Crystal structure of the PepSY‐containing domain of the YpeB protein involved in germination of bacillus spores

The crystal structure of the C‐terminal domain of the Bacillus megaterium YpeB protein has been solved by X‐ray crystallography to 1.80‐Å resolution. The full‐length protein is essential in stabilising the SleB cortex lytic enzyme in Bacillus spores, and may have a role in regulating SleB activity during spore germination. The YpeB‐C crystal structure comprises three tandemly repeated PepSY domains, which are aligned to form an extended laterally compressed molecule. A predominantly positively charged region located in the second PepSY domain may provide a site for protein interactions that are important in stabilising SleB and YpeB within the spore. Proteins 2015; 83:1914–1921. © 2015 Wiley Periodicals, Inc.     

HtrC Is Involved in Proteolysis of YpeB during Germination of Bacillus anthracis and Bacillus subtilis Spores

Bacterial endospores can remain dormant for decades yet can respond to nutrients, germinate, and resume growth within minutes. An essential step in the germination process is degradation of the spore cortex peptidoglycan wall, and the SleB protein in Bacillus species plays a key role in this process. Stable incorporation of SleB into the spore requires the YpeB protein, and some evidence suggests that the two proteins interact within the dormant spore. Early during germination, YpeB is proteolytically processed to a stable fragment. In this work, the primary sites of YpeB cleavage were identified in Bacillus anthracis, and it was shown that the stable products are comprised of the C-terminal domain of YpeB. Modification of the predominant YpeB cleavage sites reduced proteolysis, but cleavage at other sites still resulted in loss of full-length YpeB. A B. anthracis strain lacking the HtrC protease did not generate the same stable YpeB products. In B. anthracis and Bacillus subtilis htrC mutants, YpeB was partially stabilized during germination but was still degraded at a reduced rate by other, unidentified proteases. Purified HtrC cleaved YpeB to a fragment similar to that observed in vivo, and this cleavage was stimulated by Mn²⁺ or Ca²⁺ ions. A lack of HtrC did not stabilize YpeB or SleB during spore formation in the absence of the partner protein, indicating other proteases are involved in their degradation during sporulation.     

In vitro studies of peptidoglycan binding and hydrolysis by the Bacillus anthracis germination-specific lytic enzyme SleB

The Bacillus anthracis endospore loses resistance properties during germination when its cortex peptidoglycan is degraded by germination-specific lytic enzymes (GSLEs). Although this event normally employs several GSLEs for complete cortex removal, the SleB protein alone can facilitate enough cortex hydrolysis to produce vulnerable spores. As a means to better understand its enzymatic function, SleB was overexpressed, purified, and tested in vitro for depolymerization of cortex by measurement of optical density loss and the solubilization of substrate. Its ability to bind peptidoglycan was also investigated. SleB functions independently as a lytic transglycosylase on both intact and fragmented cortex. Most of the muropeptide products that SleB generates are large and are potential substrates for other GSLEs present in the spore. Study of a truncated protein revealed that SleB has two domains. The N-terminal domain is required for stable peptidoglycan binding, while the C-terminal domain is the region of peptidoglycan hydrolytic activity. The C-terminal domain also exhibits dependence on cortex containing muramic-δ-lactam in order to carry out hydrolysis. As the conditions and limitations for SleB activity are further elucidated, they will enable the development of treatments that stimulate premature germination of B. anthracis spores, greatly simplifying decontamination measures.     

The Germination-Specific Lytic Enzymes SleB,CwlJ1, and CwlJ2 Each Contribute to Bacillus anthracis Spore Germination and Virulence

The bacterial spore cortex is critical for spore stability and dormancy and must be hydrolyzed by germination-specific lytic enzymes (GSLEs), which allows complete germination and vegetative cell outgrowth. We created in-frame deletions of three genes that encode GSLEs that have been shown to be active in Bacillus anthracis germination: sleB, cwlJ1, and cwlJ2. Phenotypic analysis of individual null mutations showed that the removal of any one of these genes was not sufficient to disrupt spore germination in nutrient-rich media. This finding indicates that these genes have partially redundant functions. Double and triple deletions of these genes resulted in more significant defects. Although a small subset of ΔsleB ΔcwlJ1 spores germinate with wild-type kinetics, for the overall population there is a 3-order-of-magnitude decrease in the colony-forming efficiency compared with wild-type spores. ΔsleB ΔcwlJ1 ΔcwlJ2 spores are unable to complete germination in nutrient-rich conditions in vitro. Both ΔsleB ΔcwlJ1 and ΔsleB ΔcwlJ1 ΔcwlJ2 spores are significantly attenuated, but are not completely devoid of virulence, in a mouse model of inhalation anthrax. Although unable to germinate in standard nutrient-rich media, spores lacking SleB, CwlJ1, and CwlJ2 are able to germinate in whole blood and serum in vitro, which may explain the persistent low levels of virulence observed in mouse infections. This work contributes to our understanding of GSLE activation and function during germination. This information may result in identification of useful therapeutic targets for the disease anthrax, as well as provide insights into ways to induce the breakdown of the protective cortex layer, facilitating easier decontamination of resistant spores.Bacillus anthracis, a gram-positive spore-forming bacterium, is the causative agent of anthrax. The dormant spore form is the infectious particle and produces three different forms of the disease depending on the route of entry into a suitable host (8). When spores enter through a skin lesion and when they are ingested, they cause cutaneous and gastrointestinal anthrax, respectively. Spores entering through the lungs cause the most severe form of the disease, inhalation anthrax, which is often fatal even with aggressive antibiotic therapy (1, 8, 34). Because true pneumonias are rarely seen in victims, it is believed that inhaled spores do not germinate in the lung but are phagocytosed by alveolar macrophages and germinate intracellularly en route to the mediastinal lymph nodes, which leads to dissemination, septicemia, toxemia, and often death (1, 34). It has been shown that the spores are able to germinate and the bacteria are able to multiply inside macrophages both in cell culture and in the lungs of challenged animals (7, 11, 28, 29).Independent of the route of infection, spore germination inside a susceptible host is essential for disease. The highly stable spore form of the bacterium can remain viable under harsh environmental conditions for many decades (32). However, a spore can form a rapidly dividing vegetative cell upon entry into a host and recognition of specific chemical signals, or germinants, through specialized germinant receptors (32). The spore cortex, a thick layer of modified peptidoglycan (PG), contributes much of the spore''s environmental resistance as it is necessary to maintain dehydration of the spore core (25). This protective barrier is broken down following the activation of germination-specific lytic enzymes (GSLEs), allowing full core rehydration and cell outgrowth (32). Experimentally, germination can also be triggered by nongerminant treatments, such as lysozyme treatment, high pressure, exogenous Ca²⁺-dipicolinic acid treatment, and treatment with cationic surfactants (32). Several of these treatments likely cause spore cortex hydrolysis, triggering spore germination. This indicates the importance of cortex degradation in the spore germination process.Bacterial cell wall PG consists of polysaccharide chains of repeating N-acetylglucosamine and N-acetylmuramic acid, joined by β(1,4) glycosidic bonds (25). This basic structure is modified in several ways in spore cortex PG. In one major modification, 50% of the muramic acid residues (alternating every other residue) are converted to muramic-δ-lactam residues (25). This modification is essential for the specificity of GSLEs for degrading the cortex and prevents degradation of the bacterial cell wall during cortex hydrolysis (21).Previous work on the role of GSLEs in Bacillus subtilis and, recently, in B. anthracis has shown that the enzymes SleB and CwlJ have partially redundant roles and are necessary together for full cortex hydrolysis and spore germination (6, 14). SleB is a lytic transglycosylase that, when activated by an unknown mechanism, hydrolyzes the bond between N-acetylmuramic acid and N-acetylglucosamine (5). In both B. subtilis and B. anthracis, the sleB gene is found in a bicistronic operon with ypeB. Although the function of YpeB is not known, deletion of ypeB prevents SleB activity in spore germination, and sleB and ypeB mutants have similar phenotypes (5). Expression of both gene products is necessary for the presence of SleB in the cortex and inner membrane of mature spores (2, 5).Although no specific enzymatic activity has been attributed to CwlJ, it is required for full germination and it shares a homologous catalytic domain with SleB (20). In B. subtilis and Bacillus cereus, cwlJ is found in an operon with gerQ. Similar to the finding that ypeB is necessary for a functional SleB protein, gerQ is required for CwlJ activity (26). The B. anthracis genome contains two homologs of cwlJ (designated cwlJ1 and cwlJ2 [14]), whereas a single copy is present in B. subtilis and B. cereus. As it is in the related species, cwlJ1 is found in an operon with gerQ, but cwlJ2 is in a different locus and is not in an operon with a gerQ homolog (14). It has been shown that CwlJ is localized to the spore coat and that it is necessary for spore germination with exogenous Ca²⁺-dipicolinic acid treatment (3, 24).GSLE activation represents a critical step in the complex process of germination. The relatively small number of genes involved and the apparent essential nature of their activity make them attractive targets for new therapeutics, as well as environmental decontamination compounds. The objective of this study was to test by using genetic analysis the role of the GSLE genes sleB, cwlJ1, and cwlJ2 in B. anthracis spore germination. Mutants lacking these three genes were tested to determine their effects on in vitro germination kinetics and colony-forming efficiency. Additionally, the virulence of these mutant strains was examined by comparing mutant and wild-type spores in an in vivo mouse model of inhalational anthrax.     

Activity and Regulation of Various Forms of CwlJ,SleB, and YpeB Proteins in Degrading Cortex Peptidoglycan of Spores of Bacillus Species In Vitro and during Spore Germination

Germination of Bacillus spores requires degradation of a modified layer of peptidoglycan (PG) termed the spore cortex by two redundant cortex-lytic enzymes (CLEs), CwlJ and SleB, plus SleB''s partner protein, YpeB. In this study, in vitro and in vivo analyses have been used to clarify the roles of individual SleB and YpeB domains in PG degradation. Purified mature Bacillus cereus SleB without its signal sequence (SleB^M) and the SleB C-terminal catalytic domain (SleB^C) efficiently triggered germination of decoated Bacillus megaterium and Bacillus subtilis spores lacking endogenous CLEs; previously, SleB''s N-terminal domain (SleB^N) was shown to bind PG but have no enzymatic activity. YpeB lacking its putative membrane anchoring sequence (YpeB^M) or its N- and C-terminal domains (YpeB^N and YpeB^C) alone did not exhibit degradative activity, but YpeB^N inhibited SleB^M and SleB^C activity in vitro. The severe germination defect of B. subtilis cwlJ sleB or cwlJ sleB ypeB spores was complemented by ectopic expression of full-length sleB [sleB(FL)] and ypeB [ypeB(FL)], but normal levels of SleB^FL in spores required normal spore levels of YpeB^FL and vice versa. sleB(FL) or ypeB(FL) alone, sleB(FL) plus ypeB(C) or ypeB(N), and sleB(C) or sleB(N) plus ypeB(FL) did not complement the cortex degradation defect in cwlJ sleB ypeB spores. In addition, ectopic expression of sleB(FL) or cwlJ(FL) with a Glu-to-Gln mutation in a predicted active-site residue failed to restore the germination of cwlJ sleB spores, supporting the role of this invariant glutamate as the key catalytic residue in SleB and CwlJ.     

