Carbon catabolite repression in Bacillus subtilis: quantitative analysis of repression exerted by different carbon sources

Regulation of lactose, glucose and sucrose metabolisms in S. thermophilus

Streptococcus thermophilus is a bacterium widely used in the production of yogurts and cheeses, where it efficiently ferments lactose, the saccharide naturally present in milk. It is also employed as a starter in dairy- or plant-based fermented foods that contain saccharides other than lactose (e.g., sucrose, glucose). However, little is known about how saccharide use is regulated, in particular when saccharides are mixed. Here, we determine the effect of the 5 sugars that S. thermophilus is able to use, at different concentration and when they are mixed on the promoter activities of the C-metabolism genes. Using a transcriptional fusion approach, we discovered that lactose and glucose modulated the activity of the lacS and scrA promoters in a concentration-dependent manner. When mixed with lactose, glucose also repressed the two promoter activities; when mixed with sucrose, lactose still repressed scrA promoter activity. We determined that catabolite control protein A (CcpA) played a key role in these dynamics. We also showed that promoter activity was linked with glycolytic flux, which varied depending on saccharide type and concentration. Overall, this study identified key mechanisms in carbohydrate metabolism - autoregulation and partial hierarchical control - and demonstrated that they are partly mediated by CcpA.

Co-utilization of carbon sources in microorganisms for the bioproduction of chemicals

Carbon source is crucial for the cell growth and metabolism in microorganisms, and its utilization significantly affects the synthesis efficiency of target products in microbial cell factories. Compared with a single carbon source, co-utilizing carbon sources provide an alternative approach to optimize the utilization of different carbon sources for efficient biosynthesis of many chemicals with higher titer/yield/productivity. However, the efficiency of bioproduction is significantly limited by the sequential utilization of a preferred carbon source and secondary carbon sources, attributed to carbon catabolite repression (CCR). This review aimed to introduce the mechanisms of CCR and further focus on the summary of the strategies for co-utilization of carbon sources, including alleviation of CCR, engineering of the transport and metabolism of secondary carbon sources, compulsive co-utilization in single culture, co-utilization of carbon sources via co-culture, and evolutionary approaches. The findings of representative studies with a significant improvement in the bioproduction of chemicals via the co-utilization of carbon sources were discussed in this review. It suggested that by combining rational metabolic engineering and irrational evolutionary approaches, co-utilizing carbon sources can significantly contribute to the bioproduction of chemicals.

The Complex GH32 Enzyme Orchestra from Priestia megaterium Holds the Key to Better Discriminate Sucrose-6-phosphate Hydrolases from Other β-Fructofuranosidases in Bacteria

Inulin is widely used as a prebiotic and emerging as a priming compound to counteract plant diseases. We isolated inulin-degrading strains from the lettuce phyllosphere, identified as Bacillus subtilis and Priestia megaterium, species hosting well-known biocontrol organisms. To better understand their varying inulin degradation strategies, three intracellular β-fructofuranosidases from P. megaterium NBRC15308 were characterized after expression in Escherichia coli: a predicted sucrose-6-phosphate (Suc6P) hydrolase (SacAP1, supported by molecular docking), an exofructanase (SacAP2), and an invertase (SacAP3). Based on protein multiple sequence and structure alignments of bacterial glycoside hydrolase family 32 enzymes, we identified conserved residues predicted to be involved in binding phosphorylated (Suc6P hydrolases) or nonphosphorylated substrates (invertases and fructanases). Suc6P hydrolases feature positively charged residues near the structural catalytic pocket (histidine, arginine, or lysine), whereas other β-fructofuranosidases contain tryptophans. This correlates with our phylogenetic tree, grouping all predicted Suc6P hydrolases in a clan associated with genomic regions coding for transporters involved in substrate phosphorylation. These results will help to discriminate between Suc6P hydrolases and other β-fructofuranosidases in future studies and to better understand the interaction of B. subtilis and P. megaterium endophytes with sucrose and/or fructans, sugars naturally present in plants or exogenously applied in the context of defense priming.

Sugar transport in thermophiles: Bridging lignocellulose deconstruction and bioconversion

Biomass degrading thermophiles play an indispensable role in building lignocellulose-based supply chains. They operate at high temperatures to improve process efficiencies and minimize mesophilic contamination, can overcome lignocellulose recalcitrance through their native carbohydrate-active enzyme (CAZyme) inventory, and can utilize a wide range of sugar substrates. However, sugar transport in thermophiles is poorly understood and investigated, as compared to enzymatic lignocellulose deconstruction and metabolic conversion of sugars to value-added chemicals. Here, we review the general modes of sugar transport in thermophilic bacteria and archaea, covering the structural, molecular, and biophysical basis of their high-affinity sugar uptake. We also discuss recent genetic studies on sugar transporter function. With this understanding of sugar transport, we discuss strategies for how sugar transport can be engineered in thermophiles, with the potential to enhance the conversion of lignocellulosic biomass into renewable products.

ONE-SENTENCE SUMMARY

Sugar transport is the understudied link between extracellular biomass deconstruction and intracellular sugar metabolism in thermophilic lignocellulose bioprocessing.

The hierarchy of sugar catabolization in Lactococcus cremoris

IMPORTANCE

The availability of nutrients to microorganisms varies considerably between different environments, and changes can occur rapidly. As a general rule, a fast growth rate-typically growth on glucose-is associated with the repression of other carbohydrate utilization genes, but it is not clear to what extent catabolite repression is exerted by other sugars. We investigated the hierarchy of sugar utilization after substrate transitions in Lactococcus cremoris. For this, we determined the proteome and carbohydrate utilization capacity after growth on different sugars. The results show that the preparedness of cells for the utilization of "slower" sugars is not strictly determined by the growth rate. The data point to individual proteins relevant for various sugar transitions and suggest that the evolutionary history of the organism might be responsible for deviations from a strictly growth rate-related sugar catabolization hierarchy.

Preventing Production Escape Using an Engineered Glucose-Inducible Genetic Circuit

A proper balance of metabolic pathways is crucial for engineering microbial strains that can efficiently produce biochemicals on an industrial scale while maintaining cell fitness. High production loads can negatively impact cell fitness and hinder industrial-scale production. To address this, fine-tuning gene expression using engineered promoters and genetic circuits can promote control over multiple targets in pathways and reduce the burden. We took advantage of the robust carbon catabolite repression system of Bacillus subtilis to engineer a glucose-inducible genetic circuit that supports growth and production. The circuit is resilient, enabling a quick switch in the production status when exposed to the correct carbon source. By performing serial cultivations for 61 generations under repressive conditions, we preserved the production capacity of the cells, which could be fully accessed by switching to glucose in the next cultivation step. Switching to glucose after 61 generations resulted in 34-fold activation and generated 70% higher production in comparison to standard cultivation in glucose. Conversely, serial cultivation under permanent induction resulted in 62% production loss after 67 generations alongside an increase in the culture growth rate. As a pathway-independent circuit activated by the preferred carbon source, our engineered glucose-inducible genetic circuit is broadly useful and imposes no additional cost to traditional production processes.

Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages

Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.

