Cloning and characterization of a gene required for assembly of the Bacillus subtilis spore coat

Bacillus subtilis spore coat

In response to starvation, bacilli and clostridia undergo a specialized program of development that results in the production of a highly resistant dormant cell type known as the spore. A proteinacious shell, called the coat, encases the spore and plays a major role in spore survival. The coat is composed of over 25 polypeptide species, organized into several morphologically distinct layers. The mechanisms that guide coat assembly have been largely unknown until recently. We now know that proper formation of the coat relies on the genetic program that guides the synthesis of spore components during development as well as on morphogenetic proteins dedicated to coat assembly. Over 20 structural and morphogenetic genes have been cloned. In this review, we consider the contributions of the known coat and morphogenetic proteins to coat function and assembly. We present a model that describes how morphogenetic proteins direct coat assembly to the specific subcellular site of the nascent spore surface and how they establish the coat layers. We also discuss the importance of posttranslational processing of coat proteins in coat morphogenesis. Finally, we review some of the major outstanding questions in the field.

Regulation of hexuronate utilization in Bacillus subtilis

We have identified a locus essential for galacturonate utilization in Bacillus subtilis. Genes homologous to Escherichia coli and Erwinia chrysanthemi glucuronate and galacturonate metabolic genes were found in a cluster consisting of 10 open reading frames (ORFs) in the B. subtilis chromosome. A mutant of B. subtilis containing a replacement of the second and third ORFs was unable to grow with galacturonate as its primary carbon source. Galacturonate induced expression from a sigmaA-dependent promoter, exuP1, located upstream from the first ORF. The eighth ORF in this cluster (the exu locus) encodes a LacI and GalR homolog that negatively regulated expression from exuP1. A 26-bp inverted repeat sequence centered 15 bp downstream from the exuP1 start point of transcription acted in cis to negatively regulate expression from exuP1 under noninducing conditions. Expression from the exuP1 promoter was repressed by high levels of glucose, which is probably mediated by CcpA (catabolite control protein A). A sigmaE-dependent promoter, exuP2, was localized between the second and third ORFs and was active during sporulation.

A spore coat protein, CotS, of Bacillus subtilis is synthesized under the regulation of sigmaK and GerE during development and is located in the inner coat layer of spores

The spore coat of Bacillus subtilis has a unique morphology and consists of polypeptides of different sizes, whose synthesis and assembly are precisely regulated by a cascade of transcription factors and regulatory proteins. We examined the factors that regulate cotS gene expression and CotS assembly into the coat layer of B. subtilis by Northern blot and Western blot analysis. Transcription of cotS mRNA was not detected in sporulating cells of sigmaK and gerE mutants by Northern blot analysis. By Western blot analysis using anti-CotS antibody, CotS was first detected in protein samples solubilized from wild-type cells at 5 h after the start of sporulation. CotS was not detected in the vegetative cells and spores of a gerE mutant or in the spores of mutants deficient in sigmaE, sigmaF, sigmaG, or sigmaK. CotS was detected in the sporangium but not in the spores of a cotE mutant. The sequence of the promoter region of cotS was similar to the consensus sequences for binding of sigmaK and GerE. These results demonstrate that sigmaK and GerE are required for cotS expression and that CotE is essential for the assembly of CotS in the coat. Immunoelectron microscopic observation using anti-CotS antibody revealed that CotS is located within the spore coat, in particular in the inner coats of dormant spores.

