A channel connecting the mother cell and forespore during bacterial endospore formation

Clostridioides difficile Sporulation

Some members of the Firmicutes phylum, including many members of the human gut microbiota, are able to differentiate a dormant and highly resistant cell type, the endospore (hereinafter spore for simplicity). Spore-formers can colonize virtually any habitat and, because of their resistance to a wide variety of physical and chemical insults, spores can remain viable in the environment for long periods of time. In the anaerobic enteric pathogen Clostridioides difficile the aetiologic agent is the oxygen-resistant spore, while the toxins produced by actively growing cells are the main cause of the disease symptoms. Here, we review the regulatory circuits that govern entry into sporulation. We also cover the role of spores in the infectious cycle of C. difficile in relation to spore structure and function and the main control points along spore morphogenesis.

Sporulation, Structure Assembly, and Germination in the Soil Bacterium Bacillus thuringiensis: Survival and Success in the Environment and the Insect Host

Bacillus thuringiensis (Bt) is a rod-shaped, Gram-positive soil bacterium that belongs to the phylum Firmicutes and the genus Bacillus. It is a spore-forming bacterium. During sporulation, it produces a wide range of crystalline proteins that are toxic to different orders of insects. Sporulation, structure assembly, and germination are essential stages in the cell cycle of B. thuringiensis. The majority of studies on these issues have focused on the model organism Bacillus subtilis, followed by Bacillus cereus and Bacillus anthracis. The machinery for sporulation and germination extrapolated to B. thuringiensis. However, in the light of recent findings concerning the role of the sporulation proteins (SPoVS), the germination receptors (Gr), and the cortical enzymes in Bt, the theory strengthened that conservation in sporulation, structure assembly, and germination programs drive the survival and success of B. thuringiensis in the environment and the insect host. In the present minireview, the latter pinpointed and reviewed.

To Feed or to Stick? Genomic Analysis Offers Clues for the Role of a Molecular Machine in Endospore Formers

Sporulation in Firmicutes starts with the formation of two adjacent cells and proceeds with the engulfment of the smaller one, the forespore, by the larger one, the mother cell. This critical step involves a core set of conserved genes, some transcribed in the forespore, such as spoIIQ, and others transcribed in the mother cell, such as the eight-gene spoIIIA operon. A model has been proposed in which the SpoIIIA and the SpoIIQ proteins form a channel connecting the mother cell and the forespore, playing the role of a secretion apparatus allowing the mother cell to nurture the fully engulfed forespore. Exploration of the genomes of Caryophanaceae and Erysipelotrichales has provided informations that are not fully congruent with data from Bacillaceae or Clostridia. The differences observed are correlated with specific physiological features, and alternate, not mutually exclusive views of the function of the SpoIIIA-SpoIIQ complex are presented.

Structural insights into ring-building motif domains involved in bacterial sporulation

Components of specialized secretion systems, which span the inner and outer membranes in Gram-negative bacteria, include ring-forming proteins whose oligomerization was proposed to be promoted by domains called RBM for "Ring-Building Motifs". During spore formation in Gram-positive bacteria, a transport system called the SpoIIIA-SpoIIQ complex also assembles in the double membrane that surrounds the forespore following its endocytosis by the mother cell. The presence of RBM domains in some of the SpoIIIA proteins led to the hypothesis that they would assemble into rings connecting the two membranes and form a conduit between the mother cell and forespore. Among them, SpoIIIAG forms homo-oligomeric rings in vitro but the oligomerization of other RBM-containing SpoIIIA proteins, including SpoIIIAH, remains to be demonstrated. In this work, we identified RBM domains in the YhcN/YlaJ family of proteins that are not related to the SpoIIIA-SpoIIQ complex. We solved the crystal structure of YhcN from Bacillus subtilis, which confirmed the presence of a RBM fold, flanked by additional secondary structures. As the protein did not show any oligomerization ability in vitro, we investigated the structural determinants of ring formation in SpoIIIAG, SpoIIIAH and YhcN. We showed that in vitro, the conserved core of RBM domains alone is not sufficient for oligomerization while the β-barrel forming region in SpoIIIAG forms rings on its own. This work suggests that some RBMs might indeed participate in the assembly of homomeric rings but others might have evolved toward other functions.

High Resolution Analysis of Proteome Dynamics during Bacillus subtilis Sporulation

Bacillus subtilis vegetative cells switch to sporulation upon nutrient limitation. To investigate the proteome dynamics during sporulation, high-resolution time-lapse proteomics was performed in a cell population that was induced to sporulate synchronously. Here, we are the first to comprehensively investigate the changeover of sporulation regulatory proteins, coat proteins, and other proteins involved in sporulation and spore biogenesis. Protein co-expression analysis revealed four co-expressed modules (termed blue, brown, green, and yellow). Modules brown and green are upregulated during sporulation and contain proteins associated with sporulation. Module blue is negatively correlated with modules brown and green, containing ribosomal and metabolic proteins. Finally, module yellow shows co-expression with the three other modules. Notably, several proteins not belonging to any of the known transcription regulons were identified as co-expressed with modules brown and green, and might also play roles during sporulation. Finally, levels of some coat proteins, for example morphogenetic coat proteins, decreased late in sporulation.

Levels and Characteristics of mRNAs in Spores of Firmicute Species

Spores of firmicute species contain 100s of mRNAs, whose major function in Bacillus subtilis is to provide ribonucleotides for new RNA synthesis when spores germinate. To determine if this is a general phenomenon, RNA was isolated from spores of multiple firmicute species and relative mRNA levels determined by transcriptome sequencing (RNA-seq). Determination of RNA levels in single spores allowed calculation of RNA nucleotides/spore, and assuming mRNA is 3% of spore RNA indicated that only ∼6% of spore mRNAs were present at >1/spore. Bacillus subtilis, Bacillus atrophaeus, and Clostridioides difficile spores had 49, 42, and 51 mRNAs at >1/spore, and numbers of mRNAs at ≥1/spore were ∼10 to 50% higher in Geobacillus stearothermophilus and Bacillus thuringiensis Al Hakam spores and ∼4-fold higher in Bacillus megaterium spores. In all species, some to many abundant spore mRNAs (i) were transcribed by RNA polymerase with forespore-specific σ factors, (ii) encoded proteins that were homologs of those encoded by abundant B. subtilis spore mRNAs and are proteins in dormant spores, and (iii) were likely transcribed in the mother cell compartment of the sporulating cell. Analysis of the coverage of RNA-seq reads on mRNAs from all species suggested that abundant spore mRNAs were fragmented, as was confirmed by reverse transcriptase quantitative PCR (RT-qPCR) analysis of abundant B. subtilis and C. difficile spore mRNAs. These data add to evidence indicating that the function of at least the great majority of mRNAs in all firmicute spores is to be degraded to generate ribonucleotides for new RNA synthesis when spores germinate. IMPORTANCE Only ∼6% of mRNAs in spores of six firmicute species are at ≥1 molecule/spore, many abundant spore mRNAs encode proteins similar to B. subtilis spore proteins, and some abundant B. subtilis and C. difficile spore mRNAs were fragmented. Most of the abundant B. subtilis and other Bacillales spore mRNAs are transcribed under the control of the forespore-specific RNA polymerase σ factors, F or G, and these results may stimulate transcription analyses in developing spores of species other than B. subtilis. These findings, plus the absence of key nucleotide biosynthetic enzymes in spores, suggest that firmicute spores' abundant mRNAs are not translated when spores germinate but instead are degraded to generate ribonucleotides for new RNA synthesis by the germinated spore.

Asymmetric localization of the cell division machinery during Bacillus subtilis sporulation

The Gram-positive bacterium Bacillus subtilis can divide via two modes. During vegetative growth, the division septum is formed at the midcell to produce two equal daughter cells. However, during sporulation, the division septum is formed closer to one pole to yield a smaller forespore and a larger mother cell. Using cryo-electron tomography, genetics and fluorescence microscopy, we found that the organization of the division machinery is different in the two septa. While FtsAZ filaments, the major orchestrators of bacterial cell division, are present uniformly around the leading edge of the invaginating vegetative septa, they are only present on the mother cell side of the invaginating sporulation septa. We provide evidence suggesting that the different distribution and number of FtsAZ filaments impact septal thickness, causing vegetative septa to be thicker than sporulation septa already during constriction. Finally, we show that a sporulation-specific protein, SpoIIE, regulates asymmetric divisome localization and septal thickness during sporulation.

Distribution and preservation of the components of the engulfment. What is beyond representative genomes?

Engulfment requires the coordinated, targeted synthesis and degradation of peptidoglycan at the leading edge of the engulfing membrane to allow the mother cell to completely engulf the forespore. Proteins such as the DMP and Q:AH complexes in Bacillus subtilis are essential for engulfment, as are a set of accessory proteins including GerM and SpoIIB, among others. Experimental and bioinformatic studies of these proteins in bacteria distinct from Bacillus subtilis indicate that fundamental differences exist regarding the organization and mechanisms used to successfully perform engulfment. As a consequence, the distribution and prevalence of the proteins involved in engulfment and other proteins that participate in different sporulation stages have been studied using bioinformatic approaches. These works are based on the prediction of orthologs in the genomes of representative Firmicutes and have been helpful in tracing hypotheses about the origin and evolution of sporulation genes, some of which have been postulated as sporulation signatures. To date, an extensive study of these signatures outside of the representative Firmicutes is not available. Here, we asked whether phyletic profiles of proteins involved in engulfment can be used as signatures able to describe the sporulation phenotype. We tested this hypothesis in a set of 954 Firmicutes, finding preserved phyletic profiles defining signatures at the genus level. Finally, a phylogenetic reconstruction based on non-redundant phyletic profiles at the family level shows the non-monophyletic origin of these proteins due to gain/loss events along the phylum Firmicutes.

Metabolic differentiation and intercellular nurturing underpin bacterial endospore formation

Despite intensive research, the role of metabolism in bacterial sporulation remains poorly understood. Here, we demonstrate that Bacillus subtilis sporulation entails a marked metabolic differentiation of the two cells comprising the sporangium: the forespore, which becomes the dormant spore, and the mother cell, which dies as sporulation completes. Our data provide evidence that metabolic precursor biosynthesis becomes restricted to the mother cell and that the forespore becomes reliant on mother cell-derived metabolites for protein synthesis. We further show that arginine is trafficked between the two cells and that proposed proteinaceous channels mediate small-molecule intercellular transport. Thus, sporulation entails the profound metabolic reprogramming of the forespore, which is depleted of key metabolic enzymes and must import metabolites from the mother cell. Together, our results provide a bacterial example analogous to progeny nurturing.

Milestones in Bacillus subtilis sporulation research

Endospore formation has been a rich field of research for more than a century, and has benefited from the powerful genetic tools available in Bacillus subtilis. In this review, we highlight foundational discoveries that shaped the sporulation field, from its origins to the present day, tracing a chronology that spans more than one hundred eighty years. We detail how cell-specific gene expression has been harnessed to investigate the existence and function of intercellular proteinaceous channels in sporulating cells, and we illustrate the rapid progress in our understanding of the cell biology of sporulation in recent years using the process of chromosome translocation as a storyline. Finally, we sketch general aspects of sporulation that remain largely unexplored, and that we envision will be fruitful areas of future research.

Bacterial Spore mRNA - What's Up With That?

Bacteria belonging to the orders Bacillales and Clostridiales form spores in response to nutrient starvation. From a simplified morphological perspective, the spore can be considered as comprising a central protoplast or core, that is, enveloped sequentially by an inner membrane (IM), a peptidoglycan cortex, an outer membrane, and a proteinaceous coat. All of these structures are characterized by unique morphological and/or structural features, which collectively confer metabolic dormancy and properties of environmental resistance to the quiescent spore. These properties are maintained until the spore is stimulated to germinate, outgrow and form a new vegetative cell. Spore germination comprises a series of partially overlapping biochemical and biophysical events - efflux of ions from the core, rehydration and IM reorganization, disassembly of cortex and coat - all of which appear to take place in the absence of de novo ATP and protein synthesis. If the latter points are correct, why then do spores of all species examined to date contain a diverse range of mRNA molecules deposited within the spore core? Are some of these molecules "functional," serving as translationally active units that are required for efficient spore germination and outgrowth, or are they just remnants from sporulation whose sole purpose is to provide a reservoir of ribonucleotides for the newly outgrowing cell? What is the fate of these molecules during spore senescence, and indeed, are conditions within the spore core likely to provide any opportunity for changes in the transcriptional profile of the spore during dormancy? This review encompasses a historical perspective of spore ribonucleotide biology, from the earliest biochemical led analyses - some of which in hindsight have proved to be remarkably prescient - through the transcriptomic era at the turn of this century, to the latest next generation sequencing derived insights. We provide an overview of the key literature to facilitate reasoned responses to the aforementioned questions, and many others, prior to concluding by identifying the major outstanding issues in this crucial area of spore biology.

Shaping an Endospore: Architectural Transformations During Bacillus subtilis Sporulation

Endospore formation in Bacillus subtilis provides an ideal model system for studying development in bacteria. Sporulation studies have contributed a wealth of information about the mechanisms of cell-specific gene expression, chromosome dynamics, protein localization, and membrane remodeling, while helping to dispel the early view that bacteria lack internal organization and interesting cell biological phenomena. In this review, we focus on the architectural transformations that lead to a profound reorganization of the cellular landscape during sporulation, from two cells that lie side by side to the endospore, the unique cell within a cell structure that is a hallmark of sporulation in B. subtilis and other spore-forming Firmicutes. We discuss new insights into the mechanisms that drive morphogenesis, with special emphasis on polar septation, chromosome translocation, and the phagocytosis-like process of engulfment, and also the key experimental advances that have proven valuable in revealing the inner workings of bacterial cells.

Channels modestly impact compartment-specific ATP levels during Bacillus subtilis sporulation and a rise in the mother cell ATP level is not necessary for Pro-σK cleavage

Starvation of Bacillus subtilis initiates endosporulation involving formation of mother cell (MC) and forespore (FS) compartments. During engulfment, the MC membrane migrates around the FS and protein channels connect the two compartments. The channels are necessary for postengulfment FS gene expression, which relieves inhibition of SpoIVFB, an intramembrane protease that cleaves Pro-σ^K , releasing σ^K into the MC. SpoIVFB has an ATP-binding domain exposed to the MC cytoplasm, but the role of ATP in regulating Pro-σ^K cleavage has been unclear, as has the impact of the channels on MC and FS ATP levels. Using luciferase produced separately in each compartment to measure relative ATP concentrations during sporulation, we found that the MC ATP concentration rises about twofold coincident with increasing cleavage of Pro-σ^K , and the FS ATP concentration does not decline. Mutants lacking a channel protein or defective in channel protein turnover exhibited modest and varied effects on ATP levels, which suggested that low ATP concentration does not explain the lack of postengulfment FS gene expression in channel mutants. Furthermore, a rise in the MC ATP level was not necessary for Pro-σ^K cleavage by SpoIVFB, based on analysis of mutants that bypass the need for relief of SpoIVFB inhibition.

