Acetoin production enhanced by manipulating carbon flux in a newly isolated Bacillus amyloliquefaciens

Bacillus sp. as a microbial cell factory: Advancements and future prospects

Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently using cheap carbon sources and secrete a variety of useful substances, which are widely used in food, pharmaceutical, agricultural and environmental industries. At the same time, Bacillus sp. is also recognized as a safe genus with a relatively clear genetic background, which is conducive to the industrial production of target metabolites. In this review, we discuss the reasons why Bacillus sp. has been so extensively studied and summarize its advances in systems and synthetic biology, engineering strategies to improve microbial cell properties, and industrial applications in several metabolic engineering applications. Finally, we present the current challenges and possible solutions to provide a reliable basis for Bacillus sp. as a microbial cell factory.

Recent advances and prospects of Bacillus amyloliquefaciens as microbial cell factories: from rational design to industrial applications

Bacillus amyloliquefaciens is one of the most characterized Gram-positive bacteria. This species has unique characteristics that are beneficial for industrial applications, including its utilization of: cheap carbon as a substrate, a transparent genetic background, and large-scale robustness in fermentation. Indeed, the productivity characteristics of B. amyloliquefaciens have been thoroughly analyzed and further optimized through systems biology and synthetic biology techniques. Following the analysis of multiple engineering design strategies, B. amyloliquefaciens is now considered an efficient cell factory capable of producing large quantities of multiple products from various raw materials. In this review, we discuss the significant potential advantages offered by B. amyloliquefaciens as a platform for metabolic engineering and industrial applications. In addition, we systematically summarize the recent laboratory research and industrial application of B. amyloliquefaciens, including: relevant advances in systems and synthetic biology, various strategies adopted to improve the cellular performances of synthetic chemicals, as well as the latest progress in the synthesis of certain important products by B. amyloliquefaciens. Finally, we propose the current challenges and essential strategies to usher in an era of broader B. amyloliquefaciens use as microbial cell factories.

Enzymes and pathways in microbial production of 2,3-butanediol and 3-acetoin isomers

2,3-Butanediol (BD) and acetoin (AC) are products of the non-oxidative metabolism of microorganisms, presenting industrial importance due to their wide range of applications and high market value. Their optical isomers have particular applications, justifying the efforts on the selective bioproduction. Each microorganism produces different isomer mixtures, as a consequence of having different butanediol dehydrogenase (BDH) enzymes. However, the whole scene of the isomer bioproduction, considering the several enzymes and conditions, has not been completely elucidated. Here we show the BDH classification as R, S or meso by bioinformatics analysis uncovering the details of the isomers production. The BDH was compared to diacetyl reductases (DAR) and the new enoyl reductases (ER). We observed that R-BDH is the most singular BDH, while meso and S-BDHs are similar and may be better distinguished through their stereo-selective triad. DAR and ER showed distinct stereo-triads from those described for BDHs, agreeing with kinetic data from the literature and our phylogenetic analysis. The ER family probably has meso-BDH like activity as already demonstrated for a single sequence from this group. These results are of great relevance, as they organize BD producing enzymes, to our known, never shown before in the literature. This review also brings attention to nontraditional enzymes/pathways that can be involved with BD/AC synthesis, as well as oxygen conditions that may lead to the differential production of their isomers. Together, this information can provide helpful orientation for future studies in the field of BD/AC biological production, thus contributing to achieve their production on an industrial scale.

Metabolic Engineering of Zymomonas mobilis for Acetoin Production by Carbon Redistribution and Cofactor Balance

Biorefinery to produce value-added biochemicals offers a promising alternative to meet our sustainable energy and environmental goals. Acetoin is widely used in the food and cosmetic industries as taste and fragrance enhancer. The generally regarded as safe (GRAS) bacterium Zymomonas mobilis produces acetoin as an extracellular product under aerobic conditions. In this study, metabolic engineering strategies were applied including redistributing the carbon flux to acetoin and manipulating the NADH levