protein and is expressed only in the mother cell. spoVJ has an interesting pattern of regulation during sporulation because it is expressed from sequentially activated promoters. These promoters, designated P1 and P2, are under the control of different sigma factors, sigma E and sigma K, which become active at separate times during sporulation. Removal of promoter P1, leaving promoter P2 active, resulted in about a 30-minute delay in the formation of heat-resistant spores and demonstrated that the expression of spoVJ from both promoters is essential for normal sporulation. A comparison is made between the sequences of the spoVJ promoters and the promoters of other genes dependent upon sigma E and sigma K.

Conidium differentiation in Aspergillus nidulans wild-type and wet-white (wetA) mutant strains

Conidium (asexual spore) differentiation in wild-type and the wet-white (wetA) mutant of Aspergillus nidulans was compared in intact chains of successively older conidia. Carbohydrate cytochemistry helped define three stages (Stages I, II, and III) of wild-type conidium maturation on the basis of changes in the ultrastructure and composition of the conidium wall. Conidia of the wetA6 mutant strain formed normally but failed to mature during Stages II and III. Specifically, the inner wall layer of wetA6 conidia did not condense during Stage II and two wall layers that stained for carbohydrates did not form during the transition to Stage III. Concomitantly, wetA6 conidia formed large cytoplasmic vacuoles and underwent lysis. The wetA gene appears to have a conidium-specific function for the modification of the conidium wall during Stages II and III. These modifications of the conidium wall are essential for the stability of mature, dormant conidia.

The role of the sporulation gene spoIIIE in the regulation of prespore-specific gene expression in Bacillus subtilis

The spoIIIG gene encodes a sigma factor that determines prespore-specific gene expression during sporulation in Bacillus subtilis. Correct spatial and temporal expression of the spoIIIG gene depends on a number of other sporulation (spo) genes, but only one of these genes, spoIIIE, has a specific effect on spoIIIG expression and not on gene expression in the other differentiating cell, the mother cell. However, the spoIIIE gene is expressed predominantly before differentiation begins. Thus, its product must play an important role in sensing or determining the spatial localization of prespore-specific gene expression in this system.

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.

Regulatory studies on the promoter for a gene governing synthesis and assembly of the spore coat in Bacillus subtilis

gerE is a regulatory gene of Bacillus subtilis that governs the synthesis and assembly of the spore coat and is required for the production of spores that are lysozyme-resistant and germination-proficient. We report the identification of the promoter for gerE and studies on the regulation of its expression. We show that gerE is switched on at the fourth hour of sporulation (stage-V) and that this expression is restricted to the mother-cell chamber of the sporangium. Dependency studies in which the level of gerE expression was measured in 36 different developmental mutants indicate that efficient expression of gerE requires the products of almost all spo0-IV genes tested as well as certain spoV genes. On the basis of its time of induction, compartmentalization of expression and pattern of dependence on other spo genes, gerE is inferred to be regulated co-ordinately with the previously studied spore coat protein gene cotA. gerE and cotA may be members of a developmental regulon of genes whose products are involved in the assembly of the spore coat.

Cloning and dependence pattern of the sporulation operon spoVH

The spoVH locus, involved in the sporulation of Bacillus subtilis, was cloned in derivatives of the temperate bacteriophage luminal diameter 105. Two recombinant phages were obtained which contained 4.2 kilobases of chromosomal DNA. Both phages only partially complemented a mutation in the spoVH operon, spoVH516. Nevertheless, analysis of the cloned locus with integrational plasmids showed that the complete operon had been cloned. A spoVH'-lacZ transcriptional fusion was constructed, and this indicated that the spoVH operon was expressed 2.25 h after the start of sporulation. The distribution of beta-galactosidase in sporulating cells containing a spoVH'-lacZ fusion showed that spoVH was expressed in the spore compartment; lac fusion experiments were also used to study spoVH expression in the presence of other sporulation mutations. Expression of spoVH was prevented by mutations in any of the stage 0 or stage II loci and also by mutations in spoIIIA, spoIIIB, and spoIIIE. A similar pattern of dependence was found previously for the expression of spoVA, which is also expressed in the spore compartment.