Single-molecule optical microscopy of protein dynamics and computational analysis of images to determine cell structure development in differentiating Bacillus subtilis

Here we use singe-molecule optical proteomics and computational analysis of live cell bacterial images, using millisecond super-resolved tracking and quantification of fluorescently labelled protein SpoIIE in single live Bacillus subtilis bacteria to understand its crucial role in cell development. Asymmetric cell division during sporulation in Bacillus subtilis presents a model system for studying cell development. SpoIIE is a key integral membrane protein phosphatase that couples morphological development to differential gene expression. However, the basic mechanisms behind its operation remain unclear due to limitations of traditional tools and technologies. We instead used advanced single-molecule imaging of fluorescently tagged SpoIIE in real time on living cells to reveal vital changes to the patterns of expression, localization, mobility and stoichiometry as cells undergo asymmetric cell division then engulfment of the smaller forespore by the larger mother cell. We find, unexpectedly, that SpoIIE forms tetramers capable of cell- and stage-dependent clustering, its copy number rising to ~ 700 molecules as sporulation progresses. We observed that slow moving SpoIIE clusters initially located at septa are released as mobile clusters at the forespore pole as phosphatase activity is manifested and compartment-specific RNA polymerase sigma factor, σF, becomes active. Our findings reveal that information captured in its quaternary organization enables one protein to perform multiple functions, extending an important paradigm for regulatory proteins in cells. Our findings more generally demonstrate the utility of rapid live cell single-molecule optical proteomics for enabling mechanistic insight into the complex processes of cell development during the cell cycle.

Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia

Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required to evolve a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.

From Root to Tips: Sporulation Evolution and Specialization in Bacillus subtilis and the Intestinal Pathogen Clostridioides difficile

Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of highly resistant, dormant endospores. Endospores allow environmental persistence, dissemination and for pathogens, are also infection vehicles. In both the model Bacillus subtilis, an aerobic organism, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. Their expression is coordinated between the forespore and the mother cell, the two cells that participate in the process, and is kept in close register with the course of morphogenesis. The evolutionary mechanisms by which sporulation emerged and evolved in these two species, and more broadly across Firmicutes, remain largely unknown. Here, we trace the origin and evolution of sporulation using the genes known to be involved in the process in B. subtilis and C. difficile, and estimating their gain-loss dynamics in a comprehensive bacterial macroevolutionary framework. We show that sporulation evolution was driven by two major gene gain events, the first at the base of the Firmicutes and the second at the base of the B. subtilis group and within the Peptostreptococcaceae family, which includes C. difficile. We also show that early and late sporulation regulons have been coevolving and that sporulation genes entail greater innovation in B. subtilis with many Bacilli lineage-restricted genes. In contrast, C. difficile more often recruits new sporulation genes by horizontal gene transfer, which reflects both its highly mobile genome, the complexity of the gut microbiota, and an adjustment of sporulation to the gut ecosystem.

Sporulation and Germination in Clostridial Pathogens

As obligate anaerobes, clostridial pathogens depend on their metabolically dormant, oxygen-tolerant spore form to transmit disease. However, the molecular mechanisms by which those spores germinate to initiate infection and then form new spores to transmit infection remain poorly understood. While sporulation and germination have been well characterized in Bacillus subtilis and Bacillus anthracis, striking differences in the regulation of these processes have been observed between the bacilli and the clostridia, with even some conserved proteins exhibiting differences in their requirements and functions. Here, we review our current understanding of how clostridial pathogens, specifically Clostridium perfringens, Clostridium botulinum, and Clostridioides difficile, induce sporulation in response to environmental cues, assemble resistant spores, and germinate metabolically dormant spores in response to environmental cues. We also discuss the direct relationship between toxin production and spore formation in these pathogens.

The engulfasome in C. difficile: Variations on protein machineries

Clostridioides difficile infection (CDI) continues to be a substantial healthcare burden, and the changing disease profile raises new challenges in CDI management, both in clinical settings and in the community. CDI is transmitted by spores, which are formed by a subset of the cell population where an asymmetric septum is formed. A full copy of the chromosome is transported into the smaller compartment which is then engulfed by the mother cell. After engulfment, multiple metabolic and morphological changes occur, eventually resulting in the release of the mature spore. Whilst studies in the model organism Bacillus subtilis have demonstrated the importance of the DMP and Q:AH machineries in engulfment, it is becoming clear that there are fundamental differences in the way the two organisms organise these machineries. As spores are the infectious agent in CDI, it is crucial to understand how these dormant cells are formed, and how sporulation can be prevented or disrupted with the view of reducing CDI. Here, we review the current literature on the DMP and Q:AH machineries in C. difficile, and how they compare and contrast to those of B. subtilis.

•

Overview of the DMP and Q:AH engulfment machineries in C. difficile.

•

Analyses of the conservation of DMP across Bacilli, Clostridia and other bacteria.

•

Proposes a multi-protein complex required for engulfment: the engulfasome.

•

Highlights differential arrangements of engulfasome in B. subtilis and C. difficile.

Peptidoglycan degradation machinery in Clostridium difficile forespore engulfment

Clostridium difficile remains the leading cause of antibiotic‐associated diarrhoea in hospitals worldwide, linked to significant morbidity and mortality. As a strict anaerobe, it produces dormant cell forms – spores – which allow it to survive in the aerobic environment. Importantly, spores are the transmission agent of C. difficile infections. A key aspect of sporulation is the engulfment of the future spore by the mother cell and several proteins have been proposed to be involved. Here, we investigated the role of the SpoIID, SpoIIM and SpoIIP (DMP) machinery and its interplay with the SpoIIQ:SpoIIIAH (Q:AH) complex in C. difficile. We show that, surprisingly, SpoIIM, the proposed machinery anchor, is not required for efficient engulfment and sporulation. We demonstrate the requirement of DP for engulfment due to their sequential peptidoglycan degradation activity, both in vitro and in vivo. Finally, new interactions within DMP and between DMP and Q:AH suggest that both systems form a single engulfment machinery to keep the mother cell and forespore membranes together throughout engulfment. This work sheds new light upon the engulfment process and on how different sporeformers might use the same components in different ways to drive spore formation.

Differential requirements for conserved peptidoglycan remodeling enzymes during Clostridioides difficile spore formation

Spore formation is essential for the bacterial pathogen and obligate anaerobe, Clostridioides (Clostridium) difficile, to transmit disease. Completion of this process depends on the mother cell engulfing the developing forespore, but little is known about how engulfment occurs in C. difficile. In Bacillus subtilis, engulfment is mediated by a peptidoglycan degradation complex consisting of SpoIID, SpoIIP and SpoIIM, which are all individually required for spore formation. Using genetic analyses, we determined the functions of these engulfment-related proteins along with the putative endopeptidase, SpoIIQ, during C. difficile sporulation. While SpoIID, SpoIIP and SpoIIQ were critical for engulfment, loss of SpoIIM minimally impacted C. difficile spore formation. Interestingly, a small percentage of ∆spoIID and ∆spoIIQ cells generated heat-resistant spores through the actions of SpoIIQ and SpoIID, respectively. Loss of SpoIID and SpoIIQ also led to unique morphological phenotypes: asymmetric engulfment and forespore distortions, respectively. Catalytic mutant complementation analyses revealed that these phenotypes depend on the enzymatic activities of SpoIIP and SpoIID, respectively. Lastly, engulfment mutants mislocalized polymerized coat even though the basement layer coat proteins, SpoIVA and SipL, remained associated with the forespore. Collectively, these findings advance our understanding of several stages during infectious C. difficile spore assembly.

