Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

Developing Bacillus subtilis as cell factory for the production of the natural biocontrol compound pulcherrimin

Pulcherrimin, a natural metabolite produced by Bacillus subtilis, demonstrates a range of biological activities, including its potential use as a natural antimicrobial, antioxidant, or coloring agent. PS832 was selected as the host cell from four B. subtilis strains. Transcriptome data revealed that the leucine pathway has minimal impact on pulcherrimin titer, whereas the enzymes encoded by the yvmC-cypX operon are essential for achieving high pulcherrimin production. Alleviating transcriptional repression of the yvmC-cypX operon led to an increase in pulcherrimin titer representing a 9.5-fold enhancement to 487 mg/l. The mutant BSP17 showed 65 % inhibition rate on a phytopathogen, revealing its potential as a biocontrol agent. Furthermore, optimizing iron concentration in the medium resulted in pulcherrimin titers of 610 mg/l in shake flasks and 811 mg/l in a 1.5-l bioreactor. It is the highest reported titer and sets the stage for further metabolic engineering to achieve industrial-scale production of pulcherrimin.

Peering into the Bacterial Cell: From Transcription to Functional Genomics

I started my faculty career in 1981 at the UW-Madison in the Department of Bacteriology and moved to the University of California, San Francisco in 1993, where I am a Professor in the Departments of Microbiology and Immunology and Cell and Tissue Biology. In this article, I first review my contributions to understanding the molecular biology of the bacterial transcriptional apparatus and the global role of alternative sigmas (σs), a major pillar of bacterial transcriptional control. I then discuss my role in spearheading the development of bacterial systems biology, specifically to the genome-wide phenotyping approaches necessary for rapid understanding of gene function and the molecular basis of pathway connections across the bacterial universe.

Stable Isotopic Labeling of Dimethylallyl Pyrophosphate (DMAPP) Reveals Compartmentalization of Isoprenoid Biosynthesis during Sporulation in Bacillus subtilis

Isoprenoids are essential metabolites whose biosynthesis originates from two five-carbon (C5) isomers, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Although these isomers serve as the core substrates for isoprenoid biosynthesis, tracking their independent incorporation into downstream metabolites is difficult due to the lack of available chemical tools. To address this issue, we have developed a cell-permeant, stable isotope-labeled analog of DMAPP that employs self-immolating esters to mask the β-phosphate, allowing for efficient cellular uptake and direct forward isotopic labeling of downstream products of DMAPP in Bacillus subtilis. We demonstrate that 13C-labeled, ester-protected DMAPP (13C3 SIE-DMAPP) achieves significant incorporation into menaquinone-7 (MK-7), regardless of inhibition of endogenous production of IPP and DMAPP. By knocking out isopentenyl pyrophosphate isomerase (IPPI) expression, we achieve specific 13C isotopic labeling exclusively at DMAPP-derived positions of MK-7 and demonstrate that IPPI overexpression enables B. subtilis to utilize DMAPP as its sole isoprenoid source. Finally, we tracked DMAPP incorporation during the transition from vegetative growth to sporulation, revealing compartment-specific isotope labeling patterns that underscore the metabolic independence of isoprenoid metabolism in the mother cell and endospore during sporulation in B. subtilis. The introduction of this stable isotope-labeled DMAPP facilitates the tracking of DMAPP-derived metabolites in native biological contexts and opens new avenues for studying prenyl metabolism, terpene biosynthetic pathways, and the regulatory mechanisms governing cellular isoprenoid pools.

The TerC family metal chaperone MeeY enables surfactin export in Bacillus subtilis

TerC family proteins are widely conserved integral membrane proteins with functions related to metal transport. In Bacillus subtilis, the TerC proteins MeeF and MeeY play overlapping roles in the metalation of manganese-requiring membrane and extracellular enzymes. TerC proteins interact with the secretion translocon SecYEG and metalate proteins either during or after protein translocation. Here, we demonstrate that swarming motility is dependent on MeeY. This swarming defect can be complemented extracellularly and is correlated with a loss of surfactin. Surfactin export is mediated by SwrC, an RND family efflux pump previously shown to interact with MeeY in co-immunoprecipitation studies. The amendment of the growth medium with manganese has long been known to enhance surfactin production. We suggest a model in which surfactin export is enhanced by the MeeY-dependent metalation of the surfactin lipopeptide during export.IMPORTANCEBacillus subtilis produces surfactin, a powerful detergent-like compound that functions in intercellular communication, surface motility, and as a broad-spectrum antimicrobial agent. Production of surfactin, a cyclic lipopeptide, depends on a non-ribosomal peptide synthase followed by export by SwrC, a member of the resistance-nodulation-cell division (RND) family of export proteins. Here, we demonstrate that surfactin production additionally requires MeeY, a TerC family membrane protein that exports manganese ions to support the function of secreted and membrane metalloenzymes. We propose that MeeY interacts with SwrC to facilitate metal binding to the surfactin lipopeptide during export from the cell. These results may explain the long-appreciated role that divalent metal ions play in surfactin production during industrial fermentation.

A conserved nuclease facilitates environmental DNA uptake

Bacteria acquire new traits through the uptake of genetic material from the environment, a process requiring DNA processing. However, the molecular inventory mediating this process is far from being completely understood. Here, we identify YhaM in Bacillus subtilis as a conserved 3'-deoxyribonuclease essential for the uptake and processing of genetic information in the form of single-stranded DNA. Our results show that YhaM assembles into hexamers in the presence of divalent cations, enhancing substrate binding, which is achieved through its conserved oligonucleotide-binding domain. Cells lacking YhaM show a severe defect in the uptake of plasmids and genomic DNA, but the transduction of double-stranded DNA by the phage SPP1 remains unaffected. These findings highlight a critical role of YhaM in single-stranded DNA maturation during natural transformation. Importantly, this function is conserved in various Gram-positive human pathogens such as Staphylococcus aureus, suggesting that it could contribute to the spread of antibiotic resistance.

Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome

Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridioides (previously Clostridium). In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 105 independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for C. difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.

A shared alarmone-GTP switch controls persister formation in bacteria

Persisters are phenotypically switched bacteria that survive antibiotic exposure despite being genetically susceptible. Three pathways to persistence-triggered, spontaneous and antibiotic-induced-have been described, but the underlying molecular mechanisms are poorly understood. Here, we used antibiotic time-kill assays as well as single-cell approaches to show that all of the pathways depend on a common switch involving the alarmone guanosine tetra/penta-phosphate ((p)ppGpp) in Bacillus subtilis, each stemming from different alarmone synthetase(s). The accumulation of (p)ppGpp promotes persistence through depletion of intracellular GTP. We developed a fluorescent GTP reporter to visualize rare events of persister formation in wild-type bacteria, revealing a rapid switch from growth to dormancy in single cells as their GTP levels drop beneath a threshold. While a decrease in GTP in the bulk population slows growth and promotes antibiotic tolerance, (p)ppGpp drives persistence by driving rapid, switch-like decreases in GTP levels beneath the persister threshold in single cells. Persistence through alarmone-GTP antagonism is probably a widespread mechanism to survive antibiotics in B. subtilis and potentially beyond.

TlyA is a 23S and 16S 2'-O-methylcytidine methyltransferase important for ribosome assembly in Bacillus subtilis

Ribosomal RNA (rRNA) is methylated in organisms ranging from bacteria to metazoans. Despite the pervasiveness of rRNA methylation in biology, the function of rRNA methylation on ribosome function is poorly understood. In this work, we identify a biological function for the rRNA 2'-O-methylcytidine methyltransferase TlyA, conserved between Bacillus subtilis and Mycobacterium tuberculosis (Mtb). The tlyA deletion in B. subtilis confers a cold sensitive phenotype and resistance to aminoglycoside antibiotics that target the 16S rRNA. We show that ΔtlyA cells have ribosome assembly defects characterized by accumulation of the 50S subunit. Using a genetic approach and based on sequence alignments with other rRNA methyltransferases we tested the importance of potential catalytic residues and S-adenosyl-L-methionine (SAM) cofactor binding sites. We show that TlyA shares the common rRNA methyltransferase catalytic triad KDK and a SAM binding motif GxSxG which differs from Mtb TlyA. Together our work demonstrates that B. subtilis tlyA is critical for ribosome assembly and we identify key residues for TlyA function in vivo. Since E. coli lacks TlyA or a functional equivalent, our work highlights key differences in ribosome maturation between B. subtilis, Mtb and more divergent Gram-negative bacteria providing new insight into translation and antibiotic resistance mechanisms.