Spore Germination Mediated by Bacillus megaterium QM B1551 SleL and YpeB

Previous work demonstrated that Bacillus megaterium QM B1551 spores that are null for the sleB and cwlJ genes, which encode cortex-lytic enzymes (CLEs), either of which is required for efficient cortex hydrolysis in Bacillus spores, could germinate efficiently when complemented with a plasmid-borne copy of ypeB plus the nonlytic portion of sleB encoding the N-terminal domain of SleB (sleB^N). The current study demonstrates that the defective germination phenotype of B. megaterium sleB cwlJ spores can partially be restored when they are complemented with plasmid-borne ypeB alone. However, efficient germination in this genetic background requires the presence of sleL, which in this species was suggested previously to encode a nonlytic epimerase. Recombinant B. megaterium SleL showed little, or no, activity against purified spore sacculi, cortical fragments, or decoated spore substrates. However, analysis of muropeptides generated by the combined activities of recombinant SleB and SleL against spore sacculi revealed that B. megaterium SleL is actually an N-acetylglucosaminidase, albeit with apparent reduced activity compared to that of the homologous Bacillus cereus protein. Additionally, decoated spores were induced to release a significant proportion of dipicolinic acid (DPA) from the spore core when incubated with recombinant SleL plus YpeB, although optimal DPA release required the presence of endogenous CLEs. The physiological basis that underpins this newly identified dependency between SleL and YpeB is not clear, since pulldown assays indicated that the proteins do not interact physically in vitro.     

Crystal Structure of the Catalytic Domain of the Bacillus cereus SleB Protein, Important in Cortex Peptidoglycan Degradation during Spore Germination

The SleB protein is one of two redundant cortex-lytic enzymes (CLEs) that initiate the degradation of cortex peptidoglycan (PG), a process essential for germination of spores of Bacillus species, including Bacillus anthracis. SleB has been characterized as a soluble lytic transglycosylase that specifically recognizes spore cortex PG and catalyzes the cleavage of glycosidic bonds between N-acetylmuramic acid (NAM) and N-acetylglucosamine residues with concomitant formation of a 1,6-anhydro bond in the NAM residue. We found that like the full-length Bacillus cereus SleB, the catalytic C-terminal domain (SleB^C) exhibited high degradative activity on cortex PG in vitro, although SleB''s N-terminal domain, thought to bind PG, was inactive. The 1.85-Å crystal structure of SleB^C reveals an ellipsoid molecule with two distinct domains dominated by either α helices or β strands. The overall fold of SleB closely resembles that of the catalytic domain of the family 1 lytic transglycosylases but with a completely different topological arrangement. Structural analysis shows that an invariant Glu157 of SleB is in a position equivalent to that of the catalytic glutamate in other lytic transglycosylases. Indeed, SleB bearing a Glu157-to-Gln mutation lost its cortex degradative activity completely. In addition, the other redundant CLE (called CwlJ) in Bacillus species likely has a three-dimensional structure similar to that of SleB, including the invariant putative catalytic Glu residue. SleB and CwlJ may offer novel targets for the development of anti-spore agents.     

Levels of Germination Proteins in Bacillus subtilis Dormant,Superdormant, and Germinating Spores

Bacterial endospores exhibit extreme resistance to most conditions that rapidly kill other life forms, remaining viable in this dormant state for centuries or longer. While the majority of Bacillus subtilis dormant spores germinate rapidly in response to nutrient germinants, a small subpopulation termed superdormant spores are resistant to germination, potentially evading antibiotic and/or decontamination strategies. In an effort to better understand the underlying mechanisms of superdormancy, membrane-associated proteins were isolated from populations of B. subtilis dormant, superdormant, and germinated spores, and the relative abundance of 11 germination-related proteins was determined using multiple-reaction-monitoring liquid chromatography-mass spectrometry assays. GerAC, GerKC, and GerD were significantly less abundant in the membrane fractions obtained from superdormant spores than those derived from dormant spores. The amounts of YpeB, GerD, PrkC, GerAC, and GerKC recovered in membrane fractions decreased significantly during germination. Lipoproteins, as a protein class, decreased during spore germination, while YpeB appeared to be specifically degraded. Some protein abundance differences between membrane fractions of dormant and superdormant spores resemble protein changes that take place during germination, suggesting that the superdormant spore isolation procedure may have resulted in early, non-committal germination-associated changes. In addition to low levels of germinant receptor proteins, a deficiency in the GerD lipoprotein may contribute to heterogeneity of spore germination rates. Understanding the reasons for superdormancy may allow for better spore decontamination procedures.     