Analysis of the mRNAs in Spores of Bacillus subtilis

Large-scale shotgun sequencing (RNA-seq) analysis of mRNAs in dormant Bacillus subtilis spores prepared on plates or in liquid generally found the same ∼46 abundant mRNA species, with >250 mRNAs detected at much lower abundances. Knowledge of the amount of phosphate in a single B. subtilis spore allowed calculation of the amount of mRNA in an individual spore as ∼10⁶ nucleotides (nt). Given the levels of abundant spore mRNAs compared to those of other mRNAs, it was calculated that the great majority of low-abundance mRNAs are present in only small fractions of spores in populations. Almost all of the most abundant spore mRNAs are encoded by genes expressed late in sporulation in the developing spore under the control of the forespore-specific RNA polymerase sigma factor, σ^G, and most of the encoded proteins are in spores. Levels of the most abundant spore mRNAs were also relatively stable for a week at 4°C after spore harvest. RNA-seq analysis of mRNAs in highly purified and less-well-purified spores made in liquid, as well as from spores that were chemically decoated to remove possible contaminating mRNA, indicated that low-abundance mRNAs in spores were not contaminants in purified spore preparations, and several sources of low-abundance mRNAs in spores are suggested. The function of at least the great majority of spore mRNAs seems most likely to be the generation of ribonucleotides for new RNA synthesis by their degradation early in spore revival.IMPORTANCE Previous work indicates that dormant Bacillus subtilis spores have many hundreds of mRNAs, some of which are suggested to play roles in spores' "return to life" or revival. The present work finds only ∼46 mRNAs at ≥1 molecule spore, with others in only fractions of spores in populations, often very small fractions. Less-abundant spore mRNAs are not contaminants in spore preparations, but how spores accumulate them is not clear. Almost all abundant spore mRNAs are synthesized in the developing spore late in its development, most encode proteins in spores, and abundant mRNAs in spores are relatively stable at 4°C. These findings will have a major impact on thinking about the roles that spore mRNAs may play in spore revival.

Structural characterization of the sporulation protein GerM from Bacillus subtilis

The Gram-positive bacterium Bacillus subtilis responds to starvation by entering a morphological differentiation process leading to the formation of a highly resistant spore. Early in the sporulation process, the cell asymmetrically divides into a large compartment (the mother cell) and a smaller one (the forespore), which will maturate into a resistant spore. Proper development of the forespore requires the assembly of a multiprotein complex called the SpoIIIA-SpoIIQ complex or "A-Q complex". This complex involves the forespore protein SpoIIQ and eight mother cell proteins (SpoIIIAA to SpoIIIAH), many of which share structural similarities with components of specialized secretion systems and flagella found in Gram-negative bacteria. The assembly of the A-Q complex across the two membranes that separate the mother cell and forespore was recently shown to require GerM. GerM is a lipoprotein composed of two GerMN domains, a family of domains with unknown function. Here, we report X-ray crystallographic structures of the first GerMN domain of GerM at 1.0 Å resolution, and of the soluble domain of GerM (the tandem of GerMN domains) at 2.1 Å resolution. These structures reveal that GerMN domains can adopt distinct conformations and that the core of these domains display structural similarities with ring-building motifs found in components of specialized secretion system and in SpoIIIA proteins. This work provides an additional piece towards the structural characterization of the A-Q complex.

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

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

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

Levels of L-malate and other low molecular weight metabolites in spores of Bacillus species and Clostridium difficile

Dormant spores of Bacillus species lack ATP and NADH and contain notable levels of only a few other common low mol wt energy reserves, including 3-phosphoglyceric acid (3PGA), and glutamic acid. Recently, Bacillus subtilis spores were reported to contain ~ 30 μmol of L-malate/g dry wt, which also could serve as an energy reserve. In present work, L-malate levels were determined in the core of dormant spores of B. subtilis, Bacillus cereus, Bacillus megaterium and Clostridium difficile, using both an enzymatic assay and ¹³C-NMR on extracts prepared by several different methods. These assays found that levels of L-malate in B. cereus and B. megaterium spores were ≤ 0.5 μmol/g dry wt, and ≤ 1 μmol/g dry wt in B. subtilis spores, and levels of L-lactate and pyruvate in B. megaterium and B. subtilis spores were < 0.5 μmol/g dry wt. Levels of L-malate in C. difficile spores were ≤ 1 μmol/g dry wt, while levels of 3PGA were ~ 7 μmol/g; the latter value was determined by ³¹P-NMR, and is in between the 3PGA levels in B. megaterium and B. subtilis spores determined previously. ¹³C-NMR analysis of spore extracts further showed that B. megaterium, B. subtilis and C. difficile contained significant levels of carbonate/bicarbonate in the spore core. Low mol wt carbon-containing small molecules present at > 3 μmol/g dry spores are: i) dipicolinic acid, carbonate/bicarbonate and 3PGA in B. megaterium, B. subtilis and C. difficile; ii) glutamate in B. megaterium and B. subtilis; iii) arginine in B. subtilis; and iv) at least one unidentified compound in all three species.

Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis

Bacterial sporulation allows starving cells to differentiate into metabolically dormant spores that can survive extreme conditions. Following asymmetric division, the mother cell engulfs the forespore, surrounding it with two bilayer membranes. During the engulfment process, an essential channel, the so-called feeding tube apparatus, is thought to cross both membranes to create a direct conduit between the mother cell and the forespore. At least nine proteins are required to create this channel, including SpoIIQ and SpoIIIAA-AH. Here, we present the near-atomic resolution structure of one of these proteins, SpoIIIAG, determined by single-particle cryo-EM. A 3D reconstruction revealed that SpoIIIAG assembles into a large and stable 30-fold symmetric complex with a unique mushroom-like architecture. The complex is collectively composed of three distinctive circular structures: a 60-stranded vertical β-barrel that forms a large inner channel encircled by two concentric rings, one β-mediated and the other formed by repeats of a ring-building motif (RBM) common to the architecture of various dual membrane secretion systems of distinct function. Our near-atomic resolution structure clearly shows that SpoIIIAG exhibits a unique and dramatic adaptation of the RBM fold with a unique β-triangle insertion that assembles into the prominent channel, the dimensions of which suggest the potential passage of large macromolecules between the mother cell and forespore during the feeding process. Indeed, mutation of residues located at key interfaces between monomers of this RBM resulted in severe defects both in vivo and in vitro, providing additional support for this unprecedented structure.