A Staphylococcus aureus Virulence Inhibitor Identified by SaeRS Refactoring and Screening in Bacillus subtilis

Bacteria utilize two-component system (TCS) signal transduction pathways to sense environmental and physiological stimuli and mount appropriate responses. In opportunistic pathogens such as Staphylococcus aureus, TCSs activate virulence programs in response to host defense systems. Due to their critical role in pathogenesis, TCSs are important targets for antivirulence drug discovery campaigns. However, challenges associated with screening TCSs in pathogens and in vitro have limited the output of such efforts to a small number of characterized drug candidates. Here, we functionally express the S. aureus virulence-regulating TCS SaeRS from synthetic gene regulatory elements in the model bacterium Bacillus subtilis to reliably screen this system against a small molecule library under simple culturing conditions. Our approach reveals the compound NSC97920 as a strong inhibitor of SaeRS signaling. We combine in situ, in vivo, in silico, and in vitro characterization to demonstrate that NSC97920 suppresses the critical step of autophosphorylation in the SaeS histidine kinase, resulting in strong antivirulence activity. Our work shows that heterologous expression and screening of TCSs in model bacteria could accelerate the development of therapeutics against antibiotic-resistant pathogens.

Protein Homeostasis Impairment Alters Phenotypic Heterogeneity of Biofilm Communities

Biofilms are highly organized, cooperating communities of microorganisms encased in a self-produced extracellular matrix, providing resilience against external stress such as antimicrobial agents and host defenses. A hallmark of biofilms is their phenotypic heterogeneity, which enhances the overall growth and survival of the community. In this study, we demonstrate that removing the dnaK and tig genes encoding the core molecular chaperones DnaK (Hsp70 homolog) and Trigger factor disrupted protein homeostasis in Bacillus subtilis and resulted in the formation of an extremely mucoid biofilm with aberrant architecture, compromised structural integrity, and altered phenotypic heterogeneity. These changes include a large reduction in the motile subpopulation and an overrepresentation of matrix producers and endospores. Overproduction of poly-γ-glutamic acid contributed crucially to the mucoid phenotype and aberrant biofilm architecture. Homeostasis impairment, triggered by elevated temperatures, in wild-type cells led to mucoid and aberrant biofilm phenotypes similar to those observed in strains lacking both dnaK and tig. Our findings show that disruption of protein homeostasis, whether due to the absence of molecular chaperones or because of environmental factors, severely changes biofilm features.

Antibiotic fosmidomycin protects bacteria from cell wall perturbations by antagonizing oxidative damage-mediated cell lysis

Cell wall peptidoglycan is a defining component of bacterial cells, and its biosynthesis is a major target for medically important antibiotics. Recent studies have revealed that antibiotics can kill cells not only by their direct effects on wall synthesis, but also by downstream perturbations of metabolic homeostasis, leading to oxidative damage-mediated lysis. In this paper, we have investigated the killing effects of various effectors of cell wall inhibition, including an antibiotic inhibitor of isoprenoid synthesis, fosmidomycin, in Bacillus subtilis. We show that oxidative damage largely contributes to the toxic effect (rapid cell lysis) induced by inhibition of peptidoglycan synthesis, but not by inhibition of the isoprenoid synthetic pathway. Remarkably, intermediate concentrations of fosmidomycin, confer resistance to lysis when peptidoglycan synthesis is perturbed. We show that this is because fosmidomycin not only blocks peptidoglycan synthesis, but also impairs the synthesis of menaquinone, which, protects cells from respiratory chain-associated oxidative damage and lysis. Our results provide new insights into the critical involvement of metabolic pathways, such as isoprenoid biosynthesis, on the antibiotic efficacy and evasion by bacteria. This work advances our understanding of bacterial physiology as well as antibiotic activity and resistance.

Genome-scale resources in the infant gut symbiont Bifidobacterium breve reveal genetic determinants of colonization and host-microbe interactions

Bifidobacteria represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest in bifidobacteria as a live biotic therapy, our understanding of colonization, host-microbe interactions, and the health-promoting effects of bifidobacteria is limited. To address these major knowledge gaps, we used a large-scale genetic approach to create a mutant fitness compendium in Bifidobacterium breve. First, we generated a high-density randomly barcoded transposon insertion pool and used it to determine fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. Second, to enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1,462 genes. We leveraged these tools to reveal community- and diet-specific requirements for colonization and to connect the production of immunomodulatory molecules to growth benefits. These resources will catalyze future investigations of this important beneficial microbe.

YebC2 resolves ribosome stalling and increases fitness of cells lacking EF-P and the ABCF ATPase YfmR

Ribosome stalling is a major source of cellular stress. Therefore, many specialized elongation factors help prevent ribosome stalling. One of the best characterized of these factors is EF-P, which prevents ribosome stalling at polyproline tracts and other difficult-to-translate sequences. Recent evidence suggests that other factors also facilitate translation of polyproline motifs. For example, YfmR was recently identified as a protein that prevents ribosome stalling at proline-containing sequences in the absence of EF-P. Here, we show that YebC2 (formerly YeeI) functions as a translation factor in Bacillus subtilis that resolves ribosome stalling at polyprolines. YebC2 associates with the ribosome, supporting a direct role for YebC2 in translation. Moreover, YebC2 can reduce ribosome stalling and support cellular fitness in the absence of EF-P and YfmR. Finally, we present evidence that YebC2 is evolutionarily distinct from previously characterized YebC-family transcription factors and demonstrate that these paralogs have distinct physiological roles in B. subtilis. Altogether our work identifies YebC2 as a translation factor that resolves ribosome stalling in B. subtilis and provides crucial insight into the relationship between YebC2, EF-P, and YfmR, three factors that prevent ribosome stalling at polyprolines.

Tracking Different States of Spiked Environmental DNA Using Multiplex Digital PCR Assays

The study of microbial communities based on the total environmental DNA (eDNA) is influenced by the presence of different eDNA states, i.e., intracellular (iDNA) and extracellular DNA (exDNA), and the choice of the DNA extraction method. Although the use of spike-and-recovery controls facilitates the diagnosis of such issues, appropriate experimental setups simultaneously accounting for the different eDNA states and their bacterial origins are missing. Here, we used two single-gene deletion mutants of both Escherichia coli and Bacillus subtilis to trace exDNA and iDNA spike-ins of each selected model organism within environmental samples. Unique primer/probe sets were developed for each strain, allowing their absolute quantification using multiplex digital PCR assays. The proposed spike-and-recovery controls were successfully applied to various environments including soil, sediment, sludge and compost. While the percent recovery of spiked iDNA differed significantly between E. coli and B. subtilis, results were similar for both model organisms in the case of spiked exDNA, emphasising that the fate of DNA molecules in the environment is similar irrespective of their bacterial origin. Hence, future studies may benefit from the proposed approach to better understand methodological ambiguities related to the eDNA extraction in general as well as the separation of the different eDNA states.

Autoregulation of the Master Regulator Spo0A Controls Cell-Fate Decisions in Bacillus subtilis

Spo0A in Bacillus subtilis is activated by phosphorylation (Spo0A~P) upon starvation and differentially controls a set of genes involved in biofilm formation and sporulation. The spo0A gene is transcribed by two distinct promoters, a σA-recognized upstream promoter Pv during growth, and a σH-recognized downstream promoter Ps during starvation, and appears to be autoregulated by four Spo0A~P binding sites (0A1-4 boxes) localized between two promoters. However, the autoregulatory mechanisms and their impact on differentiation remain elusive. Here, we determined the relative affinity of Spo0A~P for each 0A box and dissected each promoter in combination with the systematic 0A box mutations. The data revealed that (1) the Pv and Ps promoters are on and off, respectively, under nutrient-rich conditions without Spo0A~P, (2) the Ps promoter is activated by first 0A3 and then 0A1 during early starvation with low Spo0A~P, (3) during later starvation with high Spo0A~P, the Pv promoter is repressed by first 0A1 and then 0A2 and 0A4, and (4) during prolonged starvation, both promoters are silenced by all 0A boxes with very high Spo0A~P. Our results indicate that the autoregulation of spo0A is one of the key determinants to achieve a developmental increase in Spo0A~P, leading to a temporal window for entry into biofilm formation or sporulation.