The cAMP receptor protein (CRP) enhances the competitive nature of Salmonella Typhimurium

The cAMP receptor protein (CRP) is a global regulatory protein. We evaluated the role of CRP in starvation physiology in Salmonella Typhimurium. The Δcrp mutant survived 10 days of starvation. However, in a co-culture with the wild type in nutrient-rich medium, Δcrp died within 48 h. Similar co-culture results were observed with Escherichia coli and Staphylococcus aureus. Our study showed that the Δcrp mutant was not killed by toxins and the Type IV secretion system of the WT. The possibility of viable but non-culturable cells (VBNC) was also ruled out. However, when the overall metabolism of the co-culture was slowed down (anaerobic condition, inhibition by antibiotics and low temperature) that improved the survival of Δcrp in co-culture. But one more significant observation was that the Δcrp mutant survived in nutrient-free co-culture conditions. These two observations suggest that CRP protein is essential for efficient nutrient assimilation in a competitive environment. The cells without CRP protein are unable to evaluate the energy balance within the cell, and the cell spends energy to absorb nutrients. But the wild type cell absorbs nutrients at a faster rate than Δcrp mutant. This leads to a situation wherein the Δcrp is spending energy to absorb the nutrients but is unable to compete with the wild type. This futile metabolism leads to death. Hence, this study shows that CRP is a metabolism modulator in a complex nutrient environment. This study also highlights the need for innovative growth conditions to understand the unique function of a gene.

Application of Endoxylanases of Bacillus halodurans for Producing Xylooligosaccharides from Empty Fruit Bunch

Endo-1,4-β-xylanase catalyzes the random hydrolysis of β-1,4-D-xylosidic bonds in xylan, resulting in the formation of oligomers of xylose. This study aims to demonstrate the promise of endoxylanases from alkaliphilic Bacillus halodurans for the production of xylooligosaccharides (XOS) from oil palm empty fruit bunch (EFB) at high pH. Two enzyme preparations were employed: recombinant endoxylanase Xyn45 (GH10 xylanase) and nonrecombinant endoxylanases, a mixture of two extracellular endo-1,4-β-xylanases Xyn45 and Xyn23 (GH11 xylanase) produced by B. halodurans. EFB was first treated with an alkaline solution. Then, the dissolved xylan-containing fraction was retained, and a prepared enzyme was added to react at pH 8 to convert xylan into XOS. Compared with the use of only Xyn45, the combined use of Xyn45 and Xyn23 resulted in a higher yield of XOS, suggesting the synergistic effect of the two endoxylanases. The yield of XOS obtained from EFB was as high as 46.77% ± 1.64% (w/w), with the xylobiose-to-xylotriose ratio being 6:5. However, when the enzyme activity dose was low, the product contained more xylotriose than xylobiose. Four probiotic lactobacilli and bifidobacteria grew well on a medium containing XOS from EFB. The presence of XOS increased cell mass and reduced pH, suggesting that XOS promoted the growth of probiotics.

Biosynthesis of value-added bioproducts from hemicellulose of biomass through microbial metabolic engineering

Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed. The bioprocess for degradation and conversion of natural lignocellulose to monosaccharides and organic acids using anaerobic thermophilic bacteria and thermostable glycoside hydrolases were summarized. Xylose transmembrane transporting systems in natural microorganisms and the latest strategies for promoting the transporting capacity by metabolic engineering were summarized. The carbon catabolite repression effect restricting xylose utilization in microorganisms, and metabolic engineering strategies developed for co-utilization of glucose and xylose were discussed. Secondly, the metabolic pathways of xylose catabolism in microorganisms were comparatively analyzed. Microbial metabolic engineering for converting xylose to value-added bioproducts based on redox pathways, non-redox pathways, pentose phosphate pathway, and improving inhibitors resistance were summarized. Thirdly, strategies for degrading lignocellulosic polysaccharides and fully converting hemicellulose to value-added bioproducts through microbial metabolic engineering were proposed.

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Hemicellulose is the main carbohydrate of biomass and has valuable applications.

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Hemicellulose is underutilized in conventional biomass refinery and pretreatment.

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Microbial and enzymatic catalysis were applied for hemicellulose utilization.

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Xylose is converted to value-added bioproducts by metabolic engineering.

Boosting the Heterologous Expression of d-Allulose 3-Epimerase in Bacillus subtilis through Protein Engineering and Catabolite-Responsive Element Box Engineering

As a natural sweetener with low calories and various physiological activities, d-allulose has drawn worldwide attention. Currently, d-allulose 3-epimerase (DAEase) is mainly used to catalyze the epimerization of d-fructose to d-allulose. Therefore, it is quite necessary to enhance the food-grade expression of DAEase to meet the surging market demand for d-allulose. In this study, initially, the promising variant H207L/D281G/C289R of Clostridium cellulolyticum H10 DAEase (CcDAEase) was generated by protein engineering, the specific activity and the T_1/2 of which were 2.24-fold and 13.45-fold those of the CcDAEase wild type at 60 °C, respectively. After that, PamyE was determined as the optimal promoter for the recombinant expression of CcDAEase in Bacillus subtilis, and catabolite-responsive element (CRE) box engineering was further performed to eliminate the carbon catabolite repression (CCR) effect. Lastly, high-density fermentation was carried out and the final activity peaked at 4971.5 U mL^-1, which is the highest expression level and could effectively promote the industrial production of DAEase. This research provides a theoretical basis and technical support for the molecular modification of DAEase and its efficient fermentation preparation.

Acetoin production from lignocellulosic biomass hydrolysates with a modular metabolic engineering system in Bacillus subtilis

Background

Acetoin (AC) is a vital platform chemical widely used in food, pharmaceutical and chemical industries. With increasing concern over non-renewable resources and environmental issues, using low-cost biomass for acetoin production by microbial fermentation is undoubtedly a promising strategy.

Results

This work reduces the disadvantages of Bacillus subtilis during fermentation by regulating genes involved in spore formation and autolysis. Then, optimizing intracellular redox homeostasis through Rex protein mitigated the detrimental effects of NADH produced by the glycolytic metabolic pathway on the process of AC production. Subsequently, multiple pathways that compete with AC production are blocked to optimize carbon flux allocation. Finally, the population cell density-induced promoter was used to enhance the AC synthesis pathway. Fermentation was carried out in a 5-L bioreactor using bagasse lignocellulosic hydrolysate, resulting in a final titer of 64.3 g/L, which was 89.5% of the theoretical yield.

Conclusions

The recombinant strain BSMAY-4-PsrfA provides an economical and efficient strategy for large-scale industrial production of acetoin.

Elimination of carbon catabolite repression in Clostridium tyrobutyricum for enhanced butyric acid production from lignocellulosic hydrolysates

Clostridium tyrobutyricum, a gram-positive anaerobic bacterium, is recognized as the promising butyric acid producer. But, the existence of carbon catabolite repression (CCR) is the major drawback for C. tyrobutyricum to efficiently use the lignocellulosic biomass. In this study, the xylose pathway genes were first identified and verified. Then, the potential regulatory mechanisms of CCR in C. tyrobutyricum were proposed and the predicted engineering targets were experimental validated. Inactivation of hprK blocked the CcpA-mediated CCR and resulted in simultaneous conversion of glucose and xylose, although xylose consumption was severe lagging behind. Deletion of xylR further shortened the lag phase of xylose utilization. When hprK and xylR were inactivated together, the CCR in C. tyrobutyricum was completely eliminated. Consequently, ATCC 25755/ΔhprKΔxylR showed significant increase in butyrate productivity (1.8 times faster than the control) and excellent butyric acid fermentation performance using both mixed sugars (11.0-11.9 g/L) and undetoxified lignocellulosic hydrolysates (12.4-13.4 g/L).