Involvement of superoxide dismutase in spore coat assembly in Bacillus subtilis

Endospores of Bacillus subtilis are enclosed in a proteinaceous coat which can be differentiated into a thick, striated outer layer and a thinner, lamellar inner layer. We found that the N-terminal sequence of a 25-kDa protein present in a preparation of spore coat proteins matched that of the Mn-dependent superoxide dismutase (SOD) encoded by the sod4 locus. sod4 is transcribed throughout the growth and sporulation of a wild-type strain and is responsible for the SOD activity detected in total cell extracts prepared from B. subtilis. Disruption of the sod4 locus produced a mutant that lacked any detectable SOD activity during vegetative growth and sporulation. The sodA mutant was not impaired in the ability to form heat- or lysozyme-resistant spores. However, examination of the coat layers of sodA mutant spores revealed increased extractability of the tyrosine-rich outer coat protein CotG. We showed that this condition was not accompanied by augmented transcription of the cotG gene in sporulating cells of the sodA mutant. We conclude that SodA is required for the assembly of CotG into the insoluble matrix of the spore and suggest that CotG is covalently cross-linked into the insoluble matrix by an oxidative reaction dependent on SodA. Ultrastructural analysis revealed that the inner coat formed by a sodA mutant was incomplete. Moreover, the outer coat lacked the characteristic striated appearance of wild-type spores, a pattern that was accentuated in a cotG mutant. These observations suggest that the SodA-dependent formation of the insoluble matrix containing CotG is largely responsible for the striated appearance of this coat layer.

CotM of Bacillus subtilis, a member of the alpha-crystallin family of stress proteins, is induced during development and participates in spore outer coat formation

We cloned and characterized a gene, cotM, that resides in the 173 degrees region of the Bacillus subtilis chromosome and is involved in spore outer coat assembly. We found that expression of the cotM gene is induced during development under sigma K control and is negatively regulated by the GerE transcription factor. Disruption of the cotM gene resulted in spores with an abnormal pattern of coat proteins. Electron microscopy revealed that the outer coat in cotM mutant spores had lost its multilayered type of organization, presenting a diffuse appearance. In particular, significant amounts of material were absent from the outer coat layers, which in some areas had a lamellar structure more typical of the inner coat. Occasionally, a pattern of closely spaced ridges protruding from its surface was observed. No deficiency associated with the inner coat or any other spore structure was found. CotM is related to the alpha-crystallin family of low-molecular-weight heat shock proteins, members of which can be substrates for transglutaminase-mediated protein cross-linking. CotM was not detected among the extractable spore coat proteins. These observations are consistent with a model according to which CotM is part of a cross-linked insoluble skeleton that surrounds the spore, serves as a matrix for the assembly of additional outer coat material, and confers structural stability to the final structure.

Characterization of csgA, a new member of the forespore-expressed sigmaG-regulon from Bacillus subtilis

A new locus, csgA, has been identified in a search for developmental genes transcribed by E sigmaG in Bacillus subtilis. csgA has the potential to encode three small proteins, CsgAA, CsgAB and CsgAC. The latter two would be encoded by overlapping ORFs. csgA is expressed in the spore chamber of the differentiating cell and is under the control of sigmaG and the transcriptional regulatory protein SpoVT. Mutation of csgA did not affect spore formation but produced a subtle defect in the ability of the germinating spore to resume vegetative growth.

cse15, cse60, and csk22 are new members of mother-cell-specific sporulation regulons in Bacillus subtilis

We report on the characterization of three new transcription units expressed during sporulation in Bacillus subtilis. Two of the units, cse15 and cse60, were mapped at about 123 degrees and 62 degrees on the genetic map, respectively. Their transcription commenced around h 2 of sporulation and showed an absolute requirement for sigmaE. Maximal expression of both cse15 and cse60 further depended on the DNA-binding protein SpoIIID. Primer extension results revealed -10 and -35 sequences upstream of the cse15 and cse60 coding sequences very similar to those utilized by sigmaE-containing RNA polymerase. Alignment of these and other regulatory regions led to a revised consensus sequence for sigmaE-dependent promoters. A third transcriptional unit, designated csk22, was localized at approximately 173 degrees on the chromosome. Transcription of csk22 was activated at h 4 of sporulation, required the late mother-cell regulator sigmaK, and was repressed by the GerE protein. Sequences in the csk22 promoter region were similar to those of other sigmaK-dependent promoters. The cse60 locus was deduced to encode an acidic product of only 60 residues. A 37.6-kDa protein apparently encoded by cse15 was weakly related to the heavy chain of myosins, as well as to other myosin-like proteins, and is predicted to contain a central, 100 residue-long coiled-coil domain. Finally, csk22 is inferred to encode a 18.2-kDa hydrophobic product with five possible membrane-spanning helices, which could function as a transporter.