The catalytic domain of the germination-specific lytic transglycosylase SleB from Bacillus anthracis displays a unique active site topology

Bacillus anthracis produces metabolically inactive spores. Germination of these spores requires germination‐specific lytic enzymes (GSLEs) that degrade the unique cortex peptidoglycan to permit resumption of metabolic activity and outgrowth. We report the first crystal structure of the catalytic domain of a GSLE, SleB. The structure revealed a transglycosylase fold with unique active site topology and permitted identification of the catalytic glutamate residue. Moreover, the structure provided insights into the molecular basis for the specificity of the enzyme for muramic‐δ‐lactam‐containing cortex peptidoglycan. The protein also contains a metal‐binding site that is positioned directly at the entrance of the substrate‐binding cleft. Proteins 2012;. © 2012 Wiley Periodicals, Inc.     

Role of the gerP Operon in Germination and Outgrowth of Bacillus anthracis Spores

Germination of Bacillus anthracis spores occurs when nutrients such as amino acids or purine nucleosides stimulate specific germinant receptors located in the spore inner membrane. The gerP_ABCDEF operon has been suggested to play a role in facilitating the interaction between germinants and their receptors in spores of Bacillus subtilis and Bacillus cereus. B. anthracis mutants containing deletions in each of the six genes belonging to the orthologue of the gerP_ABCDEF operon, or deletion of the entire operon, were tested for their ability to germinate. Deletion of the entire gerP operon resulted in a significant delay in germination in response to nutrient germinants. These spores eventually germinated to levels equivalent to wild-type, suggesting that an additional entry point for nutrient germinants may exist. Deletions of each individual gene resulted in a similar phenotype, with the exception of ΔgerPF, which showed no obvious defect. The removal of two additional gerPF-like orthologues was necessary to achieve the germination defect observed for the other mutants. Upon physical removal of the spore coat, the mutant lacking the full gerP operon no longer exhibited a germination defect, suggesting that the GerP proteins play a role in spore coat permeability. Additionally, each of the gerP mutants exhibited a severe defect in calcium-dipicolinic acid (Ca-DPA)–dependent germination, suggesting a role for the GerP proteins in this process. Collectively, these data implicate all GerP proteins in the early stages of spore germination.     

Contributions of Four Cortex Lytic Enzymes to Germination of Bacillus anthracis Spores

Bacterial spores remain dormant and highly resistant to environmental stress until they germinate. Completion of germination requires the degradation of spore cortex peptidoglycan by germination-specific lytic enzymes (GSLEs). Bacillus anthracis has four GSLEs: CwlJ1, CwlJ2, SleB, and SleL. In this study, the cooperative action of all four GSLEs in vivo was investigated by combining in-frame deletion mutations to generate all possible double, triple, and quadruple GSLE mutant strains. Analyses of mutant strains during spore germination and outgrowth combined observations of optical density loss, colony-producing ability, and quantitative identification of spore cortex fragments. The lytic transglycosylase SleB alone can facilitate enough digestion to allow full spore viability and generates a variety of small and large cortex fragments. CwlJ1 is also sufficient to allow completion of nutrient-triggered germination independently and is a major factor in Ca²⁺-dipicolinic acid (DPA)-triggered germination, but its enzymatic activity remains unidentified because its products are large and not readily released from the spore''s integuments. CwlJ2 contributes the least to overall cortex digestion but plays a subsidiary role in Ca²⁺-DPA-induced germination. SleL is an N-acetylglucosaminidase that plays the major role in hydrolyzing the large products of other GSLEs into small, rapidly released muropeptides. As the roles of these enzymes in cortex degradation become clearer, they will be targets for methods to stimulate premature germination of B. anthracis spores, greatly simplifying decontamination measures.The Gram-positive bacterium Bacillus anthracis is the etiologic agent of cutaneous, gastrointestinal, and inhalational anthrax (24). An anthrax infection begins when the host is infected with highly resistant, quiescent B. anthracis spores (1, 24). Within the host, the spore''s sensory mechanism recognizes chemical signals, known as germinants, and triggers germination, which