Spore peptidoglycan structure in a cwlD dacB double mutant of Bacillus subtilis

Pressure and Temperature Combined With Microbial Supernatant Effectively Inactivate Bacillus subtilis Spores

Spores from the Bacillus species pose a challenge to the food industry because of their ubiquitous nature and extreme resistance. Accumulated evidence indicates that it is effective to induce spore germination homogenously before killing them. However, it is difficult to obtain and apply exogenous germination factors, which will affect food composition. Therefore, this study screened endogenous germinants from microorganisms by assessing the effect of Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Lactiplantibacillus plantarum, and Streptococcus thermophilus cultures (cell-free) on B. subtilis spore germination. The results showed that the supernatants from these five microorganisms induced spore germination instead of sediments. Moreover, the supernatants of E. coli, B. subtilis, and S. cerevisiae exhibited higher germination rates than L. plantarum and S. thermophilus, and the induction effects were concentration-dependent. Furthermore, plate counting confirmed that the microbial supernatants induced the lowest spore germination ratio on strains B. subtilis FB85 [germination receptors (GRs) mutant] but not strains B. subtilis PB705 (PrkC mutant). In addition, B. subtilis and S. cerevisiae supernatants, combined with pressure and temperature, were effective in spore inactivation. The findings suggested that microbial supernatants may include agents that induce spore germination and may be used for spore inactivation.

Optimization of bacterial sporulation using economic nutrient for self-healing concrete

The use of heat- and alkali-resistant bacteria is essential for the biological repair of damaged concrete. Lysinibacillus boronitolerans YS11 was isolated from the rhizosphere of Miscanthus sacchariflorus. The increased pH in the urea-minus condition during the growth of the YS11 strain promoted calcium carbonate (CaCO₃) formation. To identify the optimum medium that promoted the growth of the YS11 strain, a Plackett-Burman design was conducted for the screening process. Consequently, malt powder, rice bran, (NH₄)₂SO₄, and corn syrup were chosen to enhance YS11 growth. The optimization of these four useful factors was carried out using a central composite design. To obtain higher survivability in mortar, the sporulation process is essential, and additional factors such as Mn²⁺, Fe²⁺, and Ca²⁺ were found to contribute to sporulation. A mixture of L. boronitolerans YS11 spore powder, cement, paste, sand, yeast extract, calcium lactate, and water showed a healing effect on a 0.3 mm mortar crack in 7 days. Furthermore, calcium carbonate precipitation was observed over the crack surface. Thus, we confirmed that mortar treated with YS11 spore powder was effective in healing micro-cracks in concrete.

Accumulation and Release of Rare Earth Ions by Spores of Bacillus Species and the Location of These Ions in Spores

Two rare earth ions, Tb³⁺ and Dy³⁺, were incorporated into spores of Bacillus species in ≤5 min at neutral pH to 100 to 200 nmol per mg of dry spores, which is equivalent to 2 to 3% of the spore dry weight. The uptake of these ions had, at most, minimal effects on spore wet heat resistance or germination, and the ions were all released upon germination, probably by complex formation with the huge depot of dipicolinic acid (DPA) released when spores germinate. Adsorbed Tb³⁺/Dy³⁺ were also released by exogenous DPA within a few minutes and faster than in spore germination. The accumulation of Tb³⁺/Dy³⁺ was not reduced in Bacillus subtilis spores by several types of coat defects, significant modification of the spore cortex peptidoglycan structure, specific loss of components of the outer spore crust layer, or the absence of DPA in the spore core. All of these findings are consistent with Tb³⁺/Dy³⁺ being accumulated in spores' outer layers, and this was confirmed by transmission electron microscopy. However, the identity of the outer spore components binding the Tb³⁺/Dy³⁺ is not clear. These findings provide new information on the adsorption of rare earth ions by Bacillus spores and suggest this adsorption might have applications in capturing rare earth ions from the environment.IMPORTANCE Biosorption of rare earth ions by growing cells of Bacillus species has been well studied and has attracted attention for possible hydrometallurgy applications. However, the interaction of spores from Bacillus species with rare earth ions has not been well studied. We investigated here the adsorption and/or desorption of two rare earth ions, Tb³⁺ and Dy³⁺, by Bacillus spores, the location of the adsorbed ions, and the spore properties after ion accumulation. The significant adsorption of rare earth ions on the surfaces of Bacillus spores and the ions' rapid release by a chelator could allow the development of these spores as a biosorbent to recover rare earth ions from the environment.