Identification of additional genes under the control of the transcription factor sigma F of Bacillus subtilis

We describe the identification of five transcriptional units under the control of the sporulation transcription factor sigma F in Bacillus subtilis. These are csfA, csfB, csfC, csfD, and csfF, located at approximately 230 degrees, 2 degrees, 316 degrees, 205 degrees, and approximately 290 degrees, respectively, on the genetic map. Null mutations in csfA, csfB, csfC, or csfD, either alone or together, do not cause a noticeable defect in sporulation or germination.

A compartmentalized regulator of developmental gene expression in Bacillus subtilis

We have identified a new Bacillus subtilis gene, spoVT, whose gene product is homologous to the transcriptional regulator AbrB and serves as a regulator of E sigmaG-controlled gene expression. SpoVT acts both positively and negatively in controlling sigmaG-dependent gene expression, providing an additional level of refinement to forespore gene regulation and feedback control of spoIIIG expression.

A sigma E dependent operon subject to catabolite repression during sporulation in Bacillus subtilis

To identify genes expressed at intermediate stages of Bacillus subtilis sporulation, we screened for sigma E-dependent promoters. One promoter that we found drives expression of an operon consisting of at least five open reading frames (ORFs). The predicted products of the first three ORFs are very homologous to enzymes involved in fatty acid metabolism, including acetyl coenzyme A (acetyl-CoA) acetyltransferase (thiolase), 3-hydroxybutyryl-CoA dehydrogenase, and acyl-CoA dehydrogenase, respectively. We showed that the fourth ORF encoded a third isozyme of citrate synthase in B. subtilis. Genetic evidence and primer extension results showed that transcription of this operon is directed by the mother cell compartment-specific sigma factor, sigma E, and so the operon was named mmg (for mother cell metabolic genes). Furthermore, we found that a sequence (mmgO) with homology to a catabolite-responsive element mediates glucose repression of mmg promoter activity during sporulation and that this repression was lost in a ccpA mutant.

Adjacent and divergently oriented operons under the control of the sporulation regulatory protein GerE in Bacillus subtilis

The DNA-binding protein GerE is the latest-acting regulatory protein in the mother cell line of gene expression during sporulation in Bacillus subtilis. GerE directs the transcription of several genes that encode structural components of the protein coat that encases the mature spore. We report on the identification and characterization of a cluster of additional genes whose transcription is dependent on GerE. These genes, which are located in the replication terminus region of the chromosome (181 degrees on the genetic map), are arranged in adjacent and divergently oriented operons called cgeAB and cgeCDE, which consist of two and at least three genes, respectively. CgeD, the product of the second member of the cgeCDE operon, is strikingly similar to the product of a B. subtilis gene (ipa-63d) of unknown function and is similar at its amino terminus to certain glycosyl transferases involved in polysaccharide biosynthesis. Strains with mutations in the cgeAB and cgeCDE operons produce spores with altered surface properties, on which basis we propose that proteins encoded by these operons influence maturation of the outermost layer of the spore, perhaps by glycosylation of coat proteins at the spore surface.

Characterization of cotJ, a sigma E-controlled operon affecting the polypeptide composition of the coat of Bacillus subtilis spores