leads to the resumption of metabolism (36). Spores that have differentiated into vegetative cells produce a protective capsule and deadly toxins. These virulence factors allow the bacteria to evade the host''s immune system and establish an infection resulting in septicemia, toxemia, and frequently death (24). Although vegetative cells produce virulence factors that are potentially fatal, these cells cannot initiate infections and are much more susceptible to antimicrobial treatments than spores (24). Therefore, efficient triggering of spore germination may enhance current decontamination methods.Spores are highly resistant to many environmental insults because the spore core (cytoplasm) is dehydrated, dormant, and surrounded by multiple protective layers, including a modified layer of peptidoglycan (PG) known as the cortex (36). The cortex functions to maintain dormancy and heat resistance by preventing core rehydration (9). It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) sugars (Fig. ​(Fig.1).1). Peptide side chains on the NAM residues are either involved in interstrand cross-linking, cleaved to single l-alanine side chains, or fully removed with accompanying formation of muramic-δ-lactam (2, 31, 38). After germination is initiated by either nutrient or nonnutrient germinants, the cortex is depolymerized, resulting in complete core rehydration, resumption of metabolic activity, and outgrowth (33, 36).Open in a separate windowFIG. 1.Spore PG structure and hydrolysis. The central structure shows a representative spore PG strand with alternating NAG and NAM or muramic-δ-lactam (MδL) residues and with tetrapeptide or l-Ala side chains on the NAM residues. Forked arrows originate at sites of hydrolysis by the indicated enzymes and point to muropeptide products. The indicated “aG” muropeptide names are as previously published (7, 11). SleB lytic transglycosylase activity produces muropeptides terminating in anhydro-NAM. Cleavage at adjacent NAM residues produces the tetrasaccharide aG7a or aG7b, while cleavage further apart can produce octasaccharides or larger fragments. These can be further cleaved by muramidase treatment, resulting in the production of tetrasaccharide N, which terminates in NAM. The N-acetylglucosaminidase activity of SleL produces tetrasaccharides terminating in NAG, which can be further cleaved by muramidase to trisaccharides terminating in NAM.Cortex hydrolysis is driven by autolysins called germination-specific cortex lytic enzymes (GSLEs) that recognize the cortex-specific muramic-δ-lactam residues (2, 4, 21, 32). GSLEs fall into two classes: spore cortex lytic enzymes (SCLEs), which are thought to depolymerize intact cortical PG, and cortical fragment lytic enzymes (CFLEs), which further degrade partially hydrolyzed cortex (21). Both SCLEs and CFLEs have been identified in a variety of spore-forming species, including B. anthracis (11, 18, 19), Bacillus cereus (4, 20, 26), Bacillus megaterium (8, 34), Bacillus subtilis (13, 16, 25), Bacillus thuringiensis (12), and Clostridium perfringens (5, 23). Of the four GSLEs identified in B. anthracis, CwlJ1, CwlJ2, and SleB are predicted to be SCLEs (11), whereas SleL is thought to be a CFLE (18).Recently, independent studies showed that CwlJ1 and the lytic transglycosylase SleB (Fig. ​(Fig.1)1) play partially redundant roles and that either is sufficient for spore germination and outgrowth (10, 11). However, these same studies report conflicting results concerning the role of CwlJ2 during germination. Heffron et al. found no effect of CwlJ2 on the biochemistry of cortex hydrolysis or on colony-forming efficiency of spores (11). Giebel et al. reported that loss of CwlJ2 caused a minor defect in germination kinetics and that in the absence of SleB and CwlJ1, further loss of CwlJ2 had a major effect on colony forming efficiency (10). SleL in Bacillus anthracis is proposed to be an N-acetylglucosaminidase (Fig. ​(Fig.1)1) whose role is to further degrade cortex fragments resulting from SCLE hydrolysis (18). SleL is not essential for the completion of germination but does promote the release of small muropeptides to the spore''s surrounding environment (18).This study reports the effects of multiple deletion mutations affecting GSLEs on spore germination efficiency and kinetics of cortex hydrolysis. The data confirm the dominant roles played by CwlJ1 and SleB in the initiation of cortex hydrolysis and the major role of SleL in release of small cortex fragments. A minor role of CwlJ2 in nutrient-triggered germination and the contributions of CwlJ1 and CwlJ2 to Ca²⁺-dipicolinic acid (DPA)-triggered germination were revealed.     

Mutational Analysis of Bacillus megaterium QM B1551 Cortex-Lytic Enzymes

Molecular-genetic and muropeptide analysis techniques have been applied to examine the function in vivo of the Bacillus megaterium QM B1551 SleB and SleL proteins. In common with Bacillus subtilis and Bacillus anthracis, the presence of anhydromuropeptides in B. megaterium germination exudates, which is indicative of lytic transglycosylase activity, is associated with an intact sleB structural gene. B. megaterium sleB cwlJ double mutant strains complemented with engineered SleB variants in which the predicted N- or C-terminal domain has been deleted (SleB-ΔN or SleB-ΔC) efficiently initiate and hydrolyze the cortex, generating anhydromuropeptides in the process. Additionally, sleB cwlJ strains complemented with SleB-ΔN or SleB-ΔC, in which glutamate and aspartate residues have individually been changed to alanine, all retain the ability to hydrolyze the cortex to various degrees during germination, with concomitant release of anhydromuropeptides to the surrounding medium. These data indicate that while the presence of either the N- or C-terminal domain of B. megaterium SleB is sufficient for initiation of cortex hydrolysis and the generation of anhydromuropeptides, the perceived lytic transglycosylase activity may be derived from an enzyme(s), perhaps exclusively or in addition to SleB, which has yet to be identified. B. megaterium SleL appears to be associated with the epimerase-type activity observed previously in B. subtilis, differing from the glucosaminidase function that is apparent in B. cereus/B. anthracis.Spores of the genera Bacillus and Clostridium emerge from dormancy via the process of germination. The germination process comprises a series of sequential biophysical and biochemical reactions that result irreversibly in the spore losing its properties of metabolic dormancy and extreme resistance to various chemical and physical treatments (24, 34). Germination is initiated by the presumed binding of small molecular germinants, commonly amino acids or sugars, to cognate receptors located within the spore inner membrane (25, 28). In a process that is poorly understood at the molecular level, this interaction leads to a change in the permeability of the inner membrane, resulting in the release of various solutes from the spore core, including metal ions, calcium dipicolinate (Ca-DPA), and some amino acids (32, 33, 35). A degree of rehydration of the core is evident at or around the same time, although this is insufficient to permit a significant degree of vegetative metabolism (9, 31). These events, which appear common to all Bacillus species where examined, comprise stage I of germination (31, 32, 34).The major event in stage II of the germination process from a biochemical perspective involves depolymerization of the spore cortex. The spore cortex is a thick layer of peptidoglycan, characterized by the spore-specific muramic acid lactam (MAL) moiety (37, 38), which, together with the thin inner layer of germ cell wall peptidoglycan (36), forms contiguous layers that entirely envelope the spore protoplast. While the germ cell wall forms the initial cell wall during vegetative outgrowth, the spore cortex serves primarily to maintain the relatively dehydrated status of the spore protoplast during dormancy (13). Dissolution of the cortex permits complete hydration of the spore core and resumption of vegetative metabolism, leading ultimately to shedding of the spore coat and the emergence of a new vegetative cell (34).A number of studies have indicated that spores of various Bacillus species employ two cortex-lytic enzymes (CLEs), SleB and CwlJ, to initiate hydrolysis of the cortex during stage II of the germination process (16, 19, 32). These enzymes are semiredundant; hence, strains bearing null mutations in either structural gene can still degrade the cortex sufficiently to complete germination, whereas double mutant strains do not appear capable of degrading the cortex at all, resulting typically in a decrease of several orders of magnitude in colony-forming ability (15, 19, 32). Other enzymes, including Bacillus cereus/Bacillus anthracis SleL, are also involved in stage II of germination, apparently hydrolyzing peptidoglycan products of SleB and/or CwlJ to smaller peptidoglycan fragments that can more easily permeate through the spore coats to the surrounding germination medium (21).Studies with SleB and SleL purified from dormant and germinating spores indicate that whereas the latter enzyme degrades only cortical fragments of peptidoglycan (7), SleB has a requirement for intact peptidoglycan that has adopted the precise architecture present within the spore (12, 22). These substrate requirements appear to be important in maintenance of the respective autolysins, which are present in the spore in a mature form, in an inactive state during dormancy. Additionally, whereas the molecular mechanism of activation of SleB remains unclear—a change in cortical stress/architecture induced by stage I events has been hypothesized (12)—the efflux of Ca-DPA from the spore core to the cortex/coat boundary where CwlJ is localized (5) appears to be the mechanism by which this CLE is activated. CwlJ can also be activated by high concentrations of exogenous Ca-DPA, presenting an alternative germination pathway that bypasses the germinant receptors (27).The hydrolytic bond specificity of various CLEs has been examined by both direct and indirect biochemical means. Direct assays are typically conducted by incubation of purified or recombinant enzymes with peptidoglycan fragments or suspensions of spores in which the cortex is rendered accessible by first chemically compromising the permeability of the spore coats (7, 12, 22). Subsequent assays for the generation of reducing groups and/or free amino groups can yield information on the probable hydrolytic bond specificity of the respective enzyme(s) being assayed.More recently, the high-performance liquid chromatography/mass spectrometry (HPLC/MS)-based muropeptide analysis technique has been applied to characterize CLE activity during germination of various spore-forming species (2, 4, 10). This methodology has the resolution to reveal fine structural changes that occur to the peptidoglycan in vivo during germination, and when used in combination with CLE null mutant strains, it can be used to indirectly correlate the generation of certain classes of muropeptides, and therefore the hydrolytic bond specificity, with defined CLEs. Muropeptide analysis has revealed, for example, that an intact copy of the sleB gene in B. subtilis and B. anthracis is required for the presence of anhydromuropeptides in the germination exudates of these respective species, indicating that SleB is a lytic transglycosylase or generates substrate for subsequent lytic transglycosylase activity (6, 16). Conversely, B. cereus SleB was characterized as a probable amidase after enzyme purified from germinating spores was found to liberate a large amount of free amino groups when incubated with coat-stripped spores as a substrate (22). The hydrolytic bond specificity of SleB therefore remains ambiguous and perhaps varies between different species.Contrary to these observations, the overall structural architecture of SleB appears to be well conserved between different Bacillus species. Alignment of the primary amino acid sequence from different species indicates that the mature protein comprises an N-terminal domain that is connected to the C-terminal domain by a linker region that is variable in length and amino acid composition (Fig. ​(Fig.1).1). The N-terminal domain is thought to comprise the peptidoglycan binding domain by virtue of two direct sequence repeats that are reminiscent of cell wall-binding motifs observed in other proteins (26). The C-terminal domain shows homology with that of the other major Bacillus CLE, CwlJ, which lacks a corresponding peptidoglycan binding domain and is therefore thought to comprise the catalytic domain (19), although there is as yet no experimental evidence to substantiate this idea.Open in a separate windowFIG. 1.ClustalW alignment of SleB from various Bacillus species. Residues predicted to comprise putative structural domains are denoted. Stars indicate charged residues that were subjected to amino acid substitution in this work. BM, B. megaterium QM B1551; BC, B. cereus W; BCl, B. clausii KSM-K16; BS, B. subtilis 168.In the current study, we have investigated the molecular function of SleB during germination of Bacillus megaterium QM B1551 spores, employing engineered SleB N- and C-terminal deletion strains, site-directed mutagenesis (SDM), and muropeptide analyses. In addition to revealing several cortex-modifying activities during germination of this species, the presented data indicate that while the presence of either the N- or C-terminal domain of SleB is sufficient for the generation of anhydromuropeptides during germination, this may be an indirect effect, and at least a degree of lytic transglycosylase activity may result from the activity of another as yet unidentified enzyme.     