A ring-shaped conduit connects the mother cell and forespore during sporulation in Bacillus subtilis

During spore formation in Bacillus subtilis a transenvelope complex is assembled across the double membrane that separates the mother cell and forespore. This complex (called the "A-Q complex") is required to maintain forespore development and is composed of proteins with remote homology to components of type II, III, and IV secretion systems found in Gram-negative bacteria. Here, we show that one of these proteins, SpoIIIAG, which has remote homology to ring-forming proteins found in type III secretion systems, assembles into an oligomeric ring in the periplasmic-like space between the two membranes. Three-dimensional reconstruction of images generated by cryo-electron microscopy indicates that the SpoIIIAG ring has a cup-and-saucer architecture with a 6-nm central pore. Structural modeling of SpoIIIAG generated a 24-member ring with dimensions similar to those of the EM-derived saucer. Point mutations in the predicted oligomeric interface disrupted ring formation in vitro and impaired forespore gene expression and efficient spore formation in vivo. Taken together, our data provide strong support for the model in which the A-Q transenvelope complex contains a conduit that connects the mother cell and forespore. We propose that a set of stacked rings spans the intermembrane space, as has been found for type III secretion systems.

GerM is required to assemble the basal platform of the SpoIIIA-SpoIIQ transenvelope complex during sporulation in Bacillus subtilis

Sporulating Bacillus subtilis cells assemble a multimeric membrane complex connecting the mother cell and developing spore that is required to maintain forespore differentiation. An early step in the assembly of this transenvelope complex (called the A-Q complex) is an interaction between the extracellular domains of the forespore membrane protein SpoIIQ and the mother cell membrane protein SpoIIIAH. This interaction provides a platform onto which the remaining components of the complex assemble and also functions as an anchor for cell-cell signalling and morphogenetic proteins involved in spore development. SpoIIQ is required to recruit SpoIIIAH to the sporulation septum on the mother cell side; however, the mechanism by which SpoIIQ specifically localizes to the septal membranes on the forespore side has remained enigmatic. Here, we identify GerM, a lipoprotein previously implicated in spore germination, as the missing factor required for SpoIIQ localization. Our data indicate that GerM and SpoIIIAH, derived from the mother cell, and SpoIIQ, from the forespore, have reciprocal localization dependencies suggesting they constitute a tripartite platform for the assembly of the A-Q complex and a hub for the localization of mother cell and forespore proteins.

A Membrane-Embedded Amino Acid Couples the SpoIIQ Channel Protein to Anti-Sigma Factor Transcriptional Repression during Bacillus subtilis Sporulation

SpoIIQ is an essential component of a channel connecting the developing forespore to the adjacent mother cell during Bacillus subtilis sporulation. This channel is generally required for late gene expression in the forespore, including that directed by the late-acting sigma factor σ(G) Here, we present evidence that SpoIIQ also participates in a previously unknown gene regulatory circuit that specifically represses expression of the gene encoding the anti-sigma factor CsfB, a potent inhibitor of σ(G) The csfB gene is ordinarily transcribed in the forespore only by the early-acting sigma factor σ(F) However, in a mutant lacking the highly conserved SpoIIQ transmembrane amino acid Tyr-28, csfB was also aberrantly transcribed later by σ(G), the very target of CsfB inhibition. This regulation of csfB by SpoIIQ Tyr-28 is specific, given that the expression of other σ(F)-dependent genes was unaffected. Moreover, we identified a conserved element within the csfB promoter region that is both necessary and sufficient for SpoIIQ Tyr-28-mediated inhibition. These results indicate that SpoIIQ is a bifunctional protein that not only generally promotes σ(G)activity in the forespore as a channel component but also specifically maximizes σ(G)activity as part of a gene regulatory circuit that represses σ(G)-dependent expression of its own inhibitor, CsfB. Finally, we demonstrate that SpoIIQ Tyr-28 is required for the proper localization and stability of the SpoIIE phosphatase, raising the possibility that these two multifunctional proteins cooperate to fine-tune developmental gene expression in the forespore at late times.

IMPORTANCE

Cellular development is orchestrated by gene regulatory networks that activate or repress developmental genes at the right time and place. Late gene expression in the developing Bacillus subtilis spore is directed by the alternative sigma factor σ(G) The activity of σ(G)requires a channel apparatus through which the adjacent mother cell provides substrates that generally support gene expression. Here we report that the channel protein SpoIIQ also specifically maximizes σ(G)activity as part of a previously unknown regulatory circuit that prevents σ(G)from activating transcription of the gene encoding its own inhibitor, the anti-sigma factor CsfB. The discovery of this regulatory circuit significantly expands our understanding of the gene regulatory network controlling late gene expression in the developing B. subtilis spore.

Complex Formed between Intramembrane Metalloprotease SpoIVFB and Its Substrate, Pro-σK

Intramembrane metalloproteases (IMMPs) are conserved from bacteria to humans and control many important signaling pathways, but little is known about how IMMPs interact with their substrates. SpoIVFB is an IMMP that cleaves Pro-σ(K) during Bacillus subtilis endospore formation. When catalytically inactive SpoIVFB was coexpressed with C-terminally truncated Pro-σ(K)(1-126) (which can be cleaved by active SpoIVFB) in Escherichia coli, the substrate dramatically improved solubilization of the enzyme from membranes with mild detergents. Both the Pro(1-20) and σ(K)(21-126) parts contributed to improving SpoIVFB solubilization from membranes, but only the σ(K) part was needed to form a stable complex with SpoIVFB in a pulldown assay. The last 10 residues of SpoIVFB were required for improved solubilization from membranes by Pro-σ(K)(1-126) and for normal interaction with the substrate. The inactive SpoIVFB·Pro-σ(K)(1-126)-His6 complex was stable during affinity purification and gel filtration chromatography. Disulfide cross-linking of the purified complex indicated that it resembled the complex formed in vivo Ion mobility-mass spectrometry analysis resulted in an observed mass consistent with a 4:2 SpoIVFB·Pro-σ(K)(1-126)-His6 complex. Stepwise photobleaching of SpoIVFB fused to a fluorescent protein supported the notion that the enzyme is tetrameric during B. subtilis sporulation. The results provide the first evidence that an IMMP acts as a tetramer, give new insights into how SpoIVFB interacts with its substrate, and lay the foundation for further biochemical analysis of the enzyme·substrate complex and future structural studies.

Structural modeling of the flagellum MS ring protein FliF reveals similarities to the type III secretion system and sporulation complex

The flagellum is a large proteinaceous organelle found at the surface of many bacteria, whose primary role is to allow motility through the rotation of a long extracellular filament. It is an essential virulence factor in many pathogenic species, and is also a priming component in the formation of antibiotic-resistant biofilms. The flagellum consists of the export apparatus on the cytosolic side; the basal body and rotor, spanning the bacterial membrane(s) and periplasm; and the hook-filament, that protrudes away from the bacterial surface. Formation of the basal body MS ring region, constituted of multiple copies of the protein FliF, is one of the initial steps of flagellum assembly. However, the precise architecture of FliF is poorly understood. Here, I report a bioinformatics analysis of the FliF sequence from various bacterial species, suggesting that its periplasmic region is composed of three globular domains. The first two are homologous to that of the type III secretion system injectisome proteins SctJ, and the third possesses a similar fold to that of the sporulation complex component SpoIIIAG. I also describe that Chlamydia possesses an unusual FliF protein, lacking part of the SctJ homology domain and the SpoIIIAG-like domain, and fused to the rotor component FliG at its C-terminus. Finally, I have combined the sequence analysis of FliF with the EM map of the MS ring, to propose the first atomic model for the FliF oligomer, suggesting that FliF is structurally akin to a fusion of the two injectisome components SctJ and SctD. These results further define the relationship between the flagellum, injectisome and sporulation complex, and will facilitate future structural characterization of the flagellum basal body.

The SpoIIQ-SpoIIIAH complex of Clostridium difficile controls forespore engulfment and late stages of gene expression and spore morphogenesis

Engulfment of the forespore by the mother cell is a universal feature of endosporulation. In Bacillus subtilis, the forespore protein SpoIIQ and the mother cell protein SpoIIIAH form a channel, essential for endosporulation, through which the developing spore is nurtured. The two proteins also form a backup system for engulfment. Unlike in B. subtilis, SpoIIQ of Clostridium difficile has intact LytM zinc‐binding motifs. We show that spoIIQ or spoIIIAH deletion mutants of C. difficile result in anomalous engulfment, and that disruption of the SpoIIQ LytM domain via a single amino acid substitution (H120S) impairs engulfment differently. SpoIIQ and SpoIIQ^H120S interact with SpoIIIAH throughout engulfment. SpoIIQ, but not SpoIIQ^H120S, binds Zn²⁺, and metal absence alters the SpoIIQ‐SpoIIIAH complex in vitro. Possibly, SpoIIQ^H120S supports normal engulfment in some cells but not a second function of the complex, required following engulfment completion. We show that cells of the spoIIQ or spoIIIAH mutants that complete engulfment are impaired in post‐engulfment, forespore and mother cell‐specific gene expression, suggesting a channel‐like function. Both engulfment and a channel‐like function may be ancestral functions of SpoIIQ‐SpoIIIAH while the requirement for engulfment was alleviated through the emergence of redundant mechanisms in B. subtilis and related organisms.

High-Throughput Genetic Screens Identify a Large and Diverse Collection of New Sporulation Genes in Bacillus subtilis

The differentiation of the bacterium Bacillus subtilis into a dormant spore is among the most well-characterized developmental pathways in biology. Classical genetic screens performed over the past half century identified scores of factors involved in every step of this morphological process. More recently, transcriptional profiling uncovered additional sporulation-induced genes required for successful spore development. Here, we used transposon-sequencing (Tn-seq) to assess whether there were any sporulation genes left to be discovered. Our screen identified 133 out of the 148 genes with known sporulation defects. Surprisingly, we discovered 24 additional genes that had not been previously implicated in spore formation. To investigate their functions, we used fluorescence microscopy to survey early, middle, and late stages of differentiation of null mutants from the B. subtilis ordered knockout collection. This analysis identified mutants that are delayed in the initiation of sporulation, defective in membrane remodeling, and impaired in spore maturation. Several mutants had novel sporulation phenotypes. We performed in-depth characterization of two new factors that participate in cell–cell signaling pathways during sporulation. One (SpoIIT) functions in the activation of σ^E in the mother cell; the other (SpoIIIL) is required for σ^G activity in the forespore. Our analysis also revealed that as many as 36 sporulation-induced genes with no previously reported mutant phenotypes are required for timely spore maturation. Finally, we discovered a large set of transposon insertions that trigger premature initiation of sporulation. Our results highlight the power of Tn-seq for the discovery of new genes and novel pathways in sporulation and, combined with the recently completed null mutant collection, open the door for similar screens in other, less well-characterized processes.

Transposon sequencing enables the recovery of virtually all previously characterized genes required for the differentiation of the bacterium Bacillus subtilis into a dormant spore and identifies 24 new ones.

When starved of nutrients, the bacterium Bacillus subtilis differentiates into a dormant spore that is impervious to environmental insults. Decades of research have uncovered over 100 genes required for spore formation. Molecular dissection of these genes has revealed factors that act at every stage of this developmental process. In this study, we used a high-throughput genetic screening method called transposon sequencing to assess whether there were any sporulation genes left to be discovered. This approach identified virtually all of the known sporulation genes, as well as 24 new ones. Furthermore, transposon sequencing enabled the discovery of two new sets of mutants in which the sporulation process was either delayed or accelerated. Using fluorescence microscopy, we determined the developmental stage at which each mutant was impaired and discovered mutants that are delayed in initiation of sporulation, or defective in morphogenesis, cell–cell signaling, or spore maturation. Our findings exemplify the utility of transposon sequencing to uncover new biology in well-studied processes, suggesting that it could similarly be used to identify novel genes required for other aspects of bacterial physiology, such as natural competence, stationary phase survival, or the responses to cell envelope stress and DNA damage.

Protein Targeting during Bacillus subtilis Sporulation

The Gram-positive bacterium Bacillus subtilis initiates the formation of an endospore in response to conditions of nutrient limitation. The morphological differentiation that spores undergo initiates with the formation of an asymmetric septum near to one pole of the cell, forming a smaller compartment, the forespore, and a larger compartment, the mother cell. This process continues with the complex morphogenesis of the spore as governed by an intricate series of interactions between forespore and mother cell proteins across the inner and outer forespore membranes. Given that these interactions occur at a particular place in the cell, a critical question is how the proteins involved in these processes get properly targeted, and we discuss recent progress in identifying mechanisms responsible for this targeting.

Regulation of Clostridium difficile Spore Formation by the SpoIIQ and SpoIIIA Proteins

Sporulation is an ancient developmental process that involves the formation of a highly resistant endospore within a larger mother cell. In the model organism Bacillus subtilis, sporulation-specific sigma factors activate compartment-specific transcriptional programs that drive spore morphogenesis. σ^G activity in the forespore depends on the formation of a secretion complex, known as the “feeding tube,” that bridges the mother cell and forespore and maintains forespore integrity. Even though these channel components are conserved in all spore formers, recent studies in the major nosocomial pathogen Clostridium difficile suggested that these components are dispensable for σ^G activity. In this study, we investigated the requirements of the SpoIIQ and SpoIIIA proteins during C. difficile sporulation. C. difficile spoIIQ, spoIIIA, and spoIIIAH mutants exhibited defects in engulfment, tethering of coat to the forespore, and heat-resistant spore formation, even though they activate σ^G at wildtype levels. Although the spoIIQ, spoIIIA, and spoIIIAH mutants were defective in engulfment, metabolic labeling studies revealed that they nevertheless actively transformed the peptidoglycan at the leading edge of engulfment. In vitro pull-down assays further demonstrated that C. difficile SpoIIQ directly interacts with SpoIIIAH. Interestingly, mutation of the conserved Walker A ATP binding motif, but not the Walker B ATP hydrolysis motif, disrupted SpoIIIAA function during C. difficile spore formation. This finding contrasts with B. subtilis, which requires both Walker A and B motifs for SpoIIIAA function. Taken together, our findings suggest that inhibiting SpoIIQ, SpoIIIAA, or SpoIIIAH function could prevent the formation of infectious C. difficile spores and thus disease transmission.

The bacterial spore-forming pathogen Clostridium difficile is a leading cause of nosocomial infections in the United States and represents a significant threat to healthcare systems around the world. As an obligate anaerobe, C. difficile must form spores in order to survive exit from the gastrointestinal tract. Accordingly, spore formation is essential for C. difficile disease transmission. Since the mechanisms controlling this process remain poorly characterized, we analyzed the importance of highly conserved secretion channel components during C. difficile sporulation. In the model organism Bacillus subtilis, this channel had previously been shown to function as a “feeding tube” that allows the mother cell to nurture the developing forespore and sustain transcription in the forespore. We show here that conserved components of this structure in C. difficile are dispensable for forespore transcription, although they are important for completing forespore engulfment and retaining the protective spore coat around the forespore, in contrast with B. subtilis. The results of our study suggest that targeting these conserved proteins could prevent C. difficile spore formation and thus disease transmission.