Germination of Bacillus spores by LiCl

Spores of Bacillus subtilis have been found to germinate when incubated with LiCl, but not with other monovalent or divalent metal cations. Bacillus megaterium spores also germinated with LiCl, but B. cereus spores did not. In B. subtilis, the LiCl germination was via the activation of spores' GerA germinant receptor (GR), and in B. megaterium, it was the GerU GR. Notably, LiCl germination was much slower than normal physiological germinant triggered GR germination. In B. subtilis spores, rates of LiCl germination were increased in spores with a more fluid IM and decreased in spores with a less fluid IM. Analyses of the GerA germinant binding site suggested that Li+ could bind in a specific site in the B. subtilis GerAB subunit where normally a Na+ likely binds. Importantly, NaCl strongly inhibited LiCl germination of B. subtilis spores, much more so than the larger cation in KCl, although neither salt inhibited L-alanine germination via the GerA GR. These findings increase the understanding of features of mechanisms of germination of Bacillus spores.IMPORTANCEThe ability of some bacteria to form spores upon nutrient starvation confers properties of metabolic dormancy and enhanced resistance to environmental stressors that would otherwise kill vegetative cells. Since spore-forming bacteria include several notable pathogens and economically significant spoilage organisms, insight into how spores are stimulated to germinate and form new vegetative cells is important. Here, we reveal that relatively high concentrations of the inorganic salt lithium chloride trigger the germination of Bacillus subtilis and Bacillus megaterium spores by stimulating one of the spores of each species cohort of nutrient germinant receptors. This is significant since novel germinants and increased knowledge of the germination process should provide opportunities for improved control of spores in healthcare, food, and environmental sectors.

Inhibition of pneumococcal growth and biofilm formation by human isolates of Streptococcus mitis and Streptococcus oralis

In a world facing the unprecedented threat of antibiotic-resistant bacteria, targeted approaches to control colonization and prevent disease caused by common pathobionts offer a promising solution. Streptococcus pneumoniae (pneumococcus) is a leading cause of infections worldwide, affecting both children and adults despite available antimicrobials and vaccines. Colonization, which occurs in the form of a biofilm in the upper respiratory tract, is frequent and a prerequisite for disease and transmission. The use of live bacterial strains as biotherapeutics for infectious diseases is actively being explored. Here, we investigated the potential of commensal streptococci to control S. pneumoniae. Screening of over 300 human isolates led to the identification of seven strains (one Streptococcus oralis and six Streptococcus mitis, designated A22 to G22) with inhibitory activity against S. pneumoniae of multiple serotypes and genotypes. Characterization of A22 to G22 cell-free supernatants indicated the involvement of secreted proteins or peptides in the inhibitory effect of all S. mitis isolates. Genome analyses revealed the presence of 64 bacteriocin loci, encoding 70 putative bacteriocins, several of which are novel and absent or rare in over 7,000 publicly available pneumococcal genomes. Deletion mutants indicated that bacteriocins partially or completely explained the anti-pneumococcal activity of the commensal strains. Importantly, strains A22 to G22 were further able to prevent and disrupt pneumococcal biofilms, a proxy for nasopharyngeal colonization. These results highlight the intricacy of the interactions among nasopharyngeal colonizers and support the potential of strains A22 to G22 to be used as live biotherapeutics, alone or in combination, to control S. pneumoniae colonization.

IMPORTANCE

Streptococcus pneumoniae (pneumococcus) infections remain a major public health issue despite the use of vaccines and antibiotics. Pneumococci asymptomatically colonize the human upper respiratory tract, a niche shared with several commensal Streptococcus species. Competition for space and nutrients among species sharing the same niche is well documented and tends to be more intense among closely related species. Based on this rationale, a screening of several commensal streptococci isolated from the human upper respiratory tract led to the identification of strains of Streptococcus mitis and Streptococcus oralis capable of inhibiting most pneumococcal strains, across diverse serotypes and genotypes. This inhibition was partially or wholly linked to the expression of novel bacteriocins. The selected S. mitis and S. oralis strains significantly disrupted pneumococcal biofilms, indicating a potential for using commensals as biotherapeutics to control pneumococcal colonization, a key step in preventing disease and transmission.

Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved

Although the textbook definition of gene function is the effect for which the gene was selected and/or by which it is maintained, gene function is commonly inferred from the phenotypic effects of deleting the gene. Because some of the deletion effects are byproducts of other effects, they may not reflect the gene's selected-effect function. To evaluate the degree to which the phenotypic effects of gene deletion inform gene function, we compare the transcriptomic and proteomic effects of systematic gene deletions in budding yeast (Saccharomyces cerevisiae) with those effects in fission yeast (Schizosaccharomyces pombe). Despite evidence for functional conservation of orthologous genes, their deletions result in no more sharing of transcriptomic or proteomic effects than that from deleting nonorthologous genes. Because the wild-type mRNA and protein levels of orthologous genes are significantly correlated between the two yeasts and because transcriptomic effects of deleting the same gene strongly overlap between studies in the same S. cerevisiae strain by different laboratories, our observation cannot be explained by rapid evolution or large measurement error of gene expression. Analysis of transcriptomic and proteomic effects of gene deletions in multiple S. cerevisiae strains by the same laboratory reveals a high sensitivity of these effects to the genetic background, explaining why these effects are not evolutionarily conserved. Together, our results suggest that most transcriptomic and proteomic effects of gene deletion do not inform selected-effect function. This finding has important implications for assessing and/or understanding gene function, pleiotropy, and biological complexity.

Developmentally regulated proteolysis by MdfA and ClpCP mediates metabolic differentiation during Bacillus subtilis sporulation

Bacillus subtilis sporulation entails a dramatic transformation of the two cells required to assemble a dormant spore, with the larger mother cell engulfing the smaller forespore to produce the "cell within a cell" structure that is a hallmark of endospore formation. Sporulation also entails metabolic differentiation, whereby key metabolic enzymes are depleted from the forespore but maintained in the mother cell. This reduces the metabolic potential of the forespore, which becomes dependent on mother cell metabolism and the SpoIIQ-SpoIIIA channel to obtain metabolic building blocks necessary for development. We demonstrate that metabolic differentiation depends on the ClpCP protease and a forespore-produced protein encoded by the yjbA gene, which we have renamed MdfA (metabolic differentiation factor A). MdfA is conserved in aerobic endospore formers and required for spore resistance to hypochlorite. Using mass spectrometry and quantitative fluorescence microscopy, we show that MdfA mediates the depletion of dozens of metabolic enzymes and key transcription factors from the forespore. An accompanying study by Massoni and colleagues demonstrates that MdfA is a ClpC adaptor protein that directly interacts with and stimulates ClpCP activity. Together, these results document a developmentally regulated proteolytic pathway that reshapes forespore metabolism, reinforces differentiation, and enhances spore resistance to the oxidant hypochlorite.

Identification of two glycosyltransferases required for synthesis of membrane glycolipids in Clostridioides difficile

Clostridioides difficile infections cause over 12,000 deaths and an estimated one billion dollars in healthcare costs annually in the United States. The cell membrane is an essential structure that is important for protection from the extracellular environment, signal transduction, and transport of nutrients. The polar membrane lipids of C. difficile are ~50% glycolipids, a higher percentage than most other organisms. The glycolipids of C. difficile consist of monohexosyldiradylglycerol (MHDRG) (~14%), dihexosyldiradylglycerol (DHDRG) (~15%), trihexosyldiradylglycerol (THDRG) (~5%), and a unique glycolipid aminohexosyl-hexosyldiradylglycerol (HNHDRG) (~16%). Previously, we found that HexSDF are required for the synthesis of HNHDRG. The enzymes required for the synthesis of MHDRG, DHDRG, and THDRG are not known. In this study, we identified the glycosyltransferases UgtA (CDR20291_0008), which is required for the synthesis of all glycolipids, and UgtB (CDR20291_1186), which is required for the synthesis of DHDRG and THDRG. We propose a model where UgtA synthesizes only MHDRG, HexSDF synthesize HNHDRG from MHDRG, and UgtB synthesizes DHDRG and potentially THDRG from MHDRG. We also report that glycolipids are important for critical cell functions, including sporulation, cell size and morphology, maintaining membrane fluidity, colony morphology, and resistance to some membrane-targeting antimicrobials.