Identification of L-Valine-initiated-germination-active genes in Bacillus subtilis using Tn-seq

Bacterial endospores can survive harsh environmental conditions and long-term dormancy in the absence of nutrients, but can rapidly germinate under favorable conditions. In the present study, we employed transposon sequencing (Tn-seq) to identify genes with previously uncharacterized roles in spore germination. Identified genes that encoded spore inner membrane proteins were chosen for study of defined mutants, which exhibited delayed germination in several assays in response to varying germinants. Significantly slowed release of DPA indicated that mutants were affected in Stage I of germination. Several mutants exhibited phenotypic traits consistent with failure of a GerA germinant receptor-mediated response, while others appeared to have a more general loss of response to varied germinants. Use of a gerA-lacZ transcriptional fusion and quantitative western blotting of GerAC allowed mutants to be classified based upon normal or decreased gerA transcription and normal or reduced GerA accumulation. Fourteen genes were identified to have newly described roles within Bacillus spore germination. A more complete understanding of this process can contribute to the development of better spore decontamination procedures.

Characterization of putative DD-carboxypeptidase-encoding genes in Mycobacterium smegmatis

Penicillin binding proteins (PBPs) are the target of numerous antimicrobial agents that disrupt bacterial cell wall synthesis. In mycobacteria, cell elongation occurs through insertion of nascent cell wall material in the sub-polar region, a process largely driven by High Molecular Weight PBPs. In contrast, the function of DD-carboxypeptidases (DD-CPases), which are Low Molecular Weight Class 1C PBPs, in mycobacteria remains poorly understood. Mycobacterium smegmatis encodes four putative DD-CPase homologues, which display homology to counterparts in Escherichia coli. Herein, we demonstrate that these are expressed in varying abundance during growth. Deletion of MSMEG_1661, MSMEG_2433 or MSMEG_2432, individually resulted in no defects in growth, cell morphology, drug susceptibility or spatial incorporation of new peptidoglycan. In contrast, deletion of MSMEG_6113 (dacB) was only possible in a merodiploid strain expressing the homologous M. tuberculosis operon encoding Rv3627c (dacB), Rv3626c, Rv3625c (mesJ) and Rv3624c (hpt), suggestive of essentiality. To investigate the role of this operon in mycobacterial growth, we depleted gene expression using anhydrotetracycline-responsive repressors and noted reduced bipolar peptidoglycan synthesis. These data point to a possible role for this four gene operon, which is highly conserved across all mycobacterial species, in regulating spatial localization of peptidoglycan synthesis.

Spore Peptidoglycan

Bacterial endospores possess multiple integument layers, one of which is the cortex peptidoglycan wall. The cortex is essential for the maintenance of spore core dehydration and dormancy and contains structural modifications that differentiate it from vegetative cell peptidoglycan and determine its fate during spore germination. Following the engulfment stage of sporulation, the cortex is synthesized within the intermembrane space surrounding the forespore. Proteins responsible for cortex synthesis are produced in both the forespore and mother cell compartments. While some of these proteins also contribute to vegetative cell wall synthesis, others are sporulation specific. In order for the bacterial endospore to germinate and resume metabolism, the cortex peptidoglycan must first be degraded through the action of germination-specific lytic enzymes. These enzymes are present, yet inactive, in the dormant spore and recognize the muramic-δ-lactam modification present in the cortex. Germination-specific lytic enzymes across Bacillaceae and Clostridiaceae share this specificity determinant, which ensures that the spore cortex is hydrolyzed while the vegetative cell wall remains unharmed. Bacillus species tend to possess two redundant enzymes, SleB and CwlJ, capable of sufficient cortex degradation, while the clostridia have only one, SleC. Additional enzymes are often present that cannot initiate the cortex degradation process, but which can increase the rate of release of small fragments into the medium. Between the two families, the enzymes also differ in the enzymatic activities they possess and the mechanisms acting to restrict their activation until germination has been initiated.

Spore Germination

Despite being resistant to a variety of environmental insults, the bacterial endospore can sense the presence of small molecules and respond by germinating, losing the specialized structures of the dormant spore, and resuming active metabolism, before outgrowing into vegetative cells. Our current level of understanding of the spore germination process in bacilli and clostridia is reviewed, with particular emphasis on the germinant receptors characterized in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. The recent evidence for a local clustering of receptors in a "germinosome" would begin to explain how signals from different receptors could be integrated. The SpoVA proteins, involved in the uptake of Ca2+-dipicolinic acid into the forespore during sporulation, are also responsible for its release during germination. Lytic enzymes SleB and CwlJ, found in bacilli and some clostridia, hydrolyze the spore cortex: other clostridia use SleC for this purpose. With genome sequencing has come the appreciation that there is considerable diversity in the setting for the germination machinery between bacilli and clostridia.

Bacillus spore wet heat resistance and evidence for the role of an expanded osmoregulatory spore cortex

Previous work reported that decoated Bacillus cereus spores incubated in 4 mol l(-1) CaCl2 are killed at lower temperatures than spores in water. This wet heat sensitization was suggested to support a role for an osmoregulatory peptidoglycan cortex in spore cores' low water content, and their wet heat resistance. Current work has replicated this finding with spores of B. cereus, Bacillus megaterium and Bacillus subtilis. However, this work found that decoated spores apparently killed at 80°C in 4 mol l(-1) CaCl2 : (i) were recovered on plates containing lysozyme; (ii) lost no dipicolinic acid (DPA) and their inner membrane remained impermeable; (iii) released no DPA upon stimulation with nutrient germinants and could not complete germination; and (iv) released DPA relatively normally upon stimulation with dodecylamine. These results indicate that decoated spores treated with 80°C- 4 mol l(-1) CaCl2 are not dead, but some protein(s) essential for spore germination, most likely germinant receptors, are inactivated by this treatment. Thus, the original finding does not support a role for an osmoregulatory cortex in spore wet heat resistance.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacillus spores' low core water content is a major factor in their wet heat resistance. One suggested mechanism for achieving low spore core water content is osmoregulated expansion of spores' peptidoglycan cortex. Evidence for this mechanism includes a report that decoated Bacillus cereus spores incubated in 4 mol l(-1) CaCl2 exhibit drastically reduced heat resistance. The current work shows that this heat sensitization of decoated spores of three Bacillus species is most likely due to inactivation of some crucial spore germination protein(s), since while treated spores appear dead, their apparent low viability is rescued by triggering spore germination with lysozyme.

Expression level of Bacillus subtilis germinant receptors determines the average rate but not the heterogeneity of spore germination

Germination of Bacillus subtilis spores can be triggered by the binding of specific nutrients, called germinants, to germinant receptors (GRs) in the spore's inner membrane. This interaction eventually initiates, with variable time delays, the release of dipicolinic acid and cations from the spore core--a key step in spore germination. The kinetics of this process are highly heterogeneous for individual spores. In this work, we sought to investigate how the germination heterogeneity was controlled. In particular, we tested whether the rates of germination were determined by GR levels, which vary from spore to spore due to stochastic gene expression. Both the expression levels of GRs and the germination rate were measured in single spores, and the experimental results were compared to theoretical predictions. Our results indicated that the variation in the expression levels of GRs was not the primary factor that controls spore germination heterogeneity. Two alternative hypotheses are discussed in light of this experimental discovery.

Effects of cortex peptidoglycan structure and cortex hydrolysis on the kinetics of Ca(2+)-dipicolinic acid release during Bacillus subtilis spore germination

The kinetic parameters of the release of Ca(2+)-dipicolinic acid (CaDPA) during germination of spore populations and multiple individual spores of Bacillus subtilis strains with major alterations in the structure of the spore peptidoglycan (PG) cortex or lacking one or both of the two redundant enzymes involved in cortex hydrolysis (cortex-lytic enzymes [CLEs]) were determined. The lack of the CLE CwlJ greatly slowed CaDPA release with a germinant receptor (GR)-dependent germinant, l-valine, or a non-GR-dependent germinant, dodecylamine. The absence of the cortex-specific PG modification muramic acid-δ-lactam also increased the time needed for full CaDPA release during germination with both types of germinants. In contrast, increased cortex PG cross-linking was associated with faster times for initiation of CaDPA release with both l-valine and dodecylamine but not with faster CaDPA release once this release had been initiated. These data suggest that the precise structure of the spore cortex plays a significant role in determining the timing and the rate of CaDPA release during B. subtilis spore germination and, further, that this effect is independent of effects of GRs.

Identification and characterization of a polysaccharide deacetylase gene from Bacillus thuringiensis

One polysaccharide deacetylase gene was cloned from Bacillus thuringiensis and designated pdaA. Disruption of pdaA did not affect vegetative growth and sporulation but obviously affected spore germination. When L-alanine was added into the spore suspension, the spores of the pdaA disruption mutant showed a slow and partial reduction in absorbance at OD600 and became phase pale gray compared with phase dark of the wild-type strain. In contrast with the outgrowing of wild-type spores after germination, the pdaA mutant spores were blocked at the stage of spore germination. Transmission electron micrographs revealed a significant difference between the pdaA mutant and the wild-type strain in the spore cortex. Introduction of the pdaA gene into the pdaA disruption mutant complemented the germination-negative phenotype. Reverse transcription--polymerase chain reaction showed that pdaA was transcribed after incubation for 10 h in CCY medium.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update covering the period 1999-2000

This review describes the use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates and continues coverage of the field from the previous review published in 1999 (D. J. Harvey, Matrix-assisted laser desorption/ionization mass spectrometry of carbohydrates, 1999, Mass Spectrom Rev, 18:349-451) for the period 1999-2000. As MALDI mass spectrometry is acquiring the status of a mature technique in this field, there has been a greater emphasis on applications rather than to method development as opposed to the previous review. The present review covers applications to plant-derived carbohydrates, N- and O-linked glycans from glycoproteins, glycated proteins, mucins, glycosaminoglycans, bacterial glycolipids, glycosphingolipids, glycoglycerolipids and related compounds, and glycosides. Applications of MALDI mass spectrometry to the study of enzymes acting on carbohydrates (glycosyltransferases and glycosidases) and to the synthesis of carbohydrates, are also covered.

Two class A high-molecular-weight penicillin-binding proteins of Bacillus subtilis play redundant roles in sporulation

The four class A penicillin-binding proteins (PBPs) of Bacillus subtilis appear to play functionally redundant roles in polymerizing the peptidoglycan (PG) strands of the vegetative-cell and spore walls. The ywhE product was shown to bind penicillin, so the gene and gene product were renamed pbpG and PBP2d, respectively. Construction of mutant strains lacking multiple class A PBPs revealed that, while PBP2d plays no obvious role in vegetative-wall synthesis, it does play a role in spore PG synthesis. A pbpG null mutant produced spore PG structurally similar to that of the wild type; however, electron microscopy revealed that in a significant number of these spores the PG did not completely surround the spore core. In a pbpF pbpG double mutant this spore PG defect was apparent in every spore produced, indicating that these two gene products play partially redundant roles. A normal amount of spore PG was produced in the double mutant, but it was frequently produced in large masses on either side of the forespore. The double-mutant spore PG had structural alterations indicative of improper cortex PG synthesis, including twofold decreases in production of muramic delta-lactam and L-alanine side chains and a slight increase in cross-linking. Sporulation gene expression in the pbpF pbpG double mutant was normal, but the double-mutant spores failed to reach dormancy and subsequently degraded their spore PG. We suggest that these two forespore-synthesized PBPs are required for synthesis of the spore germ cell wall, the first layer of spore PG synthesized on the surface of the inner forespore membrane, and that in the absence of the germ cell wall the cells lack a template needed for proper synthesis of the spore cortex, the outer layers of spore PG, by proteins on the outer forespore membrane.

Negative and positive ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and positive ion nano-electrospray ionization quadrupole ion trap mass spectrometry of peptidoglycan fragments isolated from various Bacillus species

A general approach for the detailed characterization of sodium borohydride-reduced peptidoglycan fragments (syn. muropeptides), produced by muramidase digestion of the purified sacculus isolated from Bacillus subtilis (vegetative cell form of the wild type and a dacA mutant) and Bacillus megaterium (endospore form), is outlined based on UV matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nano-electrospray ionization (nESI) quadrupole ion trap (QIT) mass spectrometry (MS). After enzymatic digestion and reduction of the resulting muropeptides, the complex glycopeptide mixture was separated and fractionated by reversed-phase high-performance liquid chromatography. Prior to mass spectrometric analysis, the muropeptide samples were subjected to a desalting step and an aliquot was taken for amino acid analysis. Initial molecular mass determination of these peptidoglycan fragments (ranging from monomeric to tetrameric muropeptides) was performed by positive and negative ion MALDI-MS using the thin-layer technique with the matrix alpha-cyano-4-hydroxycinnamic acid. The results demonstrated that for the fast molecular mass determination of large sample numbers in the 0.8-10 pmol range and with a mass accuracy of +/-0.07%, negative ion MALDI-MS in the linear TOF mode is the method of choice. After this kind of muropeptide screening often a detailed primary structural analysis is required owing to ambiguous data. Structural data could be obtained from peptidoglycan monomers by post-source decay (PSD) fragment ion analysis, but not from dimers or higher oligomers and not with the necessary sensitivity. Multistage collision-induced dissociation (CID) experiments performed on an nESI-QIT instrument were found to be the superior method for structural characterization of not only monomeric but also of dimeric and trimeric muropeptides. Up to MS4 experiments were sometimes necessary to obtain unambiguous structural information. Three examples are presented: (a) CID MSn (n = 2-4) of a peptidoglycan monomer (disaccharide-tripeptide) isolated from B. subtilis (wild type, vegetative cell form), (b) CID MSn (n = 2-4) of a peptidoglycan dimer (bis-disaccharide-tetrapentapeptide) obtained from a B. subtilis mutant (vegetative cell form) and (c) CID MS2 of a peptidoglycan trimer (a linear hexasaccharide with two peptide side chains) isolated from the spore cortex of B. megaterium. All MS(n) experiments were performed on singly charged precursor ions and the MS2 spectra were dominated by fragments derived from interglycosidic bond cleavages. MS3 and MS4 spectra exhibited mainly peptide moiety fragment ions. In case of the bis-disaccharide-tetrapentapeptide, the peptide branching point could be determined based on MS3 and MS4 spectra. The results demonstrate the utility of nESI-QIT-MS towards the facile determination of the glycan sequence, the peptide linkage and the peptide sequence and branching of purified muropeptides (monomeric up to trimeric forms). The wealth of structural information generated by nESI-QIT-MSn is unsurpassed by any other individual technique.

Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome

One of the most salient features of Bacillus subtilis and related bacilli is their natural capacity to secrete a variety of proteins into their environment, frequently to high concentrations. This has led to the commercial exploitation of bacilli as major "cell factories" for secreted enzymes. The recent sequencing of the genome of B. subtilis has provided major new impulse for analysis of the molecular mechanisms underlying protein secretion by this organism. Most importantly, the genome sequence has allowed predictions about the composition of the secretome, which includes both the pathways for protein transport and the secreted proteins. The present survey of the secretome describes four distinct pathways for protein export from the cytoplasm and approximately 300 proteins with the potential to be exported. By far the largest number of exported proteins are predicted to follow the major "Sec" pathway for protein secretion. In contrast, the twin-arginine translocation "Tat" pathway, a type IV prepilin-like export pathway for competence development, and ATP-binding cassette transporters can be regarded as "special-purpose" pathways, through which only a few proteins are transported. The properties of distinct classes of amino-terminal signal peptides, directing proteins into the various protein transport pathways, as well as the major components of each pathway are discussed. The predictions and comparisons in this review pinpoint important differences as well as similarities between protein transport systems in B. subtilis and other well-studied organisms, such as Escherichia coli and the yeast Saccharomyces cerevisiae. Thus, they may serve as a lead for future research and applications.

Structural analysis of Bacillus subtilis spore peptidoglycan during sporulation

A major structural element of bacterial endospores is a peptidoglycan (PG) wall. This wall is produced between the two opposed membranes surrounding the developing forespore and is composed of two layers. The inner layer is the germ cell wall, which appears to have a structure similar to that of the vegetative cell wall and which serves as the initial cell wall following spore germination. The outer layer, the cortex, has a modified structure, is required for maintenance of spore dehydration, and is degraded during spore germination. Theories suggest that the spore PG may also play a mechanical role in the attainment of spore dehydration. Inherent in one of these models is the production of a gradient of cross-linking across the span of the spore PG. We report analyses of the structure of PG found within immature, developing Bacillus subtilis forespores. The germ cell wall PG is synthesized first, followed by the cortex PG. The germ cell wall is relatively highly cross-linked. The degree of PG cross-linking drops rapidly during synthesis of the first layers of cortex PG and then increases two- to eightfold across the span of the outer 70% of the cortex. Analyses of forespore PG synthesis in mutant strains reveal that some strains that lack this gradient of cross-linking are able to achieve normal spore core dehydration. We conclude that spore PG with cross-linking within a broad range is able to maintain, and possibly to participate in, spore core dehydration. Our data indicate that the degree of spore PG cross-linking may have a more direct impact on the rate of spore germination and outgrowth.