Characterization of the germination of Bacillus megaterium spores lacking enzymes that degrade the spore cortex

Aims:  To determine roles of cortex lytic enzymes (CLEs) in Bacillus megaterium spore germination.
Methods and Results:  Genes for B. megaterium CLEs CwlJ and SleB were inactivated and effects of loss of one or both on germination were assessed. Loss of CwlJ or SleB did not prevent completion of germination with agents that activate the spore's germinant receptors, but loss of CwlJ slowed the release of dipicolinic acid (DPA). Loss of both CLEs also did not prevent release of DPA and glutamate during germination with KBr. However, cwlJ sleB spores had decreased viability, and could not complete germination. Loss of CwlJ eliminated spore germination with Ca²⁺ chelated to DPA (Ca-DPA), but loss of CwlJ and SleB did not affect DPA release in dodecylamine germination.
Conclusions:  CwlJ and SleB play redundant roles in cortex degradation during B. megaterium spore germination, and CwlJ accelerates DPA release and is essential for Ca-DPA germination. The roles of these CLEs are similar in germination of B. megaterium and Bacillus subtilis spores.
Significance and Impact of the Study:  These results indicate that redundant roles of CwlJ and SleB in cortex degradation during germination are similar in spores of Bacillus species; consequently, inhibition of these enzymes will prevent germination of Bacillus spores.     

Proteomic Profiling and Identification of Immunodominant Spore Antigens of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis

Differentially expressed and immunogenic spore proteins of the Bacillus cereus group of bacteria, which includes Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis, were identified. Comparative proteomic profiling of their spore proteins distinguished the three species from each other as well as the virulent from the avirulent strains. A total of 458 proteins encoded by 232 open reading frames were identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analysis for all the species. A number of highly expressed proteins, including elongation factor Tu (EF-Tu), elongation factor G, 60-kDa chaperonin, enolase, pyruvate dehydrogenase complex, and others exist as charge variants on two-dimensional gels. These charge variants have similar masses but different isoelectric points. The majority of identified proteins have cellular roles associated with energy production, carbohydrate transport and metabolism, amino acid transport and metabolism, posttranslational modifications, and translation. Novel vaccine candidate proteins were identified using B. anthracis polyclonal antisera from humans postinfected with cutaneous anthrax. Fifteen immunoreactive proteins were identified in B. anthracis spores, whereas 7, 14, and 7 immunoreactive proteins were identified for B. cereus and in the virulent and avirulent strains of B. thuringiensis spores, respectively. Some of the immunodominant antigens include charge variants of EF-Tu, glyceraldehyde-3-phosphate dehydrogenase, dihydrolipoamide acetyltransferase, Δ-1-pyrroline-5-carboxylate dehydrogenase, and a dihydrolipoamide dehydrogenase. Alanine racemase and neutral protease were uniquely immunogenic to B. anthracis. Comparative analysis of the spore immunome will be of significance for further nucleic acid- and immuno-based detection systems as well as next-generation vaccine development.     

Involvement of Coat Proteins in Bacillus subtilis Spore Germination in High-Salinity Environments

The germination of spore-forming bacteria in high-salinity environments is of applied interest for food microbiology and soil ecology. It has previously been shown that high salt concentrations detrimentally affect Bacillus subtilis spore germination, rendering this process slower and less efficient. The mechanistic details of these salt effects, however, remained obscure. Since initiation of nutrient germination first requires germinant passage through the spores'' protective integuments, the aim of this study was to elucidate the role of the proteinaceous spore coat in germination in high-salinity environments. Spores lacking major layers of the coat due to chemical decoating or mutation germinated much worse in the presence of NaCl than untreated wild-type spores at comparable salinities. However, the absence of the crust, the absence of some individual nonmorphogenetic proteins, and the absence of either CwlJ or SleB had no or little effect on germination in high-salinity environments. Although the germination of spores lacking GerP (which is assumed to facilitate germinant flow through the coat) was generally less efficient than the germination of wild-type spores, the presence of up to 2.4 M NaCl enhanced the germination of these mutant spores. Interestingly, nutrient-independent germination by high pressure was also inhibited by NaCl. Taken together, these results suggest that (i) the coat has a protective function during germination in high-salinity environments; (ii) germination inhibition by NaCl is probably not exerted at the level of cortex hydrolysis, germinant accessibility, or germinant-receptor binding; and (iii) the most likely germination processes to be inhibited by NaCl are ion, Ca²⁺-dipicolinic acid, and water fluxes.     

Bacillus anthracis Spore Surface Protein BclA Mediates Complement Factor H Binding to Spores and Promotes Spore Persistence

Spores of Bacillus anthracis, the causative agent of anthrax, are known to persist in the host lungs for prolonged periods of time, however the underlying mechanism is poorly understood. In this study, we demonstrated that BclA, a major surface protein of B. anthracis spores, mediated direct binding of complement factor H (CFH) to spores. The surface bound CFH retained its regulatory cofactor activity resulting in C3 degradation and inhibition of downstream complement activation. By comparing results from wild type C57BL/6 mice and complement deficient mice, we further showed that BclA significantly contributed to spore persistence in the mouse lungs and dampened antibody responses to spores in a complement C3-dependent manner. In addition, prior exposure to BclA deletion spores (ΔbclA) provided significant protection against lethal challenges by B. anthracis, whereas the isogenic parent spores did not, indicating that BclA may also impair protective immunity. These results describe for the first time an immune inhibition mechanism of B. anthracis mediated by BclA and CFH that promotes spore persistence in vivo. The findings also suggested an important role of complement in persistent infections and thus have broad implications.     