Relaxed control of sugar utilization in Parageobacillus thermoglucosidasius DSM 2542

Though carbon catabolite repression (CCR) has been intensively studied in some more characterised organisms, there is a lack of information of CCR in thermophiles. In this work, CCR in the thermophile, Parageobacillus thermoglucosidasius DSM 2542 has been studied during growth on pentose sugars in the presence of glucose. Physiological studies under fermentative conditions revealed a loosely controlled CCR when DSM 2542 was grown in minimal medium supplemented with a mixture of glucose and xylose. This atypical CCR pattern was also confirmed by studying xylose isomerase expression level by qRT-PCR. Fortuitously, the pheB gene, which encodes catechol 2, 3-dioxygenase was found to have a cre site highly similar to the consensus catabolite-responsive element (cre) at its 3' end and was used to confirm that expression of pheB from a plasmid was under stringent CCR control. Bioinformatic analysis suggested that the CCR regulation of xylose metabolism in P. thermoglucosidasius DSM 2542 might occur primarily via control of expression of pentose transporter operons. Relaxed control of sugar utilization might reflect a lower affinity of the CcpA-HPr (Ser46-P) or CcpA-Crh (Ser46-P) complexes to the cre(s) in these operons.

PRD-Containing Virulence Regulators (PCVRs) in Pathogenic Bacteria

Bacterial pathogens rely on a complex network of regulatory proteins to adapt to hostile and nutrient-limiting host environments. The phosphoenolpyruvate phosphotransferase system (PTS) is a conserved pathway in bacteria that couples transport of sugars with phosphorylation to monitor host carbohydrate availability. A family of structurally homologous PTS-regulatory-domain-containing virulence regulators (PCVRs) has been recognized in divergent bacterial pathogens, including Streptococcus pyogenes Mga and Bacillus anthracis AtxA. These paradigm PCVRs undergo phosphorylation, potentially via the PTS, which impacts their dimerization and their activity. Recent work with predicted PCVRs from Streptococcus pneumoniae (MgaSpn) and Enterococcus faecalis (MafR) suggest they interact with DNA like nucleoid-associating proteins. Yet, Mga binds to promoter sequences as a homo-dimeric transcription factor, suggesting a bi-modal interaction with DNA. High-resolution crystal structures of 3 PCVRs have validated the domain structure, but also raised additional questions such as how ubiquitous are PCVRs, is PTS-mediated histidine phosphorylation via potential PCVRs widespread, do specific sugars signal through PCVRs, and do PCVRs interact with DNA both as transcription factors and nucleoid-associating proteins? Here, we will review known and putative PCVRs based on key domain and functional characteristics and consider their roles as both transcription factors and possibly chromatin-structuring proteins.

Functional dissection of the phosphotransferase system provides insight into the prevalence of Faecalibacterium prausnitzii in the host intestinal environment

Faecalibacterium prausnitzii is a dominant member of healthy human colon microbiota, regarded as a beneficial gut bacterium due to its ability to produce anti-inflammatory substances. However, little is known about how F. prausnitzii utilizes the nutrients present in the human gut, influencing its prevalence in the host intestinal environment. The phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) is a widely distributed and highly efficient carbohydrate transport system found in most bacterial species that catalyses the simultaneous phosphorylation and import of cognate carbohydrates; its components play physiological roles through interaction with other regulatory proteins. Here, we performed a systematic analysis of the 16 genes encoding putative PTS components (2 enzyme I, 2 HPr, and 12 enzyme II components) in F. prausnitzii A2-165. We identified the general PTS components responsible for the PEP-dependent phosphotransfer reaction and the sugar-specific PTS components involved in the transport of two carbohydrates, N-acetylglucosamine and fructose, among five enzyme II complexes. We suggest that the dissection of the functional PTS in F. prausnitzii may help to understand how this species outcompetes other bacterial species in the human intestine.

The impact of carbon and nitrogen catabolite repression in microorganisms

Organisms have cellular machinery that is focused on optimum utilization of resources to maximize growth and survival depending on various environmental and developmental factors. Catabolite repression is a strategy utilized by various species of bacteria and fungi to accommodate changes in the environment such as the depletion of resources, or an abundance of less-favored nutrient sources. Catabolite repression allows for the rapid use of certain substrates like glucose over other carbon sources. Effective handling of carbon and nitrogen catabolite repression in microorganisms is crucial to outcompete others in nutrient limiting conditions. Investigations into genes and proteins linked to preferential uptake of different nutrients under various environmental conditions can aid in identifying regulatory mechanisms that are crucial for optimum growth and survival of microorganisms. The exact time and way bacteria and fungi switch their utilization of certain nutrients is of great interest for scientific, industrial, and clinical reasons. Catabolite repression is of great significance for industrial applications that rely on microorganisms for the generation of valuable bio-products. The impact catabolite repression has on virulence of pathogenic bacteria and fungi and disease progression in hosts makes it important area of interest in medical research for the prevention of diseases and developing new treatment strategies. Regulatory networks under catabolite repression exemplify the flexibility and the tremendous diversity that is found in microorganisms and provides an impetus for newer insights into these networks.

Ribozyme-Mediated Downregulation Uncovers DNA Integrity Scanning Protein A (DisA) as a Solventogenesis Determinant in Clostridium beijerinckii

Carbon catabolite repression (CCR) limits microbial utilization of lignocellulose-derived pentoses. To relieve CCR in Clostridium beijerinckii NCIMB 8052, we sought to downregulate catabolite control protein A (CcpA) using the M1GS ribozyme technology. A CcpA-specific ribozyme was constructed by tethering the catalytic subunit of Escherichia coli RNase P (M1 RNA) to a guide sequence (GS) targeting CcpA mRNA (M1GS^CcpA). As negative controls, the ribozyme M1GS^CcpA–Sc (constructed with a scrambled GS^CcpA) or the empty plasmid pMTL500E were used. With a ∼3-fold knockdown of CcpA mRNA in C. beijerinckii expressing M1GS^CcpA (C. beijerinckii_M1GS^CcpA) relative to both controls, a modest enhancement in mixed-sugar utilization and solvent production was achieved. Unexpectedly, C. beijerinckii_M1GS^CcpA–Sc produced 50% more solvent than C. beijerinckii_pMTL500E grown on glucose + arabinose. Sequence complementarity (albeit suboptimal) suggested that M1GS^CcpA–Sc could target the mRNA encoding DNA integrity scanning protein A (DisA), an expectation that was confirmed by a 53-fold knockdown in DisA mRNA levels. Therefore, M1GS^CcpA–Sc was renamed M1GS^DisA. Compared to C. beijerinckii_M1GS^CcpA and _pMTL500E, C. beijerinckii_M1GS^DisA exhibited a 7-fold decrease in the intracellular c-di-AMP level after 24 h of growth and a near-complete loss of viability upon exposure to DNA-damaging antibiotics. Alterations in c-di-AMP-mediated signaling and cell cycling likely culminate in a sporulation delay and the solvent production gains observed in C. beijerinckii_M1GS^DisA. Successful knockdown of the CcpA and DisA mRNAs demonstrate the feasibility of using M1GS technology as a metabolic engineering tool for increasing butanol production in C. beijerinckii.

Carbon catabolite regulation of secondary metabolite formation, an old but not well-established regulatory system

Secondary microbial metabolites have various functions for the producer microorganisms, which allow them to interact and survive in adverse environments. In addition to these functions, other biological activities may have clinical relevance, as diverse as antimicrobial, anticancer and hypocholesterolaemic effects. These metabolites are usually formed during the idiophase of growth and have a wide diversity in their chemical structures. Their synthesis is under the impact of the type and concentration of the culture media nutrients. Some of the molecular mechanisms that affect the synthesis of secondary metabolites in bacteria (Gram‐positive and negative) and fungi are partially known. Moreover, all microorganisms have their peculiarities in the control mechanisms of carbon sources, even those belonging to the same genus. This regulatory knowledge is necessary to establish culture conditions and manipulation methods for genetic improvement and product fermentation. As the carbon source is one of the essential nutritional factors for antibiotic production, its study has been imperative both at the industrial and research levels. This review aims to draw the utmost recent advances performed to clarify the molecular mechanisms of the negative effect exerted by the carbon source on the secondary metabolite formation, emphasizing those found in Streptomyces, one of the genera most profitable antibiotic producers.

Production of poly-γ-glutamic acid (γ-PGA) from xylose-glucose mixtures by Bacillus amyloliquefaciens C1

Due to the promising applications, the demand to enhance poly-γ-glutamic acid (γ-PGA) production while decreasing the cost has increased in the past decade. Here, xylose/glucose mixture and corncob hydrolysate (CCH) was evaluated as alternatives for γ-PGA production by Bacillus amyloliquefaciens C1. Although both have been validated to support cell growth, glucose and xylose were not simutaneously consumed and exhibited a diauxic growth pattern due to carbon catabolite repression (CCR) in B. amyloliquefaciens C1, while the enhanced transcription of araE alleviated the xylose transport bottleneck across a cellular membrane. Additionally, the xyl operon (xylA and xylB), which was responsible for xylose metabolism, was strongly induced by xylose at the transcriptional level. When cultured in a mixed medium, xylR was sharply induced to 3.39-folds during the first 8-h while reduced to the base level similar to that in xylose medium. Finally, pre-treated CCH mainly contained a mixture of glucose and xylose was employed for γ-PGA fermentation, which obtained a final concentration of 6.56 ± 0.27 g/L. Although the glucose utilization rate (84.91 ± 1.81%) was lower than that with chemical substrates, the xylose utilization rate (43.41 ± 2.14%) and the sodium glutamate conversion rate (77.22%) of CCH were acceptable. Our study provided a promising approach for the green production of γ-PGA from lignocellulosic biomass and circumvent excessive non-food usage of glucose.

Microbial single-cell RNA sequencing by split-pool barcoding

Single-cell RNA sequencing (scRNA-seq) has become an essential tool for characterizing gene expression in eukaryotes, but current methods are incompatible with bacteria. Here, we introduce microSPLiT (microbial split-pool ligation transcriptomics), a high-throughput scRNA-seq method for Gram-negative and Gram-positive bacteria that can resolve heterogeneous transcriptional states. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating an atlas of changes in metabolism and lifestyle. We retrieved detailed gene expression profiles associated with known, but rare, states such as competence and prophage induction and also identified unexpected gene expression states, including the heterogeneous activation of a niche metabolic pathway in a subpopulation of cells. MicroSPLiT paves the way to high-throughput analysis of gene expression in bacterial communities that are otherwise not amenable to single-cell analysis, such as natural microbiota.

Environmental and Physiological Factors Affecting High-Throughput Measurements of Bacterial Growth

Bacterial growth under nutrient-rich and starvation conditions is intrinsically tied to the environmental history and physiological state of the population. While high-throughput technologies have enabled rapid analyses of mutant libraries, technical and biological challenges complicate data collection and interpretation. Here, we present a framework for the execution and analysis of growth measurements with improved accuracy over that of standard approaches. Using this framework, we demonstrate key biological insights that emerge from consideration of culturing conditions and history. We determined that quantification of the background absorbance in each well of a multiwell plate is critical for accurate measurements of maximal growth rate. Using mathematical modeling, we demonstrated that maximal growth rate is dependent on initial cell density, which distorts comparisons across strains with variable lag properties. We established a multiple-passage protocol that alleviates the substantial effects of glycerol on growth in carbon-poor media, and we tracked growth rate-mediated fitness increases observed during a long-term evolution of Escherichia coli in low glucose concentrations. Finally, we showed that growth of Bacillus subtilis in the presence of glycerol induces a long lag in the next passage due to inhibition of a large fraction of the population. Transposon mutagenesis linked this phenotype to the incorporation of glycerol into lipoteichoic acids, revealing a new role for these envelope components in resuming growth after starvation. Together, our investigations underscore the complex physiology of bacteria during bulk passaging and the importance of robust strategies to understand and quantify growth.IMPORTANCE How starved bacteria adapt and multiply under replete nutrient conditions is intimately linked to their history of previous growth, their physiological state, and the surrounding environment. While automated equipment has enabled high-throughput growth measurements, data interpretation and knowledge gaps regarding the determinants of growth kinetics complicate comparisons between strains. Here, we present a framework for growth measurements that improves accuracy and attenuates the effects of growth history. We determined that background absorbance quantification and multiple passaging cycles allow for accurate growth rate measurements even in carbon-poor media, which we used to reveal growth-rate increases during long-term laboratory evolution of Escherichia coli Using mathematical modeling, we showed that maximum growth rate depends on initial cell density. Finally, we demonstrated that growth of Bacillus subtilis with glycerol inhibits the future growth of most of the population, due to lipoteichoic acid synthesis. These studies highlight the challenges of accurate quantification of bacterial growth behaviors.

Comparative Analysis of Structural Variations Due to Genome Shuffling of Bacillus Subtilis VS15 for Improved Cellulase Production

Cellulose is one of the most abundant and renewable biomass products used for the production of bioethanol. Cellulose can be efficiently hydrolyzed by Bacillus subtilis VS15, a strain isolate obtained from decomposing logs. A genome shuffling approach was implemented to improve the cellulase activity of Bacillus subtilis VS15. Mutant strains were created using ethyl methyl sulfonate (EMS), N-Methyl-N′ nitro-N-nitrosoguanidine (NTG), and ultraviolet light (UV) followed by recursive protoplast fusion. After two rounds of shuffling, the mutants Gb2, Gc8, and Gd7 were produced that had an increase in cellulase activity of 128%, 148%, and 167%, respectively, in comparison to the wild type VS15. The genetic diversity of the shuffled strain Gd7 and wild type VS15 was compared at whole genome level. Genomic-level comparisons identified a set of eight genes, consisting of cellulase and regulatory genes, of interest for further analyses. Various genes were identified with insertions and deletions that may be involved in improved celluase production in Gd7. Strain Gd7 maintained the capability of hydrolyzing wheatbran to glucose and converting glucose to ethanol by fermentation with Saccharomyces cerevisiae of the wild type VS17. This ability was further confirmed by the acidified potassium dichromate (K₂Cr₂O₇) method.

Carprofen-induced depletion of proton motive force reverses TetK-mediated doxycycline resistance in methicillin-resistant Staphylococcus pseudintermedius

We previously showed that doxycycline (DOX) and carprofen (CPF), a veterinary non-steroidal anti-inflammatory drug, have synergistic antimicrobial activity against methicillin-resistant Staphylococcus pseudintermedius (MRSP) carrying the tetracycline resistance determinant TetK. To elucidate the molecular mechanism of this synergy, we investigated the effects of the two drugs, individually and in combination, using a comprehensive approach including RNA sequencing, two-dimensional differential in-gel electrophoresis, macromolecule biosynthesis assays and fluorescence spectroscopy. Exposure of TetK-positive MRSP to CPF alone resulted in upregulation of pathways that generate ATP and NADH, and promote the proton gradient. We showed that CPF is a proton carrier that dissipates the electrochemical potential of the membrane. In the presence of both CPF and DOX, the energy compensation strategy was attenuated by downregulation of all the processes involved, such as citric acid cycle, oxidative phosphorylation and ATP-providing arginine deiminase pathway. Furthermore, protein biosynthesis inhibition increased from 20% under DOX exposure alone to 75% upon simultaneous exposure to CPF. We conclude that synergistic interaction of the drugs restores DOX susceptibility in MRSP by compromising proton-motive-force-dependent TetK-mediated efflux of the antibiotic. MRSP is unable to counterbalance CPF-mediated PMF depletion by cellular metabolic adaptations, resulting in intracellular accumulation of DOX and inhibition of protein biosynthesis.

The Absence of Pyruvate Kinase Affects Glucose-Dependent Carbon Catabolite Repression in Bacillus subtilis

Pyruvate is a key intermediate of diverse metabolic pathways of central carbon metabolism. In addition to being the end product of glycolysis, pyruvate is an essential carbon distribution point to oxidative metabolism, amino acid and fatty acid syntheses, and overflow metabolite production. Hence, a tight regulation of pyruvate kinase (Pyk) activity is of great importance. This study aimed to analyze targeted metabolites from several pathways and possible changes in Bacillus subtilis lacking Pyk. Wild type and Δpyk cells were cultivated in chemically defined medium with glucose and pyruvate as carbon sources, and the extracted metabolites were analyzed by ¹H-NMR, GC-MS, HPLC-MS, and LC-MS/MS. The results showed that the perturbation created in the pyruvate node drove an adaptation to new conditions by altering the nutritional compounds’ consumption. In Δpyk, pyruvate, which is subject to glucose-dependent carbon catabolite repression, did not comply with the hierarchy in carbon source utilization. Other metabolic alterations were observed such as the higher secretion of the overflow metabolites acetoin and 2,3-butanediol by Δpyk. Our results help to elucidate the regulatory transport of glucose and pyruvate in B. subtilis and possible metabolic reroute to alternative pathways in the absence of Pyk.

Alteration of Proteomes in First-Generation Cultures of Bacillus pumilus Spores Exposed to Outer Space

Bacillus pumilus SAFR-032 was originally isolated from the Jet Propulsion Lab Spacecraft Assembly Facility and thoroughly characterized for its enhanced resistance to UV irradiation and oxidative stress. This unusual resistance of SAFR-032 is of particular concern in the context of planetary protection and calls for development of novel disinfection techniques to prevent extraterrestrial contamination. Previously, spores of SAFR-032 were exposed for 18 months to a variety of space conditions on board the International Space Station to investigate their resistance to Mars-like conditions and space travel. Here, proteomic characterization of vegetative SAFR-032 cells from space-surviving spores is presented in comparison to a ground control. Vegetative cells of the first passage were processed and subjected to quantitative proteomics using tandem mass tags. Approximately 60% of all proteins encoded by SAFR-032 were identified, and 301 proteins were differentially expressed among the strains. We found that proteins predicted to be involved in carbohydrate transport/metabolism and energy production/conversion had lower abundance than those of the ground control. For three proteins, we showed that the expected metabolic activities were decreased, as expected with direct enzymatic assays. This was consistent with a decrease of ATP production in the space-surviving strains. The same space-surviving strains showed increased abundance of proteins related to survival, growth advantage, and stress response. Such alterations in the proteomes provide insights into possible molecular mechanisms of B. pumilus SAFR-032 to adapt to and resist extreme extraterrestrial environments.IMPORTANCE Spore-forming bacteria are well known for their resistance to harsh environments and are of concern for spreading contamination to extraterrestrial bodies during future life detection missions. Bacillus pumilus has been regularly isolated from spacecraft-associated surfaces and exhibited unusual resistance to ultraviolet light and other sterilization techniques. A better understanding of the mechanisms of microbial survival and enhanced resistance is essential for developing novel disinfection protocols for the purpose of planetary protection. While genomic analyses did not reveal the unique characteristics that explain elevated UV resistance of space-exposed B. pumilus, the proteomics study presented here provided intriguing insight on key metabolic changes. The observed proteomics aberrations reveal a complex biological phenomenon that plays a role in bacterial survival and adaptation under long-term exposure to outer space. This adaptive ability of microorganisms needs to be considered by those tasked with eliminating forward contamination.

A metabolomic approach to understand the solid-state fermentation of okara using Bacillus subtilis WX-17 for enhanced nutritional profile

Okara is a major agro-waste produced from the soybean industry. To hydrolyze the okara and enable nutrient release, a strategy to valorize okara using solid-state fermentation with food grade Bacillus subtilis (B. subtilis) WX-17 was carried out. The study showed that fermentation of okara with B. subtilis WX-17 improved its overall nutritional content. The total amino acids content increased from 3.04 ± 0.14 mg/g in unfermented okara to 5.41 ± 1.21 mg/g in okara fermented with B. subtilis WX-17. Total fatty acids content increased from 153.04 ± 5.10 to 166.78 ± 2.41 mg/g okara, after fermentation. Antioxidant content (DPPH) also increased by 6.4 times after fermentation. To gain insight into the mechanism, gas chromatography–mass spectrometry analysis was carried out. In total, 49 metabolites were detected, which could be classified mainly into carbohydrates, TCA cycle metabolites, amino acids and fatty acids. The decrease in carbohydrate metabolites, showed that glycolysis was upregulated. This would have provided the energy and metabolic flux towards the amino acid and fatty acid pathway. This is also in line with the increased amino acids and fatty acid production seen in okara fermented with B. subtilis WX-17. The findings of this work demonstrated the potential of using B. subtilis WX-17 fermentation, to enhance the nutritional profile of okara. This could serve as a potential low-cost animal feed or incorporated into the human diet.

Identification of soil bacteria capable of utilizing a corn ethanol fermentation byproduct

A commercial corn ethanol production byproduct (syrup) was used as a bacterial growth medium with the long-term aim to repurpose the resulting microbial biomass as a protein supplement in aquaculture feeds. Anaerobic batch reactors were used to enrich for soil bacteria metabolizing the syrup as the sole nutrient source over an eight-day period with the goal of obtaining pure cultures of facultative organisms from the reactors. Amplification of the V4 variable region of the 16S rRNA gene was performed using barcoded primers to track the succession of microbes enriched for during growth on the syrup. The resulting PCR products were sequenced using Illumina MiSeq protocols, analyzed via the program QIIME, and the alpha-diversity was calculated. Seven bacterial families were the most prevalent in the bioreactor community after eight days of enrichment: Clostridiaceae, Alicyclobacillaceae, Ruminococcaceae, Burkholderiaceae, Bacillaceae, Veillonellaceae, and Enterobacteriaceae. Pure culture isolates obtained from the reactors, and additional laboratory stock strains, capable of facultative growth, were grown aerobically in microtiter plates with the syrup substrate to monitor growth yield. Reactor isolates of interest were identified at a species level using the full 16S rRNA gene and other biomarkers. Bacillus species, commonly used as probiotics in aquaculture, showed the highest biomass yield of the monocultures examined. Binary combinations of monocultures yielded no apparent synergism between organisms, suggesting competition for nutrients instead of cooperative metabolite conversion.

Introducing substrate limitations to overcome catabolite repression in a protease producing Bacillus licheniformis strain using membrane-based fed-batch shake flasks

To overcome catabolite repression, industrial fermentation processes are usually operated in substrate-limited fed-batch mode. Therefore, the implementation of such an operating mode at small scale is crucial to maintain comparable process conditions. In this study, Bacillus licheniformis, a well-known producer of proteases, was cultivated with carbon (glucose)- and nitrogen (ammonium)-limited fed-batch conditions using the previously introduced membrane-based fed-batch shake flasks. A repression of protease production by glucose and ammonium was thus avoided and yields increased 1.5- and 2.1-fold relative to batch, respectively. An elevated feeding rate of glucose caused depletion of ammonium, which was recognizable within the oxygen transfer rate (OTR) signal measured with the Respiration Activity MOnitoring System (RAMOS). Ammonium limitation was prevented by feeding ammonium simultaneously with glucose. The OTR signal clearly indicated the initiation of the fed-batch phase and gave direct feedback on the nutrient release kinetics. Increased feeding rates of glucose and ammonium led to an elevated protease activity without affecting the protease yield (Y_P/Glu ). In addition to Y_P/Glu , protease yields were determined based on the metabolized amount of oxygen ( Y P / O 2 ) . The results showed that the protease production correlated with the amount of consumed glucose as well as with the amount of consumed oxygen. The membrane-based fed-batch shake flask in combination with the RAMOS device is a powerful combination to investigate the effect of substrate-limited fed-batch conditions.

