Acetoin metabolism in bacteria

Fermentative production of chiral acetoin by wild-type Bacillus strains

In recent years, there have been many studies on producing acetoin by microbial fermentation, while only a few studies have focused on chiral acetoin biosynthesis. The weight assignment method was first applied to balance the chiral purity (expressed as the enantiomeric excess value) and the titer of acetoin. Bacillus sp. H-18W, a thermophile, was selected from seven Bacillus strains for chiral acetoin production. To lower the cost of the fermentation medium, soybean meal was used as a feedstock. Four kinds of frequently used commercial proteinases with different active sites were tested for the hydrolyzation of the soybean meal, and the combination of the acidic proteinase and the neutral proteinase showed the best results. In a fermentation medium containing 100 g L-1 glucose and 200 g L-1 hydrolysate, Bacillus sp. H-18W produced 21.84 g L-1 acetoin with an ee value of 96.25% at 60 h. This is the first report of using a thermophilic strain to produce chiral acetoin by microbial fermentation. Thermophilic fermentation can reduce the risk of bacterial contamination and can save cooling water. Using soybean meal hydrolysate and glucose as feedstocks, this work provides an economical and alternative method for the production of chiral pure acetoin.

Microbial production of 2,3-butanediol for industrial applications

2,3-Butanediol (2,3-BD) has great potential for diverse industries, including chemical, cosmetics, agriculture, and pharmaceutical areas. However, its industrial production and usage are limited by the fairly high cost of its petro-based production. Several bio-based 2,3-BD production processes have been developed and their economic advantages over petro-based production process have been reported. In particular, many 2,3-BD-producing microorganisms including bacteria and yeast have been isolated and metabolically engineered for efficient production of 2,3-BD. In addition, several fermentation processes have been tested using feedstocks such as starch, sugar, glycerol, and even lignocellulose as raw materials. Since separation and purification of 2,3-BD from fermentation broth account for the majority of its production cost, cost-effective processes have been simultaneously developed. The construction of a demonstration plant that can annually produce around 300 tons of 2,3-BD is scheduled to be mechanically completed in Korea in 2019. In this paper, core technologies for bio-based 2,3-BD production are reviewed and their potentials for use in the commercial sector are discussed.

Synthetic engineering of Corynebacterium crenatum to selectively produce acetoin or 2,3-butanediol by one step bioconversion method

BACKGROUND

Acetoin (AC) and 2,3-butanediol (2,3-BD) as highly promising bio-based platform chemicals have received more attentions due to their wide range of applications. However, the non-efficient substrate conversion and mutually transition between AC and 2,3-BD in their natural producing strains not only led to a low selectivity but also increase the difficulty of downstream purification. Therefore, synthetic engineering of more suitable strains should be a reliable strategy to selectively produce AC and 2,3-BD, respectively.

RESULTS

In this study, the respective AC (alsS and alsD) and 2,3-BD biosynthesis pathway genes (alsS, alsD, and bdhA) derived from Bacillus subtilis 168 were successfully expressed in non-natural AC and 2,3-BD producing Corynebacterium crenatum, and generated recombinant strains, C. crenatum SD and C. crenatum SDA, were proved to produce 9.86 g L-1 of AC and 17.08 g L-1 of 2,3-BD, respectively. To further increase AC and 2,3-BD selectivity, the AC reducing gene (butA) and lactic acid dehydrogenase gene (ldh) in C. crenatum were then deleted. Finally, C. crenatumΔbutAΔldh SD produced 76.93 g L-1 AC in one-step biocatalysis with the yield of 0.67 mol mol-1. Meanwhile, after eliminating the lactic acid production and enhancing 2,3-butanediol dehydrogenase activity, C. crenatumΔldh SDA synthesized 88.83 g L-1 of 2,3-BD with the yield of 0.80 mol mol-1.

CONCLUSIONS

The synthetically engineered C. crenatumΔbutAΔldh SD and C. crenatumΔldh SDA in this study were proved as an efficient microbial cell factory for selective AC and 2,3-BD production. Based on the insights from this study, further synthetic engineering of C. crenatum for AC and 2,3-BD production is suggested.

Effect of ethanol supplementation on the transcriptional landscape of bionanocellulose producer Komagataeibacter xylinus E25

Ethanol exerts a strong positive effect on the cellulose yields from the widely exploited microbial producers of the Komagataeibacter genus. Ethanol is postulated to provide an alternative energy source, enabling effective use of glucose for cellulose biosynthesis rather than for energy acquisition. In this paper, we investigate the effect of ethanol supplementation on the global gene expression profile of Komagataeibacter xylinus E25 using RNA sequencing technology (RNA-seq). We demonstrate that when ethanol is present in the culture medium, glucose metabolism is directed towards cellulose production due to the induction of genes related to UDP-glucose formation and the repression of genes involved in glycolysis and acetan biosynthesis. Transcriptional changes in the pathways of cellulose biosynthesis and c-di-GMP metabolism are also described. The transcript level profiles suggest that Schramm-Hestrin medium supplemented with ethanol promotes bacterial growth by inducing protein biosynthesis and iron uptake. We observed downregulation of genes encoding transposases of the IS110 family which may provide one line of evidence explaining the positive effect of ethanol supplementation on the genotypic stability of K. xylinus E25. The results of this study increase knowledge and understanding of the regulatory effects imposed by ethanol on cellulose biosynthesis, providing new opportunities for directed strain improvement, scaled-up bionanocellulose production, and wider industrial exploitation of the Komagataeibacter species as bacterial cellulose producers.