Extra-chromosomal DNA maintenance in Bacillus subtilis, dependence on flagellation factor FliF and moonlighting mediator EdmS

Extra-chromosomal DNA maintenance (EDM) as an important process in the propagation and genetic engineering of microbes. Bacillus subtilis EdmS (formerly PgsE), a protein comprising 55 amino acids, is a mediator of the EDM process. In this study, the effect of mutation of global regulators on B. subtilis EDM was examined. Mutation of the swrA gene abolished EdmS-mediated EDM. It is known that swrA predominantly regulates expression of the fla/che operon in B. subtilis. We therefore performed EDM analysis using fla/che-deletion mutants and identified an EDM-mediated EDM cooperator in the flgB-fliL region. Further genetic investigation identified the flagellation factor FliF is a crucial EDM cooperator. To our knowledge, this is the first observation of the moonlighting function of FliF in DNA maintenance.

Diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes

Sporulation allows bacteria to survive adverse conditions and is essential to the lifecycle of some obligate anaerobes. In Bacillus subtilis, the sporulation-specific sigma factors, σ(F), σ(E), σ(G), and σ(K), activate compartment-specific transcriptional programs that drive sporulation through its morphological stages. The regulation of these sigma factors was predicted to be conserved across the Firmicutes, since the regulatory proteins controlling their activation are largely conserved. However, recent studies in (Pepto)Clostridium difficile, Clostridium acetobutylicum, Clostridium perfringens, and Clostridium botulinum have revealed striking differences in the order, activation, and function of sporulation sigma factors. These studies indicate that gene conservation does not necessarily predict gene function and that new mechanisms for controlling cell fate determination remain to be discovered in the anaerobic Clostridia.

Pressure-Based Strategy for the Inactivation of Spores

Since the first application of high hydrostatic pressure (HHP) for food preservation more than 100 years ago, a wealth of knowledge has been gained on molecular mechanisms underlying the HHP-mediated destruction of microorganisms. However, one observation made back then is still valid, i.e. that HHP alone is not sufficient for the complete inactivation of bacterial endospores. To achieve "commercial sterility" of low-acid foods, i.e. inactivation of spores capable of growing in a specific product under typical storage conditions, a combination of HHP with other hurdles is required (most effectively with heat (HPT)). Although HPT processes are not yet industrially applied, continuous technical progress and increasing consumer demand for minimally processed, additive-free food with long shelf life, makes HPT sterilization a promising alternative to thermal processing.In recent years, considerable progress has been made in understanding the response of spores of the model organism B. subtilis to HPT treatments and detailed insights into some basic mechanisms in Clostridium species shed new light on differences in the HPT-mediated inactivation of Bacillus and Clostridium spores. In this chapter, current knowledge on sporulation and germination processes, which presents the basis for understanding development and loss of the extreme resistance properties of spores, is summarized highlighting commonalities and differences between Bacillus and Clostridium species. In this context, the effect of HPT treatments on spores, inactivation mechanism and kinetics, the role of population heterogeneity, and influence factors on the results of inactivation studies are discussed.

A love affair with Bacillus subtilis

My career in science was launched when I was an undergraduate at Princeton University and reinforced by graduate training at the Massachusetts Institute of Technology. However, it was only after I moved to Harvard University as a junior fellow that my affections were captured by a seemingly mundane soil bacterium. What Bacillus subtilis offered was endless fascinating biological problems (alternative sigma factors, sporulation, swarming, biofilm formation, stochastic cell fate switching) embedded in a uniquely powerful genetic system. Along the way, my career in science became inseparably interwoven with teaching and mentoring, which proved to be as rewarding as the thrill of discovery.

SpoIIID-mediated regulation of σK function during Clostridium difficile sporulation

The spore-forming bacterial pathogen Clostridium difficile is a leading cause of health-care-associated diarrhea worldwide. Although C. difficile spore formation is essential for disease transmission, the regulatory pathways that control this developmental process have only been partially characterized. In the well-studied spore-former Bacillus subtilis, the highly conserved σ(E) , SpoIIID and σ(K) regulatory proteins control gene expression in the mother cell to ensure proper spore formation. To define the precise requirement for SpoIIID and σ(K) during C. difficile sporulation, we analyzed spoIIID and sigK mutants using heterologous expression systems and RNA-Seq transcriptional profiling. These analyses revealed that expression of sigK from a SpoIIID-independent promoter largely bypasses the need for SpoIIID to produce heat-resistant spores. We also observed that σ(K) is active upon translation, suggesting that SpoIIID primarily functions to activate sigK. SpoIIID nevertheless plays auxiliary roles during sporulation, as it enhances levels of the exosporium morphogenetic protein CdeC in a σ(K) -dependent manner. Analyses of purified spores further revealed that SpoIIID and σ(K) control the adherence of the CotB coat protein to C. difficile spores, indicating that these proteins regulate multiple stages of spore formation. Collectively, these results highlight that diverse mechanisms control spore formation in the Firmicutes.

Bistable forespore engulfment in Bacillus subtilis by a zipper mechanism in absence of the cell wall

To survive starvation, the bacterium Bacillus subtilis forms durable spores. The initial step of sporulation is asymmetric cell division, leading to a large mother-cell and a small forespore compartment. After division is completed and the dividing septum is thinned, the mother cell engulfs the forespore in a slow process based on cell-wall degradation and synthesis. However, recently a new cell-wall independent mechanism was shown to significantly contribute, which can even lead to fast engulfment in 60 of the cases when the cell wall is completely removed. In this backup mechanism, strong ligand-receptor binding between mother-cell protein SpoIIIAH and forespore-protein SpoIIQ leads to zipper-like engulfment, but quantitative understanding is missing. In our work, we combined fluorescence image analysis and stochastic Langevin simulations of the fluctuating membrane to investigate the origin of fast bistable engulfment in absence of the cell wall. Our cell morphologies compare favorably with experimental time-lapse microscopy, with engulfment sensitive to the number of SpoIIQ-SpoIIIAH bonds in a threshold-like manner. By systematic exploration of model parameters, we predict regions of osmotic pressure and membrane-surface tension that produce successful engulfment. Indeed, decreasing the medium osmolarity in experiments prevents engulfment in line with our predictions. Forespore engulfment may thus not only be an ideal model system to study decision-making in single cells, but its biophysical principles are likely applicable to engulfment in other cell types, e.g. during phagocytosis in eukaryotes.

When the bacterium B. subtilis runs out of food, it undergoes a fundamental development process by which it forms durable spores. Sporulation is initiated by asymmetric cell division after which the larger mother cell engulfs the smaller forespore, followed by spore maturation and release. This survival strategy is so robust that engulfment even proceeds when cells are deprived of their protective cell wall. Under these severe perturbations, 60 of the mother cells still engulf their forespores in only 10 of the normal engulfment time, while the remaining 40 of mother cells withdraw from engulfment. This all-or-none outcome of engulfment suggests decision-making, which was recently also identified in other types of engulfment, e.g. during phagocytosis when immune cells engulf and destroy pathogens. Here, we developed a biophysical model to explain fast bistable forespore engulfment in absence of the cell wall and energy sources. Our discovered principles may prove very general, thus predicting key ingredients of successful engulfment across all kingdoms of life.

A mother cell-to-forespore channel: current understanding and future challenges

Formation of endospores allows some bacteria to survive extreme nutrient limitation. The resulting dormant cell, the spore, persists in the environment and is highly resistant to physical and chemical stresses. During spore formation, cells divide asymmetrically and the mother cell engulfs the developing spore, encasing it within a double membrane and isolating it from the medium. Communication between mother cell and isolated forespore involves a specialised connection system that allows nurturing of the forespore and continued macromolecular synthesis, required to finalise spore maturation. Here, we review current understanding of this feeding channel formed by a forespore protein, SpoIIQ, and a mother cell protein, SpoIIIAH, in the model organism Bacillus subtilis and the important human pathogen Clostridium difficile. We also analyse the presence of this channel across endospore-forming bacteria and highlight the main questions still remaining.

A conserved cysteine residue of Bacillus subtilis SpoIIIJ is important for endospore development

During sporulation in Bacillus subtilis, the onset of activity of the late forespore-specific sigma factor σ^G coincides with completion of forespore engulfment by the mother cell. At this stage, the forespore becomes a free protoplast, surrounded by the mother cell cytoplasm and separated from it by two membranes that derive from the asymmetric division septum. Continued gene expression in the forespore, isolated from the surrounding medium, relies on the SpoIIIA-SpoIIQ secretion system assembled from proteins synthesised both in the mother cell and in the forespore. The membrane protein insertase SpoIIIJ, of the YidC/Oxa1/Alb3 family, is involved in the assembly of the SpoIIIA-SpoIIQ complex. Here we show that SpoIIIJ exists as a mixture of monomers and dimers stabilised by a disulphide bond. We show that residue Cys134 within transmembrane segment 2 (TM2) of SpoIIIJ is important to stabilise the protein in the dimeric form. Labelling of Cys134 with a Cys-reactive reagent could only be achieved under stringent conditions, suggesting a tight association at least in part through TM2, between monomers in the membrane. Substitution of Cys134 by an Ala results in accumulation of the monomer, and reduces SpoIIIJ function in vivo. Therefore, SpoIIIJ activity in vivo appears to require dimer formation.

Spore formation in Bacillus subtilis

Although prokaryotes ordinarily undergo binary fission to produce two identical daughter cells, some are able to undergo alternative developmental pathways that produce daughter cells of distinct cell morphology and fate. One such example is a developmental programme called sporulation in the bacterium Bacillus subtilis, which occurs under conditions of environmental stress. Sporulation has long been used as a model system to help elucidate basic processes of developmental biology including transcription regulation, intercellular signalling, membrane remodelling, protein localization and cell fate determination. This review highlights some of the recent work that has been done to further understand prokaryotic cell differentiation during sporulation and its potential applications.

Regulated proteolysis in bacterial development

Bacteria use proteases to control three types of events temporally and spatially during the processes of morphological development. These events are the destruction of regulatory proteins, activation of regulatory proteins, and production of signals. While some of these events are entirely cytoplasmic, others involve intramembrane proteolysis of a substrate, transmembrane signaling, or secretion. In some cases, multiple proteolytic events are organized into pathways, for example turnover of a regulatory protein activates a protease that generates a signal. We review well-studied and emerging examples and identify recurring themes and important questions for future research. We focus primarily on paradigms learned from studies of model organisms, but we note connections to regulated proteolytic events that govern bacterial adaptation, biofilm formation and disassembly, and pathogenesis.

Biochemical and structural insights into intramembrane metalloprotease mechanisms

Intramembrane metalloproteases are nearly ubiquitous in living organisms and they function in diverse processes ranging from cholesterol homeostasis and the unfolded protein response in humans to sporulation, stress responses, and virulence of bacteria. Understanding how these enzymes function in membranes is a challenge of fundamental interest with potential applications if modulators can be devised. Progress is described toward a mechanistic understanding, based primarily on molecular genetic and biochemical studies of human S2P and bacterial SpoIVFB and RseP, and on the structure of the membrane domain of an archaeal enzyme. Conserved features of the enzymes appear to include transmembrane helices and loops around the active site zinc ion, which may be near the membrane surface. Extramembrane domains such as PDZ (PSD-95, DLG, ZO-1) or CBS (cystathionine-β-synthase) domains govern substrate access to the active site, but several different mechanisms of access and cleavage site selection can be envisioned, which might differ depending on the substrate and the enzyme. More work is needed to distinguish between these mechanisms, both for enzymes that have been relatively well-studied, and for enzymes lacking PDZ and CBS domains, which have not been studied. This article is part of a Special Issue entitled: Intramembrane Proteases.

The spore differentiation pathway in the enteric pathogen Clostridium difficile

Endosporulation is an ancient bacterial developmental program that culminates with the differentiation of a highly resistant endospore. In the model organism Bacillus subtilis, gene expression in the forespore and in the mother cell, the two cells that participate in endospore development, is governed by cell type-specific RNA polymerase sigma subunits. σ(F) in the forespore, and σ(E) in the mother cell control early stages of development and are replaced, at later stages, by σ(G) and σ(K), respectively. Starting with σ(F), the activation of the sigma factors is sequential, requires the preceding factor, and involves cell-cell signaling pathways that operate at key morphological stages. Here, we have studied the function and regulation of the sporulation sigma factors in the intestinal pathogen Clostridium difficile, an obligate anaerobe in which the endospores are central to the infectious cycle. The morphological characterization of mutants for the sporulation sigma factors, in parallel with use of a fluorescence reporter for single cell analysis of gene expression, unraveled important deviations from the B. subtilis paradigm. While the main periods of activity of the sigma factors are conserved, we show that the activity of σ(E) is partially independent of σ(F), that σ(G) activity is not dependent on σ(E), and that the activity of σ(K) does not require σ(G). We also show that σ(K) is not strictly required for heat resistant spore formation. In all, our results indicate reduced temporal segregation between the activities of the early and late sigma factors, and reduced requirement for the σ(F)-to-σ(E), σ(E)-to-σ(G), and σ(G)-to-σ(K) cell-cell signaling pathways. Nevertheless, our results support the view that the top level of the endosporulation network is conserved in evolution, with the sigma factors acting as the key regulators of the pathway, established some 2.5 billion years ago upon its emergence at the base of the Firmicutes Phylum.

Stably bridging a great divide: localization of the SpoIIQ landmark protein in Bacillus subtilis

Many bacterial proteins involved in fundamental processes such as cell shape maintenance, cell cycle regulation, differentiation, division and motility localize dynamically to specific subcellular regions. However, the mechanisms underlying dynamic protein localization are incompletely understood. Using the SpoIIQ protein in Bacillus subtilis as a case study, two reports present important novel insights into how a protein finds its right place at the right time and remains stably bound. During sporulation, SpoIIQ localizes in clusters in the forespore membrane at the interface that separates the forespore and mother cell and functions as a landmark protein for SpoIIIAH in the mother cell membrane. The extracellular domains of SpoIIQ and SpoIIIAH interact directly effectively bridging the gap between the two membranes. Here, SpoIIQ localization is shown to depend on two pathways, one involves SpoIIIAH, the second involves two peptidoglycan-degrading enzymes SpoIIP and SpoIID; and, SpoIIQ is only delocalized in the absence of all three proteins. Importantly, in the absence of SpoIIIAH, SpoIIQ apparently localizes normally. However, FRAP experiments demonstrated that SpoIIQ is not stably maintained in the clusters in this mutant. Thus, a second targeting pathway can mask significant changes in the localization of a protein.