Enhanced Production of Polymyxin E in Paenibacillus polymyxa by Replacement of Glucose by Starch

Polymyxin E or colistin, produced by Paenibacillus polymyxa, is an important antibiotic against Gram-negative pathogens. The objective of this study is to evaluate the effect of starch in fermentation medium on colistin biosynthesis in P. polymyxa. The results indicated that replacement of glucose by starch stimulated colistin production and biosynthesis rate. Overall, the stimulation extent was starch concentration-dependent. As expected, addition of starch induced the expression of amyE encoding amylase and increased amylase activity in fermentation solution. Additionally, replacement of glucose by starch resulted in residue reducing sugar and pH of fermentation mixture low relative to glucose as the sole sugar source. At the molecular level, it was found that replacement of glucose by starch has enhanced the relative expression level of ccpA encoding catabolite control protein A. Therefore, the repression of starch utilization by glucose could be probably relieved. In addition, use of starch stimulated the expression of regulatory gene spo0A but repressed the expression of another regulatory gene abrB. As a result, the expression of genes directly involved in colistin biosynthesis and secretion increased, indicating that at the transcriptional level spo0A and abrB played opposite roles in regulating colistin biosynthesis in P. polymyxa. Taken together, our data demonstrated that starch instead of glucose can promote colistin production probably by affecting the expression of colistin biosynthesis-related genes, as well as reducing the repression of glucose to a secondary metabolic product.

Diauxic growth of Clostridium acetobutylicum ATCC 824 when grown on mixtures of glucose and cellobiose

Clostridium acetobutylicum, a promising organism for biomass transformation, has the capacity to utilize a wide variety of carbon sources. During pre-treatments of (ligno) cellulose through thermic and/or enzymatic processes, complex mixtures of oligo saccharides with beta 1,4-glycosidic bonds can be produced. In this paper, the capability of C. acetobutylicum to ferment glucose and cellobiose, alone and in mixtures was studied. Kinetic studies indicated that a diauxic growth occurs when both glucose and cellobiose are present in the medium. In mixtures, D-glucose is the preferred substrate even if cells were pre grown with cellobiose as the substrate. After the complete consumption of glucose, the growth kinetics exhibits an adaptation time, of few hours, before to be able to use cellobiose. Because of this diauxic phenomenon, the nature of the carbon source deriving from a cellulose hydrolysis pre-treatment could strongly influence the kinetic performances of a fermentation process with C. acetobutylicum.

Structural basis for the regulatory interaction of the methylglyoxal synthase MgsA with the carbon flux regulator Crh in

Utilization of energy-rich carbon sources such as glucose is fundamental to the evolutionary success of bacteria. Glucose can be catabolized via glycolysis for feeding the intermediary metabolism. The methylglyoxal synthase MgsA produces methylglyoxal from the glycolytic intermediate dihydroxyacetone phosphate. Methylglyoxal is toxic, requiring stringent regulation of MgsA activity. In the Gram-positive bacterium Bacillus subtilis, an interaction with the phosphoprotein Crh controls MgsA activity. In the absence of preferred carbon sources, Crh is present in the nonphosphorylated state and binds to and thereby inhibits MgsA. To better understand the mechanism of regulation of MgsA, here we performed biochemical and structural analyses of B. subtilis MgsA and of its interaction with Crh. Our results indicated that MgsA forms a hexamer (i.e. a trimer of dimers) in the crystal structure, whereas it seems to exist in an equilibrium between a dimer and hexamer in solution. In the hexamer, two alternative dimers could be distinguished, but only one appeared to prevail in solution. Further analysis strongly suggested that the hexamer is the biologically active form. In vitro cross-linking studies revealed that Crh interacts with the N-terminal helices of MgsA and that the Crh-MgsA binding inactivates MgsA by distorting and thereby blocking its active site. In summary, our results indicate that dimeric and hexameric MgsA species exist in an equilibrium in solution, that the hexameric species is the active form, and that binding to Crh deforms and blocks the active site in MgsA.

Impact of Seed Exudates on Growth and Biofilm Formation of Bacillus amyloliquefaciens ALB629 in Common Bean

We aimed to unravel the events which favor the seed-rhizobacterium Bacillus amyloliquefaciens strain ALB629 (hereafter ALB629) interaction and which may interfere with the rhizobacterium colonization and growth on the spermosphere of common bean. Seed exudates from common bean were tested in vitro for ALB629 biofilm formation and bacterial growth. Furthermore, the performance of ALB629 on plant-related variables under drought stress was checked. Seed exudates (1 and 5% v/v) increased ALB629 biofilm formation. Additionally, the colony forming units for ALB629 increased both in culture and on the bean seed surface. The bean seed exudates up-regulated biofilm operons in ALB629 TasA and EpsD by ca. two and sixfold, respectively. The high-performance liquid chromatography (HPLC)-coupled with MS showed that malic acid is present as a major organic acid component in the seed exudates. Seeds treated with ALB629 and amended with malic acid resulted in seedlings with a higher bacterial concentration, induced plant drought tolerance, and promoted plant growth. We showed that seed exudates promote growth of ALB629 and malic acid was identified as a major organic acid component in the bean seed exudates. Our results also show that supplementation of ALB629 induced drought tolerance and growth in plants. The research pertaining to the biological significance of seed exudates in plant–microbe interaction is unexplored field and our work shows the importance of seed exudates in priming both growth and tolerance against abiotic stress.

The MsmX ATPase plays a crucial role in pectin mobilization by Bacillus subtilis

Carbohydrates from plant cell walls are often found as heteropolysaccharides intertwined with each other. For competitive advantage against other microorganisms, and ability to fully exploit available carbon and energy sources, Bacillus subtilis possesses a high number of proteins dedicated to the uptake of mono- and oligosaccharides. Here, we characterize transporter complexes, belonging to the ATP-binding cassette (ABC) superfamily, involved in the uptake of oligosaccharides commonly found in pectin. The uptake of these carbohydrates is shown to be MsmX-dependent, assigning a key role in pectin mobilization for MsmX, a multipurpose ATPase serving several distinct ABC-type I sugar importers. Mutagenesis analysis of the transmembrane domains of the AraNPQ MsmX-dependent importer revealed putative residues for MsmX interaction. Interestingly however, although MsmX is shown to be essential for energizing various ABC transporters we found that a second B. subtilis ATPase, YurJ, is able to complement its function when placed in trans at a different locus of the chromosome.