IMPORTANCE

Clostridioides difficile infections are the leading cause of healthcare-associated diarrhea. C. difficile poses a risk to public health due to its ability to form spores and cause recurrent infections. Glycolipids make up ~50% of the polar lipids in the C. difficile membrane, a higher percentage than other common pathogens and include a unique glycolipid not present in other organisms. Here, we identify glycosyltransferases required for the synthesis of glycolipids in C. difficile and demonstrate the important role glycolipids play in C. difficile physiology.

Phosphorelay changes and plasticity underlie the life history evolution of Bacillus subtilis sporulation and germination in serial batch culture

Bacterial endospores facilitate survival in extreme and unpredictably fluctuating environments. However, under abundant nutrient conditions, the production of endospores is quickly reduced or lost. We hypothesized that endospore-forming bacteria exposed to frequent cycling of nutrient availability would evolve reduced sporulation efficiency. We employed replicated batch culture for 11 transfers to test the effects of rapid nutrient cycles on the evolution of the life history traits of sporulation, germination and growth in Bacillus subtilis. We periodically measured total cell and endospore densities during the period between transfers. Replicates evolved in parallel behaviourally and genetically. By the fourth transfer, we saw a reduction in endospore production, which continued to decline throughout the experiment. Our results support a decreased likelihood of sporulation being driven by frequent nutrient renewal. The proportion of endospores germinating after transfer increased significantly by the end of the experiment through the effects of plasticity alone. Every evolved replicate culture displayed colony dimorphism: the dominant morphology being translucent with reduced sporulation ability and the rarer being opaque with accelerated sporulation and highly efficient germination. Colony dimorphism was reflected in the genomes, with all isolates with reduced sporulation having mutations in elements of the sporulation phosphorelay, particularly kinA. Some opaque colonies had no mutations, indicating that those adaptive changes occurred through plasticity. These results suggest that our selection conditions of nutrient cycling resulted in the parallel evolution of communities of ecologically diverse strains, where most reduced sporulation while a smaller proportion accelerated it.

The mutational landscape of Bacillus subtilis conditional hypermutators shows how proofreading skews DNA polymerase error rates

Polymerase errors during DNA replication are a major source of point mutations in genomes. The spontaneous mutation rate also depends on the counteracting activity of DNA repair mechanisms, with mutator phenotypes appearing constantly and allowing for periods of rapid evolution in nature and in the laboratory. Here, we use the Gram-positive model bacterium Bacillus subtilis to disentangle the contributions of DNA polymerase initial nucleotide selectivity, DNA polymerase proofreading, and mismatch repair (MMR) to the mutation rate. To achieve this, we constructed several conditional hypermutators with a proofreading-deficient allele of polC and/or a deficient allele of mutL and performed mutation accumulation experiments. These conditional hypermutators enrich the B. subtilis synthetic biology toolbox for directed evolution. Using mathematical models, we investigated how to interpret the apparent probabilities with which errors escape MMR and proofreading, highlighting the difficulties of working with counts that aggregate potentially heterogeneous mutations and with unknowns about the pathways leading to mutations in the wild-type. Aware of these difficulties, the analysis shows that proofreading prevents partial saturation of the MMR in B. subtilis and that an inherent drawback of proofreading is to skew the net polymerase error rates by amplifying intrinsic biases in nucleotide selectivity.

A mutation in RNA polymerase imparts resistance to β-lactams by preventing dysregulation of amino acid and nucleotide metabolism

Resistance to diverse antibiotics can result from mutations in RNA polymerase (RNAP), but the underlying mechanisms remain poorly understood. In this study, we compare two Bacillus subtilis RNAP mutations: one in β' (rpoC G1122D) that increases resistance to cefuroxime (CEF; a model β-lactam) and one in β (rpoB H482Y) that increases sensitivity. CEF resistance is mediated by a decrease in branched-chain amino acid (BCAA), methionine, and pyrimidine pathways. These same pathways are upregulated by CEF, and their derepression increases CEF sensitivity and antibiotic-induced production of reactive oxygen species. The CEF-resistant rpoC G1122D mutant evades these metabolic perturbations, and repression of the BCAA and pyrimidine pathways may function to restrict membrane biogenesis, which is beneficial when cell wall synthesis is impaired. These findings provide a vivid example of how RNAP mutations, which commonly arise in response to diverse selection conditions, can rewire cellular metabolism to enhance fitness.

Recent progress in proteins regulating the germination of Bacillus subtilis spores

Bacterial spores can remain dormant for years, but they maintain the ability to recommence life through a process termed germination. Although spore germination has been reviewed many times, recent work has provided novel conceptual and molecular understandings of this important process. By using Bacillus subtilis as a model organism, here we thoroughly describe the signal transduction pathway and events that lead to spore germination, incorporating the latest findings on transcription and translation that are likely detected during germination. Then, we comprehensively review the proteins associated with germination and their respective functions. Notably, the typical germinant receptor GerA and the SpoVAF/FigP complex have been newly established as channels for ions release at early stage of germination. Moreover, given that germination is also affected by spore quality, such as molecular cargo, we collect the data about the proteins regulating sporulation to affect spore quality. Specifically, RocG-mediated glutamate catabolism during sporulation to ensure spore quality; GerE-regulated coat protein expression, and CotH-modified coat protein by phosphorylation to ensure normal coat assembly; and RNase Y-degraded RNA in newly released spores to promote dormancy. The latest progress in our understanding of these germination proteins provides valuable insights into the mechanism underlying germination.

The extracytoplasmic sigma factor σX supports biofilm formation and increases biocontrol efficacy in Bacillus velezensis 118

Plant growth promoting rhizobacteria (PGPR) offer an environmentally friendly and sustainable approach to combat pathogens and enhance crop production. The biocontrol activity of PGPR depends on their ability to colonize plant roots and synthesize antimicrobial compounds that inhibit pathogens. However, the regulatory mechanisms underlying these processes remain unclear. In this study, we isolated and characterized Bacillus velezensis 118, a soil isolate that exhibits potent biocontrol activity against Fusarium wilt of banana. Deletion of sigX, encoding an extracytoplasmic function (ECF) sigma factor previously implicated in controlling biofilm architecture in B. subtilis, reduced biocontrol efficacy. The B. velezensis 118 sigX mutant displayed reduced biofilm formation but had only a minor defect in swarming motility and a negligible impact on lipopeptide production. These findings highlight the importance of regulatory processes important for root colonization in the effectiveness of Bacillus spp. as biocontrol agents against phytopathogens.

Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection

To overtake competitors, microbes produce and secrete secondary metabolites that kill neighbouring cells and sequester nutrients. This metabolite-mediated competition probably evolved in complex microbial communities in the presence of viral pathogens. We therefore hypothesized that microbes secrete natural products that make competitors sensitive to phage infection. We used a binary-interaction screen and chemical characterization to identify a secondary metabolite (coelichelin) produced by Streptomyces sp. that sensitizes its soil competitor Bacillus subtilis to phage infection in vitro. The siderophore coelichelin sensitized B. subtilis to a panel of lytic phages (SPO1, SP10, SP50, Goe2) via iron sequestration, which prevented the activation of B. subtilis Spo0A, the master regulator of the stationary phase and sporulation. Metabolomics analysis revealed that other bacterial natural products may also provide phage-mediated competitive advantages to their producers. Overall, this work reveals that synergy between natural products and phages can shape the outcomes of competition between microbes.

Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome

Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridum. In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 105 independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for Clostridium difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.

Ribosome pausing in amylase producing Bacillus subtilis during long fermentation

BACKGROUND

Ribosome pausing slows down translation and can affect protein synthesis. Improving translation efficiency can therefore be of commercial value. In this study, we investigated whether ribosome pausing occurs during production of the α-amylase AmyM by the industrial production organism Bacillus subtilis under repeated batch fermentation conditions.

RESULTS

We began by assessing our ribosome profiling procedure using the antibiotic mupirocin that blocks translation at isoleucine codons. After achieving single codon resolution for ribosome pausing, we determined the genome wide ribosome pausing sites for B. subtilis at 16 h and 64 h growth under batch fermentation. For the highly expressed α-amylase gene amyM several strong ribosome pausing sites were detected, which remained during the long fermentation despite changes in nutrient availability. These pause sites were neither related to proline or rare codons, nor to secondary protein structures. When surveying the genome, an interesting finding was the presence of strong ribosome pausing sites in several toxins genes. These potential ribosome stall sites may prevent inadvertent activity in the cytosol by means of delayed translation.

CONCLUSIONS

Expression of the α-amylase gene amyM in B. subtilis is accompanied by several ribosome pausing events. Since these sites can neither be predicted based on codon specificity nor on secondary protein structures, we speculate that secondary mRNA structures are responsible for these translation pausing sites. The detailed information of ribosome pausing sites in amyM provide novel information that can be used in future codon optimization studies aimed at improving the production of this amylase by B. subtilis.

A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis

RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches-transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites-that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5'- and 3'-exonuclease-deficient cells revealed >103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.

A noncanonical polyamine from bacteria antagonizes animal mitochondrial function

Canonical polyamines such as agmatine, putrescine, and spermidine are evolutionarily conserved metabolites found in nearly all forms of life ranging from bacteria to humans. Recently, interactions between polyamines produced by gut bacteria and human intestinal cells have been proposed to contribute to both Irritable Bowel Syndrome with Diarrhea (IBS-D) and inflammatory bowel diseases. However, the molecular mechanisms that underlie these effects are often unclear due in part to limitations in the methods used to manipulate and study polyamine functions in vivo. Here, we developed a Caenorhabditis elegans based screening platform and a modified LC-MS approach for profiling polyamine metabolites. We combined these methods to make the unexpected discovery that dysfunctional polyamine metabolism in both Gram-negative (E. coli) and Gram-positive (B. subtilis) bacteria can result in the accumulation of a noncanonical polyamine intermediate, N1-Aminopropylagmatine (N1-APA). We further find that N1-APA is produced via spermidine synthase (SpeE) and that it is bioactive when encountered by animals. Specifically, we find that when N1-APA is produced by bacteria in animal intestines it can be transported into intestinal cells via the polyamine transporter CATP-5 where it antagonizes both animal development and mitochondrial function across diverse animal species. Lastly, we find that N1-APA functions analogously to the deoxyhypusine synthase inhibitor GC7. For example, like GC7, N1-APA antagonizes eIF5A hypusination and inhibits the alternative activation of mammalian macrophages. To our knowledge, these findings are the first to demonstrate that N1-APA is a bioactive metabolite and that bacteria can produce a small molecule that functions similarly to existing deoxyhypusine synthase inhibitors. Furthermore, these results suggest an exciting new mechanistic hypothesis for why the loss of speB in gut microbes, including E. coli, has been both linked to inflammatory bowel disease (IBD) in humans and found to drive IBD in germ free mice.

Identification of two glycosyltransferases required for synthesis of membrane glycolipids in Clostridioides difficile

Clostridioides difficile infections cause over 12,000 deaths and an estimated one billion dollars in healthcare costs annually in the United States. The cell membrane is an essential structure that is important for protection from the extracellular environment, signal transduction, and transport of nutrients. The polar membrane lipids of C. difficile are ~50% glycolipids, a higher percentage than most other organisms. The glycolipids of C. difficile consist of monohexosyldiradylglycerol (MHDRG) (~14%), dihexosyldiradylglycerol (DHDRG) (~15%), trihexosyldiradylglycerol (THDRG) (~5%), and a unique glycolipid aminohexosyl-hexosyldiradylglycerol (HNHDRG) (~16%). Previously, we found HexSDF are required for synthesis of HNHDRG. The enzymes required for synthesis of MHDRG, DHDRG, and THDRG are not known. In this study, we identified the glycosyltransferases UgtA (CDR20291_0008), which is required for synthesis of all glycolipids, and UgtB (CDR20291_1186), which is required for synthesis of DHDRG and THDRG. We propose a model where UgtA synthesizes only MHDRG, HexSDF synthesize HNHDRG from MHDRG, and UgtB synthesizes DHDRG and potentially THDRG from MHDRG. We also report that glycolipids are important for critical cell functions, including sporulation, cell size and morphology, maintaining membrane fluidity, colony morphology, and resistance to some membrane targeting antimicrobials.

Mode of Action and Mechanisms of Resistance to the Unusual Polyglycosylated Thiopeptide Antibiotic Persiathiacin A

Persiathiacin A is a novel thiopeptide antibiotic produced by Actinokineospora species UTMC 2448. It has potent activity against methicillin-resistant Staphylococcus aureus (MRSA) and Mycobacterium tuberculosis. Thiopeptides, including persiathiacin A, exhibit antibacterial activity by inhibiting protein synthesis. In this study, we characterize the mechanism of action of persiathiacin A and investigate how resistance to this antibiotic can emerge. In vitro assays revealed that persiathiacin A inhibits translation elongation, leading to ribosome stalling. Genetic analysis of resistant Bacillus subtilis mutants identified mutations primarily in the rplK gene encoding ribosomal protein L11, which is the binding site for other 26-membered macrocycle-containing thiopeptides. The resistant mutants showed growth impairment and an increased lag time, even in the absence of persiathiacin. Comparative proteomic analysis of a resistant mutant versus the parental strain revealed multiple changes, indicative of negative effects on protein synthesis. Thus, although persiathiacin-resistant mutants can arise readily by the loss of L11 function, it is likely that such mutants would be severely compromised in pathogenesis. Furthermore, bioinformatics analysis identified differences in the key amino acids within the thiopeptide-binding region of L11 in the persiathiacin producer. These probably prevent the antibiotic from associating with its target, providing a mechanism for self-resistance.

A new framework for SubtiWiki, the database for the model organism Bacillus subtilis

Bacillus subtilis is a Gram-positive model bacterium and one of the most-studied and best understood organisms. The complex information resulting from its investigation is compiled in the database SubtiWiki (https://subtiwiki.uni-goettingen.de/v5) in an integrated and intuitive manner. To enhance the utility of SubtiWiki, we have added novel features such as a viewer to interrogate conserved genomic organization, a widget that shows mutant fitness data for all non-essential genes, and a widget showing protein structures, structure predictions and complex structures. Moreover, we have integrated metabolites as new entities. The new framework also includes a documented API, enabling programmatic access to data for computational tasks. Here we present the recent developments of SubtiWiki and the current state of the data for this organism.

A shared alarmone-GTP switch underlies triggered and spontaneous persistence

Persisters describe phenotypically switched cells refractory to antibiotic killing in a genetically susceptible population, while preserving the ability to resume growth when antibiotics are discontinued1,2. Since its proposal 70 years ago, great strides were made to build the framework regarding persistence, including defining triggered, spontaneous and antibiotic-induced persisters. However, challenges remain in characterizing the molecular determinants underlying the phenotypic switch into persistence3. Here we document triggered, spontaneous and antibiotic-induced persistence in a Gram-positive bacterium, all through a common switch involving the alarmone (p)ppGpp and each stemming from a different alarmone synthesis pathway. Starvation-triggered persistence is mediated by Rel synthetase, and spontaneous persistence is through self-amplification via allosteric enzyme activation of alarmone synthetases Rel and SasB, whereas lethal and sublethal concentrations of cell wall antibiotics induce alarmones through an antibiotic-induced alarmone synthetase SasA, consequently enabling adaptive persistence that promotes survival. (p)ppGpp accumulation promotes persistence by depleting intracellular GTP and antagonizing its action. We developed a fluorescent GTP reporter to visualize rare events of persister formation in wild type bacteria, revealing a rapid switch from growth to dormancy in single cells as their GTP levels drop beneath a threshold. While a modest drop of GTP in bulk population slows down growth and promotes antibiotic tolerance, (p)ppGpp drives persistence by allowing the switch-like dynamics to drop GTP beneath the persister threshold in single cells. Persistence through alarmone-GTP antagonism is likely a widespread mechanism to survive antibiotics in Gram positive bacteria and possibly beyond.