Quorum and Light Signals Modulate Acetoin/Butanediol Catabolism in Acinetobacter spp

Acinetobacter spp. are found in all environments on Earth due to their extraordinary capacity to survive in the presence of physical and chemical stressors. In this study, we analyzed global gene expression in airborne Acinetobacter sp. strain 5-2Ac02 isolated from hospital environment in response to quorum network modulators and found that they induced the expression of genes of the acetoin/butanediol catabolism, volatile compounds shown to mediate interkingdom interactions. Interestingly, the acoN gene, annotated as a putative transcriptional regulator, was truncated in the downstream regulatory region of the induced acetoin/butanediol cluster in Acinetobacter sp. strain 5-2Ac02, and its functioning as a negative regulator of this cluster integrating quorum signals was confirmed in Acinetobacter baumannii ATCC 17978. Moreover, we show that the acetoin catabolism is also induced by light and provide insights into the light transduction mechanism by showing that the photoreceptor BlsA interacts with and antagonizes the functioning of AcoN in A. baumannii, integrating also a temperature signal. The data support a model in which BlsA interacts with and likely sequesters AcoN at this condition, relieving acetoin catabolic genes from repression, and leading to better growth under blue light. This photoregulation depends on temperature, occurring at 23°C but not at 30°C. BlsA is thus a dual regulator, modulating different transcriptional regulators in the dark but also under blue light, representing thus a novel concept. The overall data show that quorum modulators as well as light regulate the acetoin catabolic cluster, providing a better understanding of environmental as well as clinical bacteria.

Comparison of Volatile and Nonvolatile Compounds in Rice Fermented by Different Lactic Acid Bacteria

The production of rice-based beverages fermented by lactic acid bacteria (LAB) can increase the consumption of rice in the form of a dairy replacement. This study investigated volatile and nonvolatile components in rice fermented by 12 different LABs. Volatile compounds of fermented rice samples were analyzed using gas chromatography-mass spectrometry (GC-MS) combined with solid-phase microextraction (SPME), while nonvolatile compounds were determined using gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) after derivatization. The 47 identified volatile compounds included acids, aldehydes, esters, furan derivatives, ketones, alcohols, benzene and benzene derivatives, hydrocarbons, and terpenes, while the 37 identified nonvolatile components included amino acids, organic acids, and carbohydrates. The profiles of volatile and nonvolatile components generally differed significantly between obligatorily homofermentative/facultatively heterofermentative LAB and obligatorily heterofermentative LAB. The rice sample fermented by Lactobacillus sakei (RTCL16) was clearly differentiated from the other samples on principal component analysis (PCA) plots. The results of PCA revealed that the rice samples fermented by LABs could be distinguished according to microbial strains.

The changes of microbial community and flavor compound in the fermentation process of Chinese rice wine using Fagopyrum tataricum grain as feedstock

Chinese rice wine (CRW), a unique wine species, has a long history in China. Fagopyrum tataricum grain is a kind of high-quality grain with function in health care. The production of CRW wine with F. tataricum grain is beneficial to the development of new rice wine products. The flavor compounds and microorganisms in F. tataricum grain rice wine were studied. One hundred and seven volatile compounds (including 11 kinds of pyrazines that were rarely detected in wine) were detected and eight organic acids were measured. The microecological diversity in the fermentation process of F. tataricum rice wine was studied. It was found that Bacillus was the main bacterial genus, and the unclassfied_O_Saccharomycetales was the main fungi. Correlation analysis between microorganism and flavor compound shown there are 838 correlations. A total of 108 microbial genera maybe participate in the formation of flavor compounds. In addition, fourteen genera included unclassified_O_Saccharomycetales, Lactococcus, Pediococcus, Aspergillus, Cladosporium, Cochliobolus, Sporidiobolus, Pichia and Saccharomycopsis et al. were screened as functional significant microbiota and built correlation with flavor compounds. This work provides a perspective for bridging the gap between flavor compound and microbial community, and advances our understanding of mechanisms in F. tataricum rice wine fermentation.

Structural characterization of an acetolactate decarboxylase from Klebsiella pneumoniae

Acetolactate decarboxylase (ALDC) is a well-characterized anabolic enzyme involved with 3-hydroxy butanone (acetoin), an important physiological metabolite excreted by microbes. Although the enzyme is widely present in microorganisms, few atomic structures and functions of ALDC have been reported to date. Here we report the crystal structure of ALDC from Klebsiella pneumoniae KP (KpALDC). KpALDC crystallizes in space group P3₁21 with one monomer per asymmetric unit. Analytical ultracentrifugation data shows that KpALDC forms a stable dimer but can exist as a tetramer in solution. A Zn²⁺ ion is coordinated by three strictly-conserved histidines (His198, His200 and His211) and a conserved glutamate (Glu69), but the C-terminal tail that forms part of the active site in ALDC enzymes is disordered. A complex structure with ethane-1,2-diol shows a unusual mode of binding, whereby the ligand does not coordinate the Zn²⁺ ion. MicroScale Thermophoresis analysis shows that KpALDC binds Zn²⁺ ions, but no binding of Mg²⁺, Ca²⁺ and Mn²⁺ ions was detected.

Simultaneous biosynthesis of (R)-acetoin and ethylene glycol from D-xylose through in vitro metabolic engineering

(R)-acetoin is a four-carbon platform compound used as the precursor for synthesizing novel optically active materials. Ethylene glycol (EG) is a large-volume two-carbon commodity chemical used as the anti-freezing agent and building-block molecule for various polymers. Currently established microbial fermentation processes for converting monosaccharides to either (R)-acetoin or EG are plagued by the formation of undesirable by-products. We show here that a cell-free bioreaction scheme can generate enantiomerically pure acetoin and EG as co-products from biomass-derived D-xylose. The seven-step, ATP-free system included in situ cofactor regeneration and recruited enzymes from Escherichia coli W3110, Bacillus subtilis shaijiu 32 and Caulobacter crescentus CB 2. Optimized in vitro biocatalytic conditions generated 3.2 mM (R)-acetoin with stereoisomeric purity of 99.5% from 10 mM D-xylose at 30 °C and pH 7.5 after 24 h, with an initial (R)-acetoin productivity of 1.0 mM/h. Concomitantly, EG was produced at 5.5 mM, with an initial productivity of 1.7 mM/h. This in vitro biocatalytic platform illustrates the potential for production of multiple value-added biomolecules from biomass-based sugars with no ATP requirement.

Interspecific formation of the antimicrobial volatile schleiferon

Microorganisms release a plethora of volatile secondary metabolites. Up to now, it has been widely accepted that these volatile organic compounds are produced and emitted as a final product by a single organism e.g. a bacterial cell. We questioned this commonly assumed perspective and hypothesized that in diversely colonized microbial communities, bacterial cells can passively interact by emitting precursors which non-enzymatically react to form the active final compound. This hypothesis was inspired by the discovery of the bacterial metabolite schleiferon A. This bactericidal volatile compound is formed by a non-enzymatic reaction between acetoin and 2-phenylethylamine. Both precursors are released by Staphylococcus schleiferi cells. In order to provide evidence for our hypothesis that these precursors could also be released by bacterial cells of different species, we simultaneously but separately cultivated Serratia plymuthica 4Rx13 and Staphylococcus delphini 20771 which held responsible for only one precursor necessary for schleiferon A formation, respectively. By mixing their headspace, we demonstrated that these two species were able to deliver the active principle schleiferon A. Such a joint formation of a volatile secondary metabolite by different bacterial species has not been described yet. This highlights a new aspect of interpreting multispecies interactions in microbial communities as not only direct interactions between species might determine and influence the dynamics of the community. Events outside the cell could lead to the appearance of new compounds which could possess new community shaping properties.

2,3-Butanediol catabolism in Pseudomonas aeruginosa PAO1

2,3-Butanediol (2,3-BD) is a primary microbial metabolite that enhances the virulence of Pseudomonas aeruginosa and alters the lung microbiome. 2,3-BD exists in three stereoisomeric forms: (2R,3R)-2,3-BD, meso-2,3-BD and (2S,3S)-2,3-BD. In this study, we investigated whether and how P. aeruginosa PAO1 utilizes these 2,3-BD stereoisomers and showed that all three stereoisomers were transformed into acetoin by (2R,3R)-2,3-butanediol dehydrogenase (BDH) or (2S,3S)-2,3-BDH. Acetoin was cleaved to form acetyl-CoA and acetaldehyde by acetoin dehydrogenase enzyme system (AoDH ES). Genes encoding (2R,3R)-2,3-BDH, (2S,3S)-2,3-BDH and the E1 and E2 components of AoDH ES were identified as part of a new 2,3-BD utilization operon. In addition, the regulatory protein AcoR promoted the expression of this operon using acetaldehyde, a cleavage product of acetoin, as its direct effector. The results of this study elucidate the integrated catabolic role of 2,3-BD and may provide new insights in P. aeruginosa-related infections.

NMR-based metabolic profiling of urine, serum, fecal, and pancreatic tissue samples from the Ptf1a-Cre; LSL-KrasG12D transgenic mouse model of pancreatic cancer

Pancreatic cancer is the third leading cause of cancer deaths in the United States with more than 53,000 expected to be diagnosed with the disease in 2018. The median survival time after diagnosis is four to six months. The poor survival statistics are due in part to the fact that pancreatic cancer is typically asymptomatic until it reaches advanced stages of the disease. Although surgical resection provides the best chance of survival, pancreatic cancer is rarely detected when surgery is still possible due, in part, to lack of effective biomarkers for early detection. The goal of the research reported here was to determine if it was possible to identify metabolic biomarkers for detection of pre-cancerous pancreatic intraepithelial neoplasia (PanIN) that precede pancreatic adenocarcinoma. The transgenic Ptf1a-Cre; LSL-KrasG12D mouse strain was used as a model of pancreatic cancer progression. Nuclear magnetic resonance (NMR) spectroscopy was employed to compare metabolic profiles of urine, sera, fecal extracts, and pancreatic tissue extracts collected from control and study mice aged 5, 11, and 15 months, including 47 mice with tumors. We were able to identify the following potential biomarkers: decreased 3-indoxylsulfate, benzoate and citrate in urine, decreased glucose, choline, and lactate in blood, and decreased phenylalanine and benzoate and increased acetoin in fecal extracts. Potential biomarkers were validated by p-values, PLS-DA VIP scores, and accuracies based on area under ROC curve analyses. Essentially, all of the metabolic profiling changes could be explained as being associated with the consequences of bicarbonate wasting caused by a complete substitution of the normal pancreatic acinar tissue by tissue entirely composed of PanIN. Given the nature of the mouse model used here, our results indicate that it may be possible to use NMR-based metabolic profiling to identify biomarkers for detection of precancerous PanIN that immediately precede pancreatic cancer.

Effect of medium compositions on microbially mediated volatile organic compounds release profile

AIMS

To monitor temporal changes in the volatile organic compounds' (VOCs) profile generated by the metabolic activities of Pseudomonads in real time.

METHODS AND RESULTS

Three Pseudomonas strains were cultivated in Vogel's broth, supplemented with glucose (0·5 or 1%) and/or protein (egg white powder at 0 or 2%) at 25°C. Glucose or egg white protein contents influenced the VOCs' release profile for alcohols, carbonyls and sulphur derivatives. Increasing glucose content resulted in higher alcohol and ketone contents. Glucose showed a lower effect on the VOCs' release profile, mainly impacting on individual compounds, such as m/z 89 (3-methyl-1-butanol). In contrast, egg white protein enhanced production of VOCs such as m/z 75 (2-methyl-1-propanol) and m/z 63 (dimethyl sulphide) regardless of glucose level present in the medium. At the end of bacteria growth phase (54, 60 and 72 h), the fingerprint of VOCs was different from the early growth phase. Cells near to the end of their growth phase (54, 60 and 72 h) produced a distinctly different array of compounds compared to those produced in early growth phase, for example, cyclic compounds were detected in early growth phase, whereas sulphur derivatives were more common in late growth phase.

CONCLUSIONS

Pseudomonads-mediated VOCs' fingerprint as a response to varying growth conditions can be identified as latent biomarkers.

SIGNIFICANCE AND IMPACT OF THE STUDY

Understanding how microbially mediated VOCs' release profile responds to varying growth conditions can potentially be used as a rapid method for detecting microbial activities in controlled conditions such as food quality systems.

Identification of attractive blend for spotted wing drosophila, Drosophila suzukii, from apple juice

Drosophila suzukii, commonly known as the spotted wing drosophila (SWD), is an exotic fruit fly from Southeast Asia that was introduced to the temperate regions of North America and Europe in 2008. It attacks a wide variety of fruits and has become a devastating pest of soft-skinned fruit crops. Due to the rapid spread of SWD across the newly invaded continents, fresh fruit markets have a zero-tolerance policy regarding D. suzukii infestation. Specific and efficient D. suzukii detection tools are urgently needed so that farmers can deliver timely management interventions to meet market demands. Since SWD is known to be attracted to damaged and rotting fruits, headspace volatiles from fresh and fermented apple juices were collected and analyzed by gas chromatography-mass spectrometry. Special attention was given to the compounds produced and/or enriched during the fermentation process. After performing a series of laboataory and field tests, we identified a quinary blend, which is more efficient and selective for D. suzukii than the currently standard apple cider vinegar and commercially available SWD lure under field conditions. Identification of SWD attractant will help growers accurately detect D. suzukii adult infestations in orchards, thereby allowing for timely pest management interventions while reducing conventional insecticidal usage to protect our crops, environment, and ecosystem.

Metabolic interactions between dynamic bacterial subpopulations

Individual microbial species are known to occupy distinct metabolic niches within multi-species communities. However, it has remained largely unclear whether metabolic specialization can similarly occur within a clonal bacterial population. More specifically, it is not clear what functions such specialization could provide and how specialization could be coordinated dynamically. Here, we show that exponentially growing Bacillus subtilis cultures divide into distinct interacting metabolic subpopulations, including one population that produces acetate, and another population that differentially expresses metabolic genes for the production of acetoin, a pH-neutral storage molecule. These subpopulations exhibit distinct growth rates and dynamic interconversion between states. Furthermore, acetate concentration influences the relative sizes of the different subpopulations. These results show that clonal populations can use metabolic specialization to control the environment through a process of dynamic, environmentally-sensitive state-switching.

The chemical reactions that occur within a living organism are collectively referred to as its metabolism. Many metabolic reactions produce byproducts that will poison the cells if they are not dealt with: fermenting bacteria, for example, release harmful organic acids and alcohols. How the bacteria respond to these toxins has been most studied at the level of entire microbial populations, meaning the activities of individual cells are effectively “averaged” together. Yet, even two bacteria with the same genes and living in the same environment can behave in different ways. This raises the question: do bacterial populations specialize into distinct subpopulations that play distinct roles when dealing with metabolic products, or do all cells in the community act in unison?

Rosenthal et al. set out to answer this question for a community of Bacillus subtilis, a bacterium that is commonly studied in the laboratory and used for the industrial production of enzymes. The analysis focused on genes involved in fundamental metabolic processes, known as the TCA cycle, which the bacteria use to generate energy and build biomass. The experiments revealed that, even when all the cells are genetically identical, different Bacillus subtilis cells do indeed specialize into metabolic subpopulations with distinct growth rates.

Time-lapse movies of bacteria that made fluorescent markers of different colors whenever certain metabolic genes became active showed cells switching different colors on and off, indicating that they switch between metabolic subpopulations. Further biochemical studies and measures of gene activity revealed that the different subpopulations produce and release distinct metabolic products, including toxic byproducts. Notably, the release of these metabolites by one subpopulation appeared to activate other subpopulations within the community.

This example of cells specializing into unique interacting metabolic subpopulations provides insight into several fundamental issues in microbiology and beyond. It is relevant to evolutionary biologists, since the fact that fractions of the population can switch in and out of a metabolic state, instead of evolving into several inflexible specialists, may provide an evolutionary advantage in fluctuating natural environments by reducing the risk of extinction. It also has implications for industrial fermentation processes and metabolic engineering, and may help biotechnologists design more efficient ways to harness bacterial metabolism to produce useful products.

Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6

Plant-growth promotion has been linked to the Pseudomonas genus since the beginning of this research field. In this work, we mined the genome of an Argentinean isolate of the recently described species P. donghuensis. Strain SVBP6, isolated from bulk soil of an agricultural plot, showed a broad antifungal activity and several other plant-probiotic activities. As this species has been recently described, and it seems like some plant-growth promoting (PGP) traits do not belong to the classical pseudomonads toolbox, we decide to explore the SVBP6 genome via an bioinformatic approach. Genome inspection confirmed our previous in vitro results about genes involved in several probiotic activities. Other genetic traits possibly involved in survival of SVBP6 in highly competitive environments, such as rhizospheres, were found. Tn5 mutagenesis revealed that the antifungal activity against the soil pathogen Macrophomina phaseolina was dependent on a functional gacS gene, from the regulatory cascade Gac-Rsm, but it was not due to volatile compounds. Altogether, our genomic analyses and in vitro tests allowed the phylogenetic assignment and provided the first insights into probiotic properties of the first P. donghuensis isolate from the Americas.

Stereoisomers of the Bacterial Volatile Compound 2,3-Butanediol Differently Elicit Systemic Defense Responses of Pepper against Multiple Viruses in the Field

The volatile compound 2,3-butanediol, which is produced by certain strains of root-associated bacteria, consists of three stereoisomers, namely, two enantiomers (2R,3R- and 2S,3S-butanediol) and one meso compound (2R,3S-butanediol). The ability of 2,3-butanediol to induce plant resistance against pathogenic fungi and bacteria has been investigated; however, little is known about its effects on induced resistance against viruses in plants. To investigate the effects of 2,3-butanediol on plant systemic defense against viruses, we evaluated the disease control capacity of each of its three stereoisomers in pepper. Specifically, we investigated the optimal concentration of 2,3-butanediol to use for disease control against Cucumber mosaic virus and Tobacco mosaic virus in the greenhouse and examined the effects of drench application of these compounds in the field. In the field trial, treatment with 2R,3R-butanediol and 2R,3S-butanediol significantly reduced the incidence of naturally occurring viruses compared with 2S,3S-butanediol and control treatments. In addition, 2R,3R-butanediol treatment induced the expression of plant defense marker genes in the salicylic acid, jasmonic acid, and ethylene signaling pathways to levels similar to those of the benzothiadiazole-treated positive control. This study reports the first field trial showing that specific stereoisomers of 2,3-butanediol trigger plant immunity against multiple viruses.

Metabolic engineering of carbon overflow metabolism of Bacillus subtilis for improved N-acetyl-glucosamine production

Bacillus subtilis is widely used as cell factories for the production of important industrial biochemicals. Although many studies have demonstrated the effects of organic acidic byproducts, such as acetate, on microbial fermentation, little is known about the effects of blocking the neutral byproduct overflow, such as acetoin, on bioproduction. In this study, we focused on the influences of modulating overflow metabolism on the production of N-acetyl-d-glucosamine (GlcNAc) in engineered B. subtilis. We found that acetoin overflow competes with GlcNAc production, and blocking acetoin overflow increased GlcNAc titer and yield by 1.38- and 1.39-fold, reaching 48.9 g/L and 0.32 g GlcNAc/g glucose, respectively. Further blocking acetate overflow inhibited cell growth and GlcNAc production may be induced by inhibiting glucose uptake. Taken together, our results show that blocking acetoin overflow is a promising strategy for enhancing GlcNAc production. The strategies developed in this work may be useful for engineering strains of B. subtilis for producing other important biochemicals.

Deacidification of grass silage press juice by continuous production of acetoin from its lactate via an immobilized enzymatic reaction cascade

An immobilized enzymatic reaction cascade was designed and optimized for the deacidification of grass silage press juice (SPJ), thus facilitating the production of bio-based chemicals. The cascade involves a three-step process using four enzymes immobilized in a Ca-alginate gel and uses lactic acid to form acetoin, a value-added product. The reaction is performed with a continuous, pH-dependent substrate feed under oxygenation. With titrated lactic acid yields of up to 91% and reaction times of ca. 6h was achieved. Using SPJ as titrant yields of 49% were obtained within 6h. In this deacidification process, with acetoin one value-added bio-based chemical is produced while simultaneously the remaining press juice can be used in applications that require a higher pH. Such, this system can be applied in a multi-product biorefinery concept to take full advantage of nutrient-rich SPJ, which is a widely available and easily storable renewable resource.

Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease

Lipoylation is a rare, but highly conserved lysine posttranslational modification. To date, it is known to occur on only four multimeric metabolic enzymes in mammals, yet these proteins are staples in the core metabolic landscape. The dysregulation of these mitochondrial proteins is linked to a range of human metabolic disorders. Perhaps most striking is that lipoylation itself, the proteins that add or remove the modification, as well as the proteins it decorates are all evolutionarily conserved from bacteria to humans, highlighting the importance of this essential cofactor. Here, we discuss the biological significance of protein lipoylation, the importance of understanding its regulation in health and disease states, and the advances in mass spectrometry-based proteomic technologies that can aid these studies.

Conversion of cellulose and hemicellulose of biomass simultaneously to acetoin by thermophilic simultaneous saccharification and fermentation

BACKGROUND

Acetoin (3-hydroxy-2-butanone), the precursor of biofuel 2,3-butanediol, is an important bio-based platform chemical with wide applications. Fermenting the low-cost and renewable plant biomass is undoubtedly a promising strategy for acetoin production. Isothermal simultaneous saccharification and fermentation (SSF) is regarded as an efficient method for bioconversion of lignocellulosic biomass, in which the temperature optima fitting for both lignocellulose-degrading enzymes and microbial strains.

RESULTS

A thermotolerant (up to 52 °C) acetoin producer Bacillus subtilis IPE5-4 which simultaneously consumed glucose and xylose was isolated and identified. By compound mutagenesis, the mutant IPE5-4-UD-4 with higher acetoin productivity was selected. When fermenting at 50 °C in a 5-L bioreactor using glucose as the feedstock by strain IPE5-4-UD-4, the acetoin concentration reached 28.83 ± 0.91 g L^-1 with the acetoin yield and productivity of 0.34 g g^-1 glucose and 0.60 g L^-1 h^-1, respectively. Furthermore, an optimized and thermophilic SSF process operating at 50 °C was conducted for acetoin production from alkali-pretreated corncob (APC). An acetoin concentration of 12.55 ± 0.28 g L^-1 was achieved by strain IPE5-4-UD-4 in shake flask SSF, with the acetoin yield and productivity of 0.25 g g^-1 APC and 0.17 g L^-1 h^-1. Meanwhile, the utilization of cellulose and hemicellulose in the SSF approach reached 96.34 and 93.29%, respectively. When further fermented at 50 °C in a 5-L bioreactor, the concentration of acetoin reached the maximum of 22.76 ± 1.16 g L^-1, with the acetoin yield and productivity reaching, respectively, 0.46 g g^-1 APC and 0.38 g L^-1 h^-1. This was by far the highest acetoin yield in SSF from lignocellulosic biomass.

CONCLUSIONS

This thermophilic SSF process provided an efficient and economical route for acetoin production from lignocellulosic biomass at ideal temperature for both enzymatic hydrolysis and microbial fermentation.

Volatiles emitted by Bacillus sp. BCT9 act as growth modulating agents on Lactuca sativa seedlings

Chemical products are applied during horticulture to increase food production, but the environmental problems resulting from these applications have led to a search for more sustainable products. Volatile organic compounds (VOCs) demonstrating plant growth promoter (PGP) activity released by bacterial species have emerged as alternatives, but their effects on Lactuca sativa growth are unknown. In this study, VOCs released by Bacillus sp. BCT9 cultures grown in different media (Methyl Red & Voges Proskauer, Murashige & Skoog and nutrient media) at concentrations of 0.1, 0.2, 0.5 and 0.7 (measured as the absorbance, λ=600nm) were tested to evaluate their activity as growth inducers of L. sativa after 10days of exposure. Lower concentrations of BCT9 increased root length, and higher concentrations induced shoot length and lateral root length. The dry weight and number of lateral roots increased similarly, independent of concentration, for VOCs produced in all culture media. BCT9 cultures grown in Methyl Red & Voges Proskauer medium as bioactive compounds with or without lanolin. These VOCs increased shoot length, root length and dry weight at low concentrations, independent of the presence of lanolin. Lateral root length increased with the application of 2-nonanone (50ppm) and 2-undecanone (0.05ppm). Based on these results, the use of bioactive volatiles as growth inducers of horticultural species represents an alternative or complementary strategy.