The Identification of in Vitro Production of Lectin from Callus Cultures of Korean Mistletoe (Viscum album L. var. coloratum)

The hydrolysis of the bacterial spore peptidoglycan (cortex) is a crucial event in spore germination. It has been suggested that SleC and SleM, which are conserved among clostridia, are to be considered putative cortex-lytic enzymes in Clostridium perfringens. However, little is known about the details of the hydrolytic process by these enzymes during germination, except that SleM functions as a muramidase. Muropeptides derived from SleC-digested decoated spores of a Bacillus subtilis mutant that lacks the enzymes, SleB, YaaH and CwlJ, related to cortex hydrolysis were identified by amino acid analysis and mass spectrometry. The results suggest that SleC is most likely a bifunctional enzyme possessing lytic transglycosylase activity and N-acetylmuramoyl-L-alanine amidase activity confined to cross-linked tetrapeptide-tetrapeptide moieties of the cortex structure. Furthermore, it appears that during germination of Clostridium perfringens spores, SleC causes merely small and local changes in the cortex structure, which are necessary before SleM can function.     

Convergent evolution of diverse Bacillus anthracis outbreak strains toward altered surface oligosaccharides that modulate anthrax pathogenesis

Bacillus anthracis, a spore-forming gram-positive bacterium, causes anthrax. The external surface of the exosporium is coated with glycosylated proteins. The sugar additions are capped with the unique monosaccharide anthrose. The West African Group (WAG) B. anthracis have mutations rendering them anthrose deficient. Through genome sequencing, we identified 2 different large chromosomal deletions within the anthrose biosynthetic operon of B. anthracis strains from Chile and Poland. In silico analysis identified an anthrose-deficient strain in the anthrax outbreak among European heroin users. Anthrose-deficient strains are no longer restricted to West Africa so the role of anthrose in physiology and pathogenesis was investigated in B. anthracis Sterne. Loss of anthrose delayed spore germination and enhanced sporulation. Spores without anthrose were phagocytized at higher rates than spores with anthrose, indicating that anthrose may serve an antiphagocytic function on the spore surface. The anthrose mutant had half the LD₅₀ and decreased time to death (TTD) of wild type and complement B. anthracis Sterne in the A/J mouse model. Following infection, anthrose mutant bacteria were more abundant in the spleen, indicating enhanced dissemination of Sterne anthrose mutant. At low sample sizes in the A/J mouse model, the mortality of ΔantC-infected mice challenged by intranasal or subcutaneous routes was 20% greater than wild type. Competitive index (CI) studies indicated that spores without anthrose disseminated to organs more extensively than a complemented mutant. Death process modeling using mouse mortality dynamics suggested that larger sample sizes would lead to significantly higher deaths in anthrose-negative infected animals. The model was tested by infecting Galleria mellonella with spores and confirmed the anthrose mutant was significantly more lethal. Vaccination studies in the A/J mouse model showed that the human vaccine protected against high-dose challenges of the nonencapsulated Sterne-based anthrose mutant. This work begins to identify the physiologic and pathogenic consequences of convergent anthrose mutations in B. anthracis.

A study of the spontaneous loss of the spore coat monosaccharide anthrose suggests that convergent evolution in several anthrax strains towards increased pathogenicity could exacerbate global human and animal anthrax disease.     

Identification of Several Unique, Low-Molecular-Weight Basic Proteins in Dormant Spores of Clostridium bifermentans and Their Degradation During Spore Germination

Two acid-soluble, low-molecular-weight basic proteins comprise ~20% of the protein in dormant spores of Clostridium bifermentans. Both of these proteins are rapidly degraded during spore germination.     

Structural and functional analysis of SleL,a peptidoglycan lysin involved in germination of Bacillus spores

A major event in the germination of Bacillus spores concerns hydrolysis of the cortical peptidoglycan that surrounds the spore protoplast, the integrity of which is essential for maintenance of dormancy. Cortex degradation is initiated in all species of Bacillus spores by the combined activity of two semi‐redundant cortex‐lytic enzymes, SleB and CwlJ. A third enzyme, SleL, which has N‐acetylglucosaminidase activity, cleaves peptidoglycan fragments generated by SleB and CwlJ. Here we present crystal structures of B. cereus and B. megaterium SleL at 1.6 angstroms and 1.7 angstroms, respectively. The structures were determined with a view to identifying the structural basis of differences in catalytic efficiency between the respective enzymes. The catalytic (α/β)₈‐barrel cores of both enzymes are highly conserved from a structural perspective, including the spatial distribution of the catalytic residues. Both enzymes are equipped with two N‐terminal peptidoglycan‐binding LysM domains, which are also structurally highly conserved. However, the topological arrangement of the respective enzymes second LysM domain is markedly different, and this may account for differences in catalytic rates by impacting upon the position of the active sites with respect to their substrates. A chimeric enzyme comprising the B. megaterium SleL catalytic domain plus B. cereus SleL LysM domains displayed enzymatic activity comparable to the native B. cereus protein, exemplifying the importance of the LysM domains to SleL function. Similarly, the reciprocal construct, comprising the B. cereus SleL catalytic domain with B. megaterium SleL LysM domains, showed reduced activity compared with native B. cereus SleL. Proteins 2015; 83:1787–1799. © 2015 Wiley Periodicals, Inc.