The outermost protective structure found in endospores of Bacillus subtilis is a thick protein shell known as the coat, which makes a key contribution to the resistance properties of the mature spore and also plays a role in its interaction with compounds able to trigger germination. The coat is organized as a lamellar inner layer and an electron-dense outer layer and has a complex polypeptide composition. Here we report the cloning and characterization of an operon, cotJ, located at about 62 degrees on the B. subtilis genetic map, whose inactivation results in the production of spores with an altered pattern of coat polypeptides. The cotJ operon was identified by screening a random library of lacZ transcriptional fusions for a conditional (inducer-dependent) Lac+ phenotype in cells of a strain in which the structural gene (spoIIGB) for the early-acting, mother-cell-specific transcriptional factor sigma E was placed under the control of the IPTG (isopropyl-beta-D-thiogalactopyranoside)-inducible Pspac promoter. Sequence analysis of cloned DNA from the cotJ region complemented by genetic experiments revealed a tricistronic operon preceded by a strong sigma E-like promoter. Expression of an SP beta-borne cotJ-lacZ fusion commences at around h 2 of sporulation, as does expression of other sigma E-dependent genes, and shows an absolute requirement for sigma E. Studies with double-reporter strains bearing a cotJ-gusA fusion and lacZ fusions to other cot genes confirmed that expression of cotJ is initiated during sporulation prior to activation of genes known to encode coat structural proteins (with the sole exception of cotE). An in vitro-constructed insertion-deletion mutation in cotJ resulted in the formation of spores with no detectable morphological or resistance deficiency. However, examination of the profile of electrophoretically separated spore coat proteins from the null mutant revealed a pattern that was essentially identical to that of a wild-type strain in the range of 12 to 65 kDa, except for polypeptides of 17 and 24 kDa, the putative products of the second (cotJB) and third (cotJC) cistrons of the operon, that were missing or reduced in amount in the coat of the mutant. Polypeptides of the same apparent sizes are detected in spores of a cotE null mutant, on which basis we infer that the products of the cotJ operon are required for the normal formation of the inner layers of the coat or are themselves structural components of the coat. Because the onset of cotJ transcription is temporally coincident with the appearance of active sigma E, we speculate that the cotJ-encoded products may be involved in an early state of coat assembly.

Identification of a gene, spoIIR, that links the activation of sigma E to the transcriptional activity of sigma F during sporulation in Bacillus subtilis

Sporulation of Bacillus subtilis requires the coordinated expression of two separate developmental programs in the mother cell and forespore compartments by sigma E and sigma F, respectively. This coordination is maintained through the action of cross-regulatory factors that control the activities of the various sporulation-specific sigma factors. We present here the isolation and characterization of one such cross-regulatory factor, the spoIIR gene. Using a genetic screen, we have isolated four mutant alleles of spoIIR. These mutants were isolated as expressing sigma F-directed genes but not sigma E-directed genes. The block in sigma E-directed gene expression in spoIIR mutants was caused by an inability to process pro-sigma E to its active form. Cloning and characterization of the spoIIR gene determined that its transcription is directed by sigma F. Thus, SpoIIR is required for linking the activation of sigma E to the activation of sigma F and coordinating the initiation of the two developmental programs required to form a spore.

The sigma factors of Bacillus subtilis

The specificity of DNA-dependent RNA polymerase for target promotes is largely due to the replaceable sigma subunit that it carries. Multiple sigma proteins, each conferring a unique promoter preference on RNA polymerase, are likely to be present in all bacteria; however, their abundance and diversity have been best characterized in Bacillus subtilis, the bacterium in which multiple sigma factors were first discovered. The 10 sigma factors thus far identified in B. subtilis directly contribute to the bacterium's ability to control gene expression. These proteins are not merely necessary for the expression of those operons whose promoters they recognize; in many instances, their appearance within the cell is sufficient to activate these operons. This review describes the discovery of each of the known B. subtilis sigma factors, their characteristics, the regulons they direct, and the complex restrictions placed on their synthesis and activities. These controls include the anticipated transcriptional regulation that modulates the expression of the sigma factor structural genes but, in the case of several of the B. subtilis sigma factors, go beyond this, adding novel posttranslational restraints on sigma factor activity. Two of the sigma factors (sigma E and sigma K) are, for example, synthesized as inactive precursor proteins. Their activities are kept in check by "pro-protein" sequences which are cleaved from the precursor molecules in response to intercellular cues. Other sigma factors (sigma B, sigma F, and sigma G) are inhibited by "anti-sigma factor" proteins that sequester them into complexes which block their ability to form RNA polymerase holoenzymes. The anti-sigma factors are, in turn, opposed by additional proteins which participate in the sigma factors' release. The devices used to control sigma factor activity in B, subtilis may prove to be as widespread as multiple sigma factors themselves, providing ways of coupling sigma factor activation to environmental or physiological signals that cannot be readily joined to other regulatory mechanisms.