In vitro imaging of bacteria using 18F-fluorodeoxyglucose micro positron emission tomography

Positron emission tomography (PET) with fluorine-18-fluorodeoxyglucose (¹⁸F-FDG) can be applied to detect infection and inflammation. However, it was so far not known to what extent bacterial pathogens may contribute to the PET signal. Therefore, we investigated whether clinical isolates of frequently encountered bacterial pathogens take up ¹⁸F-FDG in vitro, and whether FDG inhibits bacterial growth as previously shown for 2-deoxy-glucose. 22 isolates of Gram-positive and Gram-negative bacterial pathogens implicated in fever and inflammation were incubated with ¹⁸F-FDG and uptake of ¹⁸F-FDG was assessed by gamma-counting and µPET imaging. Possible growth inhibition by FDG was assayed with Staphylococcus aureus and the Gram-positive model bacterium Bacillus subtilis. The results show that all tested isolates accumulated ¹⁸F-FDG actively. Further, ¹⁸F-FDG uptake was hampered in B. subtilis pts mutants impaired in glucose uptake. FDG inhibited growth of S. aureus and B. subtilis only to minor extents, and this effect was abrogated by pts mutations in B. subtilis. These observations imply that bacteria may contribute to the signals observed in FDG-PET infection imaging in vivo. Active bacterial FDG uptake is corroborated by the fact that the B. subtilis phosphotransferase system is needed for ¹⁸F-FDG uptake, while pts mutations protect against growth inhibition by FDG.

Regulation of the synthesis of pulp degrading enzymes in Bacillus isolated from cocoa fermentation

Pectin degrading enzymes are essential for quality of product from cocoa fermentation. Previously, we studied purified pectate lyases (Pel) produced by Bacillus strains from fermenting cocoa and characterized the cloned pel genes. This study aims to search for biological signals that modulates Pel production and regulators that influence pel gene expression. Strains were grown to the end of exponential phase in media containing various carbon sources. Pel enzymes production in Bacillus was unaffected by simple sugar content variation up to 2%. Additionally, it appeared that pel gene is not under the control of the most common carbon and pectin catabolism regulators ccpA and kdgR, which could explain the insensitivity of Pel production to carbon source variation. However, a 6-fold decrease in Pel production was observed when bacteria were grown in LB rich medium as opposed to basal mineral medium. Subsequently, bioinformatics analysis of cloned pel gene promoter region revealed the presence of DegU binding site. Furthermore, the deletion of degU gene dramatically reduces the pel gene expression, as revealed by real time quantitative PCR, showing an activation effect of DegU on Pel synthesis in Bacillus strains studied. We assumed that, during the latter stage of cocoa fermentation when simple sugars are depleted, production of Pel in Bacillus is stimulated by DegU to supply microbial cells with carbon source from polymeric pectic compounds.

GH115 α-glucuronidase and GH11 xylanase from Paenibacillus sp. JDR-2: potential roles in processing glucuronoxylans

Paenibacillus sp. JDR-2 (Pjdr2) has been studied as a model for development of bacterial biocatalysts for efficient processing of xylans, methylglucuronoxylan, and methylglucuronoarabinoxylan, the predominant hemicellulosic polysaccharides found in dicots and monocots, respectively. Pjdr2 produces a cell-associated GH10 endoxylanase (Xyn10A₁) that catalyzes depolymerization of xylans to xylobiose, xylotriose, and methylglucuronoxylotriose with methylglucuronate-linked α-1,2 to the nonreducing terminal xylose. A GH10/GH67 xylan utilization regulon includes genes encoding an extracellular cell-associated Xyn10A₁ endoxylanase and an intracellular GH67 α-glucuronidase active on methylglucuronoxylotriose generated by Xyn10A₁ but without activity on methylglucuronoxylotetraose generated by a GH11 endoxylanase. The sequenced genome of Pjdr2 contains three paralogous genes potentially encoding GH115 α-glucuronidases found in certain bacteria and fungi. One of these, Pjdr2_5977, shows enhanced expression during growth on xylans along with Pjdr2_4664 encoding a GH11 endoxylanase. Here, we show that Pjdr2_5977 encodes a GH115 α-glucuronidase, Agu115A, with maximal activity on the aldouronate methylglucuronoxylotetraose selectively generated by a GH11 endoxylanase Xyn11 encoded by Pjdr2_4664. Growth of Pjdr2 on this methylglucuronoxylotetraose supports a process for Xyn11-mediated extracellular depolymerization of methylglucuronoxylan and Agu115A-mediated intracellular deglycosylation as an alternative to the GH10/GH67 system previously defined in this bacterium. A recombinantly expressed enzyme encoded by the Pjdr2 agu115A gene catalyzes removal of 4-O-methylglucuronate residues α-1,2 linked to internal xylose residues in oligoxylosides generated by GH11 and GH30 xylanases and releases methylglucuronate from polymeric methylglucuronoxylan. The GH115 α-glucuronidase from Pjdr2 extends the discovery of this activity to members of the phylum Firmicutes and contributes to a novel system for bioprocessing hemicelluloses.

Hierarchy in pentose sugar metabolism in Clostridium acetobutylicum

Bacterial metabolism of polysaccharides from plant detritus into acids and solvents is an essential component of the terrestrial carbon cycle. Understanding the underlying metabolic pathways can also contribute to improved production of biofuels. Using a metabolomics approach involving liquid chromatography-mass spectrometry, we investigated the metabolism of mixtures of the cellulosic hexose sugar (glucose) and hemicellulosic pentose sugars (xylose and arabinose) in the anaerobic soil bacterium Clostridium acetobutylicum. Simultaneous feeding of stable isotope-labeled glucose and unlabeled xylose or arabinose revealed that,as expected, glucose was preferentially used as the carbon source. Assimilated pentose sugars accumulated in pentose phosphate pathway (PPP) intermediates with minimal flux into glycolysis. Simultaneous feeding of xylose and arabinose revealed an unexpected hierarchy among the pentose sugars, with arabinose utilized preferentially over xylose. The phosphoketolase pathway (PKP) provides an alternative route of pentose catabolism in C. acetobutylicum that directly converts xylulose-5-phosphate into acetyl-phosphate and glyceraldehyde-3-phosphate, bypassing most of the PPP. When feeding the mixture of pentose sugars, the labeling patterns of lower glycolytic intermediates indicated more flux through the PKP than through the PPP and upper glycolysis, and this was confirmed by quantitative flux modeling. Consistent with direct acetyl-phosphate production from the PKP, growth on the pentose mixture resulted in enhanced acetate excretion. Taken collectively, these findings reveal two hierarchies in clostridial pentose metabolism: xylose is subordinate to arabinose, and the PPP is used less than the PKP.

An Alternative Bacterial Expression System Using Bacillus pumilus SG2 Chitinase Promoter

BACKGROUND

Chitin is an abundant natural polysaccharide found in fungi, algae, and exoskeleton of insects. Several bacterial species are capable of utilizing chitin as their carbon source. These bacteria produce chitinases for degradation of chitin into N-acetyl-D-glucosamine. So far, regulation of the chitinase encoding genes has been studied in different bacterial species. Among Bacillus species, B. pumilus strain SG2 encodes two chitinases, ChiS and ChiL. The promoter region of chiSL genes (P _chiS ) is mainly regulated by the general carbon catabolite repression (CCR) system in B. subtilis due to the presence of a catabolite responsive element (cre).

OBJECTIVES

Use of P _chiS in constructing an inducible expression system in B. subtilis was investigated.

MATERIALS AND METHODS

In the first step, complete and shortened versions of P _chiS were inserted upstream of the lacZ on a pBS72/pUC18 shuttle plasmid. The β-galactosidase activity of B. subtilis carrying one of the relevant plasmids was measured in the presence of different carbon sources.

RESULTS

An expression system based on the chitinase promoter of B. pumilus SG2 was established. Modification of P _chiS and the culture medium resulted in production of β-galactosidase in B. subtilis up to 1,800 Miller unit (MU) activity.

CONCLUSIONS

The chitinase promoter developed in this study, has potential to be used in an expression vector that could be induced by chitin. In addition, compared to the other inducers like IPTG and lactose, chitin is definitely cheaper and more available as an inducer.

Probing the regulatory effects of specific mutations in three major binding domains of the pleiotropic regulator CcpA of Bacillus subtilis

Carbon catabolite control is required for efficient use of available carbon sources to ensure rapid growth of bacteria. CcpA is a global regulator of carbon metabolism in Gram-positive bacteria like Bacillus subtilis. In this study the genome-wide gene regulation of a CcpA knockout and three specific CcpA mutants were studied by transcriptome analysis, to further elucidate the function of specific binding sites in CcpA. The following three amino acids were mutated to characterize their function: M17(R) which is involved in DNA binding, T62(H) which is important for the allosteric switch in CcpA upon HPr-Ser46-P binding, and R304(W) which is important for binding of the coeffectors HPr-Ser46-P and fructose-1,6-bisphosphate. The results confirm that CcpA was also involved in gene regulation in the absence of glucose. CcpA-M17R showed a small relief of Carbon Catabolite Control; the CcpA-M17R mutant regulates fewer genes than the CcpA-wt and the palindromicity of the cre site is less important for CcpA-M17R. CcpA-T62H was a stronger repressor than CcpA-wt and also acted as a strong repressor in the absence of glucose. CcpA-R304W was shown here to be less dependent on HPr-Ser46-P for its carbon catabolite control activities. The results presented here provide detailed information on alterations in gene regulation for each CcpA-mutant.

NanI Sialidase, CcpA, and CodY Work Together To Regulate Epsilon Toxin Production by Clostridium perfringens Type D Strain CN3718

Clostridium perfringens type D strains are usually associated with diseases of livestock, and their virulence requires the production of epsilon toxin (ETX). We previously showed (J. Li, S. Sayeed, S. Robertson, J. Chen, and B. A. McClane, PLoS Pathog 7:e1002429, 2011, http://dx.doi.org/10.1371/journal.ppat.1002429) that BMC202, a nanI null mutant of type D strain CN3718, produces less ETX than wild-type CN3718 does. The current study proved that the lower ETX production by strain BMC202 is due to nanI gene disruption, since both genetic and physical (NanI or sialic acid) complementation increased ETX production by BMC202. Furthermore, a sialidase inhibitor that interfered with NanI activity also reduced ETX production by wild-type CN3718. The NanI effect on ETX production was shown to involve reductions in codY and ccpA gene transcription levels in BMC202 versus wild-type CN3718. Similar to CodY, CcpA was found to positively control ETX production. A double codY ccpA null mutant produced even less ETX than a codY or ccpA single null mutant. CcpA bound directly to sequences upstream of the etx or codY start codon, and bioinformatics identified putative CcpA-binding cre sites immediately upstream of both the codY and etx start codons, suggesting possible direct CcpA regulatory effects. A ccpA mutation also decreased codY transcription, suggesting that CcpA effects on ETX production can be both direct and indirect, including effects on codY transcription. Collectively, these results suggest that NanI, CcpA, and CodY work together to regulate ETX production, with NanI-generated sialic acid from the intestines possibly signaling type D strains to upregulate their ETX production and induce disease.

IMPORTANCE

Clostridium perfringens NanI was previously shown to increase ETX binding to, and cytotoxicity for, MDCK host cells. The current study demonstrates that NanI also regulates ETX production via increased transcription of genes encoding the CodY and CcpA global regulators. Results obtained using single ccpA or codY null mutants and a ccpA codY double null mutant showed that codY and ccpA regulate ETX production independently of one another but that ccpA also affects codY transcription. Electrophoretic mobility shift assays and bioinformatic analyses suggest that both CodY and CcpA may directly regulate etx transcription. Collectively, results of this study suggest that sialic acid generated by NanI from intestinal sources signals ETX-producing C. perfringens strains, via CcpA and CodY, to upregulate ETX production and cause disease.

Phosphoproteome dynamics mediate revival of bacterial spores

Background

Bacterial spores can remain dormant for decades, yet harbor the exceptional capacity to rapidly resume metabolic activity and recommence life. Although germinants and their corresponding receptors have been known for more than 30 years, the molecular events underlying this remarkable cellular transition from dormancy to full metabolic activity are only partially defined.

Results

Here, we examined whether protein phospho-modifications occur during germination, the first step of exiting dormancy, thereby facilitating spore revival. Utilizing Bacillus subtilis as a model organism, we performed phosphoproteomic analysis to define the Ser/Thr/Tyr phosphoproteome of a reviving spore. The phosphoproteome was found to chiefly comprise newly identified phosphorylation sites located within proteins involved in basic biological functions, such as transcription, translation, carbon metabolism, and spore-specific determinants. Quantitative comparison of dormant and germinating spore phosphoproteomes revealed phosphorylation dynamics, indicating that phospho-modifications could modulate protein activity during this cellular transition. Furthermore, by mutating select phosphorylation sites located within proteins representative of key biological processes, we established a functional connection between phosphorylation and the progression of spore revival.

Conclusions

Herein, we provide, for the first time, a phosphoproteomic view of a germinating bacterial spore. We further show that the spore phosphoproteome is dynamic and present evidence that phosphorylation events play an integral role in facilitating spore revival.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-015-0184-7) contains supplementary material, which is available to authorized users.

The phosphoenolpyruvate:sugar phosphotransferase system is involved in sensitivity to the glucosylated bacteriocin sublancin

The mode of action of a group of glycosylated antimicrobial peptides known as glycocins remains to be elucidated. In the current study of one glycocin, sublancin, we identified the phosphoenolpyruvate:sugar phosphotransferase system (PTS) of Bacillus species as a key player in bacterial sensitivity. Sublancin kills several Gram-positive bacteria, such as Bacillus species and Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA). Unlike other classes of bacteriocins for which the PTS is involved in their mechanism of action, we show that the addition of PTS-requiring sugars leads to increased resistance rather than increased sensitivity, suggesting that sublancin has a distinct mechanism of action. Collectively, our present mutagenesis and genomic studies demonstrate that the histidine-containing phosphocarrier protein (HPr) and domain A of enzyme II (PtsG) in particular are critical determinants for bacterial sensitivity to sublancin.

Two enzymes with redundant fructose bisphosphatase activity sustain gluconeogenesis and virulence in Mycobacterium tuberculosis

The human pathogen Mycobacterium tuberculosis (Mtb) likely utilizes host fatty acids as a carbon source during infection. Gluconeogenesis is essential for the conversion of fatty acids into biomass. A rate-limiting step in gluconeogenesis is the conversion of fructose 1,6-bisphosphate to fructose 6-phosphate by a fructose bisphosphatase (FBPase). The Mtb genome contains only one annotated FBPase gene, glpX. Here we show that, unexpectedly, an Mtb mutant lacking GLPX grows on gluconeogenic carbon sources and has detectable FBPase activity. We demonstrate that the Mtb genome encodes an alternative FBPase (GPM2, Rv3214) that can maintain gluconeogenesis in the absence of GLPX. Consequently, deletion of both GLPX and GPM2 is required for disruption of gluconeogenesis and attenuation of Mtb in a mouse model of infection. Our work affirms a role for gluconeogenesis in Mtb virulence and reveals previously unidentified metabolic redundancy at the FBPase-catalysed reaction step of the pathway.

Mycobacterium tuberculosis feeds on host fatty acids during infection, a process that requires a fructose bisphosphatase (FBPase) enzyme for gluconeogenesis. Here, Ganapathy et al. show that the bacterium has two different FBPases and that this enzymatic activity is required for full virulence.