Inflammatory bowel disease and patterns of volatile organic compounds in the exhaled breath of children: A case-control study using Ion Molecule Reaction-Mass Spectrometry

Inflammatory bowel diseases (IBD) profoundly affect quality of life and have been gradually increasing in incidence, prevalence and severity in many areas of the world, and in children in particular. Patients with suspected IBD require careful history and clinical examination, while definitive diagnosis relies on endoscopic and histological findings. The aim of the present study was to investigate whether the alveolar air of pediatric patients with IBD presents a specific volatile organic compounds’ (VOCs) pattern when compared to controls. Patients 10–17 years of age, were divided into four groups: Crohn’s disease (CD), ulcerative colitis (UC), controls with gastrointestinal symptomatology, and surgical controls with no evidence of gastrointestinal problems. Alveolar breath was analyzed by ion molecule reaction mass spectrometry. Four models were built starting from 81 molecules plus the age of subjects as independent variables, adopting a penalizing LASSO logistic regression approach: 1) IBDs vs. controls, finally based on 18 VOCs plus age (sensitivity = 95%, specificity = 69%, AUC = 0.925); 2) CD vs. UC, finally based on 13 VOCs plus age (sensitivity = 94%, specificity = 76%, AUC = 0.934); 3) IBDs vs. gastroenterological controls, finally based on 15 VOCs plus age (sensitivity = 94%, specificity = 65%, AUC = 0.918); 4) IBDs vs. controls, built starting from the 21 directly or indirectly calibrated molecules only, and finally based on 12 VOCs plus age (sensitivity = 94%, specificity = 71%, AUC = 0.888). The molecules identified by the models were carefully studied in relation to the concerned outcomes. This study, with the creation of models based on VOCs profiles, precise instrumentation and advanced statistical methods, can contribute to the development of new non–invasive, fast and relatively inexpensive diagnostic tools, with high sensitivity and specificity. It also represents a crucial step towards gaining further insights on the etiology of IBD through the analysis of specific molecules which are the expression of the particular metabolism that characterizes these patients.

Genome Comparison of Pseudomonas fluorescens UM270 with Related Fluorescent Strains Unveils Genes Involved in Rhizosphere Competence and Colonization

Pseudomonas fluorescens UM270 is a rhizosphere-colonizing bacterium that produces multiple diffusible and volatile compounds involved in plant growth-promoting activities. Strain UM270 exhibits excellent biocontrol capacities against diverse fungal pathogens.In a previous study, the general UM270 genome characteristics were published. Here, we report a deeper analysis of its gene content and compare it to other P. fluorescens strains to unveil the genetic elements that might explain UM270's great colonizing and plant growth-promoting capabilities. Our analyses found high variation in genome size and gene content among the eight Pseudomonas genomes analyzed (strains UM270, Pf0-1, A506, F113, SBW25, PICF-7, UK4 and UW4). A core genome of 3,039 coding DNA sequences (CDSs) was determined, with 599 CDSs present only in the UM270 genome. From these unique UM270 genes, a set of 192 CDSs was found to be involved in signaling, rhizosphere colonization and competence, highlighted as important traits to achieve an effective biocontrol and plant growth promotion.

Hydroxy-pentanones production by Bacillus sp. H15-1 and its complete genome sequence

Acyloins are useful organic compounds with reactive adjacent hydroxyl group and carbonyl group. Current research is usually constrained to acetoin (i.e. 3-hydroxy-2-butanone) and the biological production of other acyloins was scarcely reported. In this study, two hydroxy-pentanone metabolites (3-hydroxy-2-pentanone and 2-hydroxy-3-pentanone) of Bacillus sp. H15-1 were identified by gas chromatography-mass spectrometry and authentic standards. Then the complete genome of this strain was sequenced and de novo assembled to a single circular chromosome of 4,162,101bp with a guanine-cytosine content of 46.3%, but no special genes were found for the biosynthesis of the hydroxy-pentanones. Since hydroxy-pentanones are the homologues of acetoin, the two genes alsD and alsS (encoding α-acetolactate decarboxylase and α-acetolactate synthase, respectively) responsible for acetoin formation in this strain were respectively expressed in Escherichia coli. The purified enzymes were found to be capable of transforming pyruvate and 2-oxobutanoate to the two hydroxy-pentanones. This study extends the knowledge on the biosynthesis of acyloins and provides helpful information for further utilizing Bacillus sp. H15-1 as a source of valuable acyloins.

Mass spectrometric techniques for the analysis of volatile organic compounds emitted from bacteria

Bacteria are the main cause of many human diseases. Typical bacterial identification methods, for example culture-based, serological and genetic methods, are time-consuming, delaying the potential for an early and accurate diagnosis and the appropriate subsequent treatment. Nevertheless, there is a stringent need for in situ tests that are rapid, noninvasive and sensitive, which will greatly facilitate timely treatment of the patients. This review article presents volatile organic metabolites emitted from various micro-organism strains responsible for common bacterial infections in humans. Additionally, the manuscript shows the application of different analytical techniques for fast bacterial identification. Details of these techniques are given, which focuses on their advantages and drawbacks in using for volatile organic components analysis.