Bacillus subtilis lon protease prevents inappropriate transcription of genes under the control of the sporulation transcription factor sigma G

The Bacillus subtilis RNA polymerase sigma factor sigma G is a cell-type-specific regulatory protein that governs the transcription of genes that are expressed at an intermediate to late stage of sporulation in the forespore compartment of the sporangium. Here we report the identification of a mutation (lon-1) that causes inappropriate transcription of genes under the control of sigma G under nutritional and genetic conditions in which sporulation is prevented. The mutation is located at 245 degrees on the genetic map and lies within a newly identified open reading frame that is predicted to encode a homolog to Lon protease. Inappropriate transcription of sigma G-controlled genes in the lon-1 mutant is not prevented by mutations in genes that are normally required for the appearance of sigma G during sporulation but is prevented by a mutation in the structural gene (spoIIIG) for sigma G itself. In light of previous work showing that spoIIIG is subject to positive autoregulation, we propose that Lon protease is responsible (possibly by causing degradation of sigma G) for preventing sigma G-directed transcription of spoIIIG and hence the accumulation of sigma G in cells that are not undergoing sporulation. An integrated physical and genetic map is presented that encompasses 36 kb of uninterrupted DNA sequence from the lon pheA region of the chromosome, corresponding to 245 degrees to 239 degrees on the genetic map.

Cloning and characterization of spoVR, a gene from Bacillus subtilis involved in spore cortex formation

Screening for sigma E-dependent promoters led to the isolation of a gene from Bacillus subtilis, designated spoVR, which appears to be involved in spore cortex formation. Cultures of strains carrying mutations in spoVR had an increased proportion of phase-dark spores, which correlated with an increased proportion of cortexless spores seen by electron microscopy. The numbers of heat- and chloroform-resistant phase-bright spores produced by these mutants were decreased by about 3- to 10-fold, and accumulation of dipicolinate was decreased by more than 3-fold. The spoVR gene was located on the B. subtilis chromosome immediately upstream from, and in the opposite orientation of, the phoAIV gene. Expression of spoVR was initiated at the second hour of sporulation from a sigma E-dependent promoter, and this expression did not require any of the other known mother-cell-specific transcriptional regulators. The spoVR gene was predicted to encode a product of 468 residues.

Expression of the Bacillus subtilis spoIVCA gene, which encodes a site-specific recombinase, depends on the spoIIGB product

The Bacillus subtilis spoIVCA gene encodes a site-specific recombinase which creates a sigK gene by DNA rearrangement. We have determined the transcription initiation point of the spoIVCA gene and found that (i) the spoIVCA promoter contains sequences which are similar to -10 and -35 regions of promoters recognized by sigma E and (ii) mutation of spoIIGB, which encodes pro-sigma E, blocked the expression of spoIVCA.

Subcellular localization of proteins involved in the assembly of the spore coat of Bacillus subtilis

Spores of the bacterium Bacillus subtilis are encased in a two-layered protein shell, which consists of an electron-translucent, lamellar inner coat, and an electron-dense outer coat. The coat protein CotE is both a structural component of the coat and a morphogenetic protein that is required for the assembly of the outer coat. We now show that CotE is located in the outer coat of the mature spore and that at an intermediate stage of sporulation, when the developing spore (the forespore) is present as a free protoplast within the sporangium, CotE is localized in a ring that surrounds the forespore but is separated from it by a small gap. We propose that the ring is the site of assembly of the outer coat and that the gap is the site of formation of the inner coat. Assembly of the ring depends on the sporulation protein SpoIVA, which sits close to or on the surface of the outer membrane that encircles the forespore. We propose that SpoIVA creates a basement layer around the forespore on which coat assembly takes place. The subcellular localization and assembly of CotE and other coat proteins are therefore determined by the capacity of SpoIVA to recognize and adhere to a specific surface within the sporangium, the outer membrane of the forespore.