Ribosomes translocation into the spore of Bacillus subtilis is highly organised and requires peptidoglycan rearrangements

In the spore-forming bacterium Bacillus subtilis transcription and translation are uncoupled and the translational machinery is located at the cell poles. During sporulation, the cell undergoes morphological changes including asymmetric division and chromosome translocation into the forespore. However, the fate of translational machinery during sporulation has not been described. Here, using microscopy and mass spectrometry, we show the localisation of ribosomes during sporulation in wild type and mutant Bacillus subtilis. We demonstrate that ribosomes are associated with the asymmetric septum, a functionally important organelle in the cell's developmental control, and that SpoIIDMP-driven peptidoglycan rearrangement is crucial for ribosomes packing into the forespore. We also show that the SpoIIIA-SpoIIQ 'feeding-tube' channel is not required for ribosome translocation. Our results demonstrate that translation and translational machinery are temporally and spatially organised in B. subtilis during sporulation and that the forespore 'inherits' ribosomes from the mother cell. We propose that the movement of ribosomes in the cell may be mediated by the bacterial homologs of cytoskeletal proteins and that the cues for asymmetric division localisation may be translation-dependent. We anticipate our findings to elicit more sophisticated structural and mechanistic studies of ribosome organisation during bacterial cell development.

Bacillus subtilis ensures high spore quality in competition with Salmonella Typhimurium via the SigB-dependent pathway

The interactions between beneficial bacteria and pathogens are understudied. Here we investigate the interactions between the probiotic strain Bacillus subtilis PS-216 and the pathogen Salmonella Typhimurium SL1344. We show here that the sporulation of B. subtilis is impaired when it competes with S. Typhimurium in a nutrient-depleted medium. The sporulation impairment in B. subtilis is mediated by the sigma factor B (SigB)-dependent general stress response, as the ΔsigB mutant remains blind to manipulative cues from S. Typhimurium. Furthermore, we show that decreased sporulation frequency in B. subtilis depends on cell-cell contact between the two species involving the S. Typhimurium Type VI Secretion System, whereas B. subtilis uses the SigB-dependent response to trade spore quantity for higher spore quality.

Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics

By acquiring or evolving resistance to one antibiotic, bacteria can become cross-resistant to a second antibiotic, which further limits therapeutic choices. In the opposite scenario, initial resistance leads to collateral sensitivity to a second antibiotic, which can inform cycling or combinatorial treatments. Despite their clinical relevance, our knowledge of both interactions is limited. We used published chemical genetics data of the Escherichia coli single-gene deletion library in 40 antibiotics and devised a metric that discriminates between known cross-resistance and collateral-sensitivity antibiotic interactions. Thereby we inferred 404 cases of cross-resistance and 267 of collateral-sensitivity, expanding the number of known interactions by over threefold. We further validated 64/70 inferred interactions using experimental evolution. By identifying mutants driving these interactions in chemical genetics, we demonstrated that a drug pair can exhibit both interactions depending on the resistance mechanism. Finally, we applied collateral-sensitive drug pairs in combination to reduce antibiotic-resistance development in vitro.

Flagellar rotation facilitates the transfer of a bacterial conjugative plasmid

Conjugation-mediated DNA delivery is the primary mode for antibiotic resistance spread in bacteria; yet, molecular mechanisms regulating the conjugation process remain largely unexplored. While conjugative plasmids typically require bacterial attachment to solid surfaces for facilitation of donor-to-recipient proximity, the pLS20 conjugative plasmid, prevalent among Gram-positive Bacillus spp., uniquely requires fluid environments to enhance its transfer. Here, we show that pLS20, carried by Bacillus subtilis, induces multicellular clustering, which can accommodate various species, hence offering a stable platform for DNA delivery in a liquid milieu. We further discovered that induction of pLS20 promoters, governing crucial conjugative genes, is dependent on the presence of donor cell flagella, the major bacterial motility organelle. Moreover, the pLS20 regulatory circuit is controlled by a mechanosensing signal transduction pathway responsive to flagella rotation, thus activating conjugation gene expression exclusively during the host motile phase. This flagella-conjugation coupling strategy may allow the dissemination of the plasmid to remote destinations, allowing infiltration into new niches.

Inactivation of the conserved protease LonA increases production of xylanase and amylase in Bacillus subtilis

BACKGROUND

Bacillus subtilis is widely used for industrial enzyme production due to its capacity to efficiently secrete proteins. However, secretion efficiency of enzymes varies widely, and optimizing secretion is crucial to make production commercially viable. Previously, we have shown that overexpression of the xylanase XynA lowers expression of Clp protein chaperones, and that inactivation of CtsR, which regulates and represses clp transcription, increases the production of XynA. In the current study, we examined whether the same is the case for overexpression of the α-amylase AmyM from Geobacillus stearothermophilus by B. subtilis, and why XynA shows a different timing of secretion compared to AmyM.

RESULTS

Transcriptome analyses revealed that B. subtilis cells overexpressing AmyM exhibited a distinct profile compared to XynA overexpressing cells, however there were also similarities and in both cases expression of CtsR controlled genes was downregulated. In contrast to XynA, inactivation of CtsR did not improve AmyM production. Upregulation of other protein chaperones, including GroEL/ES and DnaJ/K, by inactivating their transcriptional repressor HrcA, had almost no effect on XynA yields and in fact considerably lowered that of AmyM. Despite using the same promoter, the production of XynA peaks well before AmyM reaches its optimal secretion rate. Transcriptome and ribosome profiling indicated that this is neither related to transcription nor to translation regulation. We show that the reduced secretion in the stationary phase is partially due to the activity of secreted proteases, but also due to the activity of the intracellular protease LonA. The absence of this protein resulted in a 140% and 20% increased production for XynA and AmyM, respectively.

CONCLUSION

The combination of transcriptome and ribosome profiling offered important information to determine at which cellular level production bottlenecks occurred. This helped us to identify LonA protease as an important factor influencing enzyme production yields in B. subtilis.

Identification and characterization of the Bacillus subtilis spore germination protein GerY

In response to starvation, endospore-forming bacteria differentiate into stress-resistant spores that can remain dormant for years yet rapidly germinate and resume growth when nutrients become available. To identify uncharacterized factors involved in the exit from dormancy, we performed a transposon-sequencing screen taking advantage of the loss of spore heat resistance that accompanies germination. We reasoned that transposon insertions that impair but do not block germination will lose resistance more slowly than wild type after exposure to nutrients and will therefore survive heat treatment. Using this approach, we identified most of the known germination genes and several new ones. We report an initial characterization of 15 of these genes and a more detailed analysis of one (ymaF). Spores lacking ymaF (renamed gerY) are impaired in germination in response to both L-alanine and L-asparagine, D-glucose, D-fructose, and K+. GerY is a soluble protein synthesized under σE control in the mother cell. A YFP-GerY fusion localizes around the developing and mature spore in a manner that depends on CotE and SafA, indicating that it is a component of the spore coat. Coat proteins encoded by the gerP operon and gerT are also required for efficient germination, and we show that spores lacking two or all three of these loci have more severe defects in the exit from dormancy. Our data are consistent with a model in which GerY, GerT, and the GerP proteins are required for efficient transit of nutrients through the coat to access the germination receptors, but each acts independently in this process.

IMPORTANCE

Pathogens in the orders Bacillales and Clostridiales resist sterilization by differentiating into stress-resistant spores. Spores are metabolically inactive and can remain dormant for decades, yet upon exposure to nutrients, they rapidly resume growth, causing food spoilage, food-borne illness, or life-threatening disease. The exit from dormancy, called germination, is a key target in combating these important pathogens. Here, we report a high-throughput genetic screen using transposon sequencing to identify novel germination factors that ensure the efficient exit from dormancy. We identify several new factors and characterize one in greater detail. This factor, renamed GerY, is part of the proteinaceous coat that encapsulates the dormant spore. Our data suggest that GerY enables efficient transit of nutrients through the coat to trigger germination.

Enhancing High-Level Food-Grade Expression of Glutamate Decarboxylase and Its Application in the Production of γ-Aminobutyric Acid

Gamma-aminobutyric acid (GABA), a non-proteinogenic amino acid, exhibits diverse physiological functions and finds extensive applications in food, medicine, and various industries. Glutamate decarboxylase (GAD) can effectively convert L-glutamic acid (L-Glu) or monosodium glutamate (MSG) into GABA. However, the low food-grade expression of GAD has hindered large-scale GABA production. In this study, we aimed to elevate GAD expression in Bacillus subtilis through cofactor synthesis enhancement, CRISPRi-based host strain modification, and fermentation optimization. In a 3-L fermenter, the optimized strain achieved a remarkable GAD activity of 319.62 U/ml without antibiotic selection pressure, representing the highest reported food-grade expression to date. Subsequently, enzymatic property analysis facilitated the optimization of GABA production using MSG and L-Glu as substrates, achieving 100% molar conversion yields of 274.40 g/l and 481.62 g/l, respectively, with the latter yielding an unprecedented productivity of 48.16 g/l/h. Finally, in vitro fermentation demonstrated that GABA supplementation promoted gut microbial growth and increased the relative abundance of Actinobacteriota and Bacteroidota.

The ribosome-associated quality control pathway supports survival in the absence of non-stop ribosome rescue factors

In bacteria, if a ribosome translates an mRNA lacking a stop codon it becomes stalled at the 3' end of the message. These ribosomes must be rescued by trans-translation or the alternative rescue factors (ArfA or ArfB). However, mounting evidence suggests that the ribosome quality control (RQC) pathway may also rescue non-stop ribosomes. Here, we surveyed the conservation of ribosome rescue pathways in >15,000 bacterial genomes. We found that trans-translation is conserved in >97% of bacterial genomes, while the other rescue pathways are restricted to particular phyla. We did not detect the gene encoding RqcH, the major mediator of RQC, in Proteobacteria (Pseudomonadota). In all Proteobacteria investigated to date, trans-translation is essential in the absence of the Arf proteins. Therefore, we tested whether expression of RQC components from Bacillus subtilis could rescue viability in the absence of trans-translation and ArfA in Escherichia coli. We found that the RQC pathway indeed functions in E. coli and rescues the well-documented synthetic lethal phenotype of ∆ssrA∆arfA. Moreover, we show that the RQC pathway in B. subtilis is essential in the absence of trans-translation and ArfA, further supporting a role for the RQC pathway in the rescue of non-stop ribosomes. Finally, we report a strong co-occurrence between RqcH and the ribosome splitting factor MutS2, but present experimental evidence that there are likely additional ribosome splitting factors beyond MutS2 in B. subtilis. Altogether, our work supports a role for RQC in non-stop ribosome rescue and provides a broad survey of ribosome rescue pathways in diverse bacteria.

IMPORTANCE

In bacteria, it is estimated that 2%-4% of all translation reactions terminate with the ribosome stalled on a damaged mRNA lacking a stop codon. Mechanisms that rescue these ribosomes are essential for viability. We determined the functional overlap between the ribosome quality control pathway and the classical non-stop rescue systems [alternative rescue factor (ArfA) and trans-translation] in a representative Firmicute and Proteobacterium, phyla that are evolutionarily distinct. Furthermore, we used a bioinformatics approach to examine the conservation and overlap of various ribosome rescue systems in >15,000 species throughout the bacterial domain. These results provide key insights into ribosome rescue in diverse phyla.

Developmentally-regulated proteolysis by MdfA and ClpCP mediates metabolic differentiation during Bacillus subtilis sporulation

Bacillus subtilis sporulation entails a dramatic transformation of the two cells required to assemble a dormant spore, with the larger mother cell engulfing the smaller forespore to produce the cell-within-a-cell structure that is a hallmark of endospore formation. Sporulation also entails metabolic differentiation, whereby key metabolic enzymes are depleted from the forespore but maintained in the mother cell. This reduces the metabolic potential of the forespore, which becomes dependent on mother-cell metabolism and the SpoIIQ-SpoIIIA channel to obtain metabolic building blocks necessary for development. We demonstrate that metabolic differentiation depends on the ClpCP protease and a forespore-produced protein encoded by the yjbA gene, which we have renamed MdfA (metabolic differentiation factor A). MdfA is conserved in aerobic endospore-formers and required for spore resistance to hypochlorite. Using mass spectrometry and quantitative fluorescence microscopy, we show that MdfA mediates the depletion of dozens of metabolic enzymes and key transcription factors from the forespore. An accompanying study by Massoni, Evans and collaborators demonstrates that MdfA is a ClpC adaptor protein that directly interacts with and stimulates ClpCP activity. Together, these results document a developmentally-regulated proteolytic pathway that reshapes forespore metabolism, reinforces differentiation, and is required to produce spores resistant to the oxidant hypochlorite.

A Multi-Omics, Machine Learning-Aware, Genome-Wide Metabolic Model of Bacillus Subtilis Refines the Gene Expression and Cell Growth Prediction

Given the extensive heterogeneity and variability, understanding cellular functions and regulatory mechanisms through the analysis of multi-omics datasets becomes extremely challenging. Here, a comprehensive modeling framework of multi-omics machine learning and metabolic network models are proposed that covers various cellular biological processes across multiple scales. This model on an extensive normalized compendium of Bacillus subtilis is validated, which encompasses gene expression data from environmental perturbations, transcriptional regulation, signal transduction, protein translation, and growth measurements. Comparison with high-throughput experimental data shows that EM_iBsu1209-ME, constructed on this basis, can accurately predict the expression of 605 genes and the synthesis of 23 metabolites under different conditions. This study paves the way for the construction of comprehensive biological databases and high-performance multi-omics metabolic models to achieve accurate predictive analysis in exploring complex mechanisms of cell genotypes and phenotypes.

Flagellar point mutation causes social aggregation in laboratory-adapted Bacillus subtilis under conditions that promote swimming

Motility allows microbes to explore and maximize success in their environment; however, many laboratory bacterial strains have a reduced or altered capacity for motility. Swimming motility in Bacillus subtilis depends on peritrichous flagella and is carried out individually as cells move by biased random walks toward attractants. Previously, we adapted Bacillus subtilis strain 3610 to the laboratory for 300 generations in lysogeny broth (LB) batch culture and isolated lab-adapted strains. Strain SH2 is motility-defective and in broth culture forms large, frequently spherical aggregates of cells. A single point mutation in the flagellin gene hag that causes amino acid 259 to switch from A to T is necessary and sufficient to cause these social cell aggregates, and aggregation occurs between flagellated cells bearing this point mutation regardless of the strain background. Cells associate when bearing this mutation, but flagellar rotation is needed to pull associating cells into spherical aggregates. Using electron microscopy, we are able to show that the SH2 flagellar filament has limited polymorphism when compared to other flagellar structures. This limited polymorphism hinders the flagellum's ability to function as a motility apparatus but appears to alter its function to that of cell aggregation/adhesion. We speculate that the genotype-specific aggregation of cells producing HagA259T flagella could have increased representation in a batch-culture experiment by allowing similar cells to go through a transfer together and also that this mutation could serve as an early step to evolve sociality in the natural world.IMPORTANCEThe first life forms on this planet were prokaryotic, and the earliest environments were aquatic, and from these relatively simple starting conditions, complex communities of microbes and ultimately multicellular organisms were able to evolve. Usually, motile cells in aqueous environments swim as individuals but become social by giving up motility and secreting extracellular substances to become a biofilm. Here, we identify a single point mutation in the flagellum that is sufficient to allow cells containing this mutation to specifically form large, suspended groups of cells. The specific change in the flagellar filament protein subunits causes a unique change in the flagellar structure. This could represent a distinct way for closely related cells to associate as an early precursor to sociality.

Overexpression of diglucosyldiacylglycerol synthase leads to daptomycin resistance in Bacillus subtilis

The lipopeptide antibiotic daptomycin exhibits bactericidal activity against Gram-positive bacteria by forming a complex with phosphatidylglycerol (PG) and lipid II in the cell membrane, causing membrane perforation. With the emergence of daptomycin-resistant bacteria, understanding the mechanisms of bacterial resistance to daptomycin has gained great importance. In this study, we aimed to identify the genetic factors contributing to daptomycin resistance in Bacillus subtilis, a model Gram-positive bacterium. Our findings demonstrated that overexpression of ugtP, which encodes diglucosyldiacylglycerol synthase, induces daptomycin resistance in B. subtilis. Specifically, overexpression of ugtP resulted in increased levels of diglucosyldiacylglycerol (Glc2DAG) and decreased levels of acidic phospholipids cardiolipin and PG, as well as the basic phospholipid lysylphosphatidylglycerol. However, ugtP overexpression did not alter the cell surface charge and the susceptibility to the cationic antimicrobial peptide nisin or the cationic surfactant hexadecyltrimethylammonium bromide. Furthermore, by serial passaging in the presence of daptomycin, we obtained daptomycin-resistant mutants carrying ugtP mutations. These mutants showed increased levels of Glc2DAG and a >4-fold increase in the minimum inhibitory concentration of daptomycin. These results suggest that increased Glc2DAG levels, driven by ugtP overexpression, modify the phospholipid composition and confer daptomycin resistance in B. subtilis without altering the cell surface charge of the bacteria.IMPORTANCEDaptomycin is one of the last-resort drugs for the treatment of methicillin-resistant Staphylococcus aureus infections, and the emergence of daptomycin-resistant bacteria has become a major concern. Understanding the mechanism of daptomycin resistance is important for establishing clinical countermeasures against daptomycin-resistant bacteria. In the present study, we found that overexpression of ugtP, which encodes diglucosyldiacylglycerol synthase, induces daptomycin resistance in B. subtilis, a model Gram-positive bacteria. The overexpression of UgtP increased diglucosyldiacylglycerol levels, resulting in altered phospholipid composition and daptomycin resistance. These findings are important for establishing clinical strategies against daptomycin-resistant bacteria, including their detection and management.

Complex sporulation-specific expression of transcription termination factor Rho highlights its involvement in Bacillus subtilis cell differentiation

Termination factor Rho, responsible for the main factor-dependent pathway of transcription termination and the major inhibitor of antisense transcription, is an emerging regulator of various physiological processes in microorganisms. In Gram-positive bacterium Bacillus subtilis, Rho is involved in the control of cell adaptation to starvation and, in particular, in the control of sporulation, a complex differentiation program leading to the formation of a highly resistant dormant spore. While the initiation of sporulation requires a decrease in Rho protein levels during the transition to stationary phase, the mechanisms regulating the expression of rho gene throughout the cell cycle remain largely unknown. Here we show that a drop in the activity of the vegetative SigA-dependent rho promoter causes the inhibition of rho expression in stationary phase. However, after the initiation of sporulation, rho gene is specifically reactivated in two compartments of the sporulating cell using distinct mechanisms. In the mother cell, rho expression occurs by read-through transcription initiated at the SigH-dependent promoter of the distal spo0F gene. In the forespore, rho gene is transcribed from the intrinsic promoter recognized by the alternative sigma factor SigF. These regulatory elements ensure the activity of Rho during sporulation, which appears important for the proper formation of spores. We provide experimental evidence that disruption of the spatiotemporal expression of rho during sporulation affects the resistance properties of spores, their morphology, and the ability to return to vegetative growth under favorable growth conditions.

YebC2 resolves ribosome stalling at polyprolines independent of EF-P and the ABCF ATPase YfmR

Polyproline motifs are essential structural features of many proteins, and recent evidence suggests that EF-P is one of several factors that facilitate their translation. For example, YfmR was recently identified as a protein that prevents ribosome stalling at proline-containing sequences in the absence of EF-P. Here, we show that the YebC-family protein YebC2 (formerly YeeI) functions as a translation factor in B. subtilis that resolves ribosome stalling at polyprolines. We demonstrate that YebC2, EF-P and YfmR act independently to support cellular fitness. Moreover, we show that YebC2 interacts directly with the 70S ribosome, supporting a direct role for YebC2 in translation. Finally, we assess the evolutionary relationship between YebC2 and other characterized YebC family proteins, and present evidence that transcription and translation factors within the YebC family have evolved separately. Altogether our work identifies YebC2 as a translation factor that resolves ribosome stalling and provides crucial insight into the relationship between YebC2, EF-P, and YfmR, three factors that prevent ribosome stalling at prolines.

Sirtuin-dependent reversible lysine acetylation of the o-succinylbenzoyl-coenzyme A synthetase of Bacillus subtilis

Reversible lysine acylation (RLA) is a conserved posttranslational modification that cells of all domains of life use to regulate the biological function of proteins, some of which have enzymatic activity. Many AMP-forming organic acid:CoA ligases are regulated via acylation in prokaryotes and eukaryotes. Here, we report the acetylation of the o-succinylbenzoyl-CoA synthetase (EC 6.2.1.26) of Bacillus subtilis (BsMenE) by the GCN5-related acetyltransferase (GNAT) AcuA enzyme of this bacterium. BsMenE is part of the metabolic pathway that assembles menaquinone (MK), an essential component of the electron transport chain in B. subtilis. We demonstrate that the active-site lysine 471 (K471) of BsMenE is acetylated specifically by BsAcuA, and that acetylated BsMenE (BsMenEAc) is deacetylated by the NAD+-dependent sirtuin (BsSrtN) of this bacterium. The in vivo analyses performed in this study were done in an Escherichia coli ΔmenE strain because the enzymatic activity of MenE is essential in B. subtilis, but not in E. coli. The use of a heterologous system allowed us to assess the effect of acetylation on BsMenE function under MK-dependent growth conditions. Based on our in vivo data, we suggest that regulation of BsMenE by RLA reduces MK production, negatively affecting the growth rate and yield of the culture.IMPORTANCEReversible lysine acylation (RLA) is a posttranslational modification used by all cells to rapidly control the biological function of proteins. Herein, we identify an acetyltransferase and deacetylase in the soil bacterium Bacillus subtilis that can modify/demodify an enzyme required for the synthesis of menaquinone (MK), an essential electron carrier involved in respiration in cells of all domains of life. Based on our data, we suggest that under some as-yet-undefined physiological conditions, B. subtilis modulates MK biosynthesis, which changes the flux of electrons through the electron transport chain of this bacterium. To our knowledge, this is the first example of control of respiration by RLA.

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the model organism Escherichia coli, as well as major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, with the Keio E. coli single-gene deletion library often regarded as a gold standard. However, it remains unclear how gene essentiality varies between related strains and species. To investigate this, we have assembled a collection of 13 sequenced high-density transposon mutant libraries from five genera within the Enterobacteriaceae. We first assess several gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations, we develop a new classifier for gene essentiality. Using this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes. Despite the presence of a large cohort of variably essential genes, we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the σE extracytoplasmic stress response, which appears to have independently acquired essentiality multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts that have emerged from within the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival and identifies several instances of essential stress responses masked by redundancy in free-living bacteria.IMPORTANCEThe essential genome, that is the set of genes absolutely required to sustain life, is a core concept in genetics. Essential genes in bacteria serve as drug targets, put constraints on the engineering of biological chassis for technological or industrial purposes, and are key to constructing synthetic life. Despite decades of study, relatively little is known about how gene essentiality varies across related bacteria. In this study, we have collected gene essentiality data for 13 bacteria related to the model organism Escherichia coli, including several human pathogens, and investigated the conservation of essentiality. We find that approximately a third of the genes essential in any particular strain are non-essential in another related strain. Surprisingly, we do not find evidence for essential genes unique to specific genera; rather it appears a substantial fraction of the essential genome rapidly gains or loses essentiality during evolution. This suggests that essentiality is not an immutable characteristic but depends crucially on the genomic context. We illustrate this through a comparison of our essential genes in free-living bacteria to genes conserved in 34 insect endosymbionts with naturally reduced genomes, finding several cases where genes generally regarded as being important for specific stress responses appear to have become essential in endosymbionts due to a loss of functional redundancy in the genome.