A thermophilic cell-free cascade enzymatic reaction for acetoin synthesis from pyruvate

Acetoin (3-hydroxy-2-butanone) is an important bio-based platform chemical with wide applications. In vitro enzyme catalysed synthesis exhibits great feasibility in the production of chemicals with high purity. In the present work, a synthetic pathway involving a two-step continuous reaction was constructed in vitro for acetoin production from pyruvate at improved temperature. Thermostable candidates, acetolactate synthase (coAHASL1 and coAHASL2 from Caldicellulosiruptor owensensis OL) and α-acetolactate decarboxylase (bsALDC from Bacillus subtilis IPE5-4) were cloned, heterologously expressed, and characterized. All the enzymes showed maximum activities at 65–70 °C and pH of 6.5. Enzyme kinetics analysis showed that coAHASL1 had a higher activity but lower affinity against pyruvate than that of coAHASL2. In addition, the activities of coAHASL1 and bsALDC were promoted by Mn²⁺ and NADPH. The cascade enzymatic reaction was optimized by using coAHASL1 and bsALDC based on their kinetic properties. Under optimal conditions, a maximum concentration of 3.36 ± 0.26 mM acetoin was produced from 10 mM pyruvate after reaction for 24 h at 65 °C. The productivity of acetoin was 0.14 mM h⁻¹, and the yield was 67.80% compared with the theoretical value. The results confirmed the feasibility of synthesis of acetoin from pyruvate with a cell-free enzyme catalysed system at improved temperature.

Selection of an endogenous 2,3-butanediol pathway in Escherichia coli by fermentative redox balance

Fermentative redox balance has long been utilized as a metabolic evolution platform to improve efficiency of NADH-dependent pathways. However, such system relies on the complete recycling of NADH and may become limited when the target pathway results in excess NADH stoichiometrically. In this study, endogenous capability of Escherichia coli for 2,3-butanediol (2,3-BD) synthesis was explored using the anaerobic selection platform based on redox balance. To address the issue of NADH excess associated with the 2,3-BD pathway, we devised a substrate-decoupled system where a pathway intermediate is externally supplied in addition to the carbon source to decouple NADH recycling ratio from the intrinsic pathway stoichiometry. In this case, feeding of the 2,3-BD precursor acetoin effectively restored anaerobic growth of the mixed-acid fermentation mutant that remained otherwise inhibited even in the presence of a functional 2,3-BD pathway. Using established 2,3-BD dehydrogenases as model enzyme, we verified that the redox-based selection system is responsive to NADPH-dependent reactions but with lower sensitivity. Based on this substrate-decoupled selection scheme, we successfully identified the glycerol/1,2-propanediol dehydrogenase (Ec-GldA) as the major enzyme responsible for the acetoin reducing activity (k_cat/K_m≈0.4mM^-1s^-1) observed in E. coli. Significant shift of 2,3-BD configuration upon withdrawal of the heterologous acetolactate decarboxylase revealed that the endogenous synthesis of acetoin occurs via diacetyl. Among the predicted diacetyl reductase in E. coli, Ec-UcpA displayed the most significant activity towards diacetyl reduction into acetoin (V_max≈6U/mg). The final strain demonstrated a meso-2,3-BD production titer of 3g/L without introduction of foreign genes. The substrate-decoupled selection system allows redox balance regardless of the pathway stoichiometry thus enables segmented optimization of different reductive pathways through enzyme bioprospecting and metabolic evolution.

Growth promotion of Lactuca sativa in response to volatile organic compounds emitted from diverse bacterial species

Agrochemicals are currently used in horticulture to increase crop production. Nevertheless, their indiscriminate use is a relevant issue for environmental and legal aspects. Alternative tools for reducing fertilizers and synthetic phytohormones are being investigated, such as the use of volatile organic compounds (VOCs) as growth inducers. Some soil bacteria, such as Pseudomonas and Bacillus, stimulate Arabidopsis and tobacco growth by releasing VOCs, but their effects on vegetables have not been investigated. Lactuca sativa was used as model vegetable to investigate bacterial VOCs as growth inducers. We selected 10 bacteria strains, belonging to Bacillus, Staphylococcus and Serratia genera that are able to produce 3-hydroxy-2-butanone (acetoin), a compound with proven growth promoting activity. Two-day old-seedlings of L. sativa were exposed to VOCs emitted by the selected bacteria grown in different media cultures for 7 days. The results showed that the VOCs released from the bacteria elicited an increase in the number of lateral roots, dry weight, root growth and shoot length, depending on the media used. Three Bacillus strains, BCT53, BCT9 and BCT4, were selected according to its their growth inducing capacity. The BCT9 strain elicited the greatest increases in dry weight and primary root length when L. sativa seedlings were subjected to a 10-day experiment. Finally, because acetoin only stimulated root growth, we suggest that other volatiles could be responsible for the growth promotion of L. sativa. In conclusion, our results strongly suggest that bacteria volatiles can be used as growth-inducers as alternative or complementary strategies for application in horticulture species.

Metabolic engineering of Serratia marcescens MG1 for enhanced production of (3R)-acetoin

Background

Optically pure acetoin (AC) is an important platform chemical which has been widely used to synthesize novel optically active α-hydroxyketone derivatives and liquid crystal composites.

Results

In this study, slaC and gldA encoding meso-2,3-butanediol dehydrogenase (meso-2,3-BDH) and glycerol dehydrogenase (GDH), respectively, in S. marcescens MG1 were knocked out to block the conversion from AC to 2,3-butanediol (2,3-BD). The resulting strain MG14 was found to produce a large amount of optically pure (3R)-AC with a little 2,3-BD, indicating that another enzyme responsible for 2,3-BD formation except meso-2,3-BDH and GDH existed in the strain MG1. Furthermore, SlaR protein, a transcriptional activator of AC cluster, was overexpressed using P_C promoter in the strain MG14, leading to enhancement of the (3R)-AC yield by 29.91%. The recombinant strain with overexpression of SlaR, designated as S. marcescens MG15, was used to perform medium optimization for improving (3R)-AC production.

Conclusion

Under the optimized conditions, 39.91 ± 1.35 g/l (3R)-AC was produced by strain MG15 with the productivity of 1.11 g/l h and the conversion rate of 80.13%.

Strain- and Substrate-Dependent Redox Mediator and Electricity Production by Pseudomonas aeruginosa

Pseudomonas aeruginosa is an important, thriving member of microbial communities of microbial bioelectrochemical systems (BES) through the production of versatile phenazine redox mediators. Pure culture experiments with a model strain revealed synergistic interactions of P. aeruginosa with fermenting microorganisms whereby the synergism was mediated through the shared fermentation product 2,3-butanediol. Our work here shows that the behavior and efficiency of P. aeruginosa in mediated current production is strongly dependent on the strain of P. aeruginosa We compared levels of phenazine production by the previously investigated model strain P. aeruginosa PA14, the alternative model strain P. aeruginosa PAO1, and the BES isolate Pseudomonas sp. strain KRP1 with glucose and the fermentation products 2,3-butanediol and ethanol as carbon substrates. We found significant differences in substrate-dependent phenazine production and resulting anodic current generation for the three strains, with the BES isolate KRP1 being overall the best current producer and showing the highest electrochemical activity with glucose as a substrate (19 μA cm(-2) with ∼150 μg ml(-1) phenazine carboxylic acid as a redox mediator). Surprisingly, P. aeruginosa PAO1 showed very low phenazine production and electrochemical activity under all tested conditions.

IMPORTANCE

Microbial fuel cells and other microbial bioelectrochemical systems hold great promise for environmental technologies such as wastewater treatment and bioremediation. While there is much emphasis on the development of materials and devices to realize such systems, the investigation and a deeper understanding of the underlying microbiology and ecology are lagging behind. Physiological investigations focus on microorganisms exhibiting direct electron transfer in pure culture systems. Meanwhile, mediated electron transfer with natural redox compounds produced by, for example, Pseudomonas aeruginosa might enable an entire microbial community to access a solid electrode as an alternative electron acceptor. To better understand the ecological relationships between mediator producers and mediator utilizers, we here present a comparison of the phenazine-dependent electroactivities of three Pseudomonas strains. This work forms the foundation for more complex coculture investigations of mediated electron transfer in microbial fuel cells.

Building Bridges: Biocatalytic C-C-Bond Formation toward Multifunctional Products

Carbon-carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. The review gives a selection of biocatalytic C-C-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. In most cases, the reactions lead to products functionalized at the site of C-C-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow to decorate aromatic and heteroaromatic molecules. Furthermore, examples for cyclization of (non)natural precursors leading to saturated carbocycles are given as well as the stereoselective cyclopropanation of olefins affording cyclopropanes. Although many tools are already available, recent research also makes it clear that nature provides an even broader set of enzymes to perform specific C-C coupling reactions. The possibilities are without limit; however, a big library of variants for different types of reactions is required to have the specific enzyme for a desired specific (stereoselective) reaction at hand.

Biotypes analysis of Corynebacterium glutamicum growing in dicarboxylic acids demonstrates the existence of industrially-relevant intra-species variations

Production enhancement of industrial microbial products or strains has been traditionally tackled by mutagenesis with chemical methods, irradiation or genetic manipulation. However, the final yield increase must go hand in hand with the resistance increasing against the usual inherent toxicity of the final products. Few studies have been carried out on resistance improvement and even fewer on the initial selection of naturally-generated biotypes, which could decrease the artificial mutagenesis. This fact is vital in the case of GRAS microorganisms as Corynebacterium glutamicum involved in food, feed and cosmetics production. The characteristic wide diversity and plasticity in terms of their genetic material of Actinobacteria eases the biotypes generation. Thus, differences in morphology, glutamate and lysine production and growth in media supplemented with dicarboxylic acids were analysed in four biotypes of C. glutamicum ATCC 13032. A 2D-DIGE analysis of these biotypes growing with itaconic acid allowed us to define their differences. Thus, an optimized central metabolism and better protection against the generated stress conditions present the CgL biotype as a suitable platform for production of itaconic acid, which is used as a building block (e.g.: acrylic plastic). This analysis highlights the preliminary biotypes screening as a way to reach optimal industrial productions.

Impact of a Bacterial Volatile 2,3-Butanediol on Bacillus subtilis Rhizosphere Robustness

Volatile compounds, such as short chain alcohols, acetoin, and 2,3-butanediol, produced by certain strains of root-associated bacteria (rhizobacteria) elicit induced systemic resistance in plants. The effects of bacterial volatile compounds (BVCs) on plant and fungal growth have been extensively studied; however, the impact of bacterial BVCs on bacterial growth remains poorly understood. In this study the effects of a well-characterized bacterial volatile, 2,3-butanediol, produced by the rhizobacterium Bacillus subtilis, were examined in the rhizosphere. The nature of 2,3-butanediol on bacterial cells was assessed, and the effect of the molecule on root colonization was also determined. Pepper roots were inoculated with three B. subtilis strains: the wild type, a 2,3-butanediol overexpressor, and a 2,3-butanediol null mutant. The B. subtilis null strain was the first to be eliminated in the rhizosphere, followed by the wild-type strain. The overexpressor mutant was maintained at roots for the duration of the experiment. Rhizosphere colonization by a saprophytic fungus declined from 14 days post-inoculation in roots treated with the B. subtilis overexpressor strain. Next, exudates from roots exposed to 2,3-butanediol were assessed for their impact on fungal and bacterial growth in vitro. Exudates from plant roots pre-treated with the 2,3-butanediol overexpressor were used to challenge various microorganisms. Growth was inhibited in a saprophytic fungus (Trichoderma sp.), the 2,3-butanediol null B. subtilis strain, and a soil-borne pathogen, Ralstonia solanacearum. Direct application of 2,3-butanediol to pepper roots, followed by exposure to R. solanacearum, induced expression of Pathogenesis-Related (PR) genes such as CaPR2, CaSAR8.2, and CaPAL. These results indicate that 2,3-butanediol triggers the secretion of root exudates that modulate soil fungi and rhizosphere bacteria. These data broaden our knowledge regarding bacterial volatiles in the rhizosphere and their roles in bacterial fitness and as important inducers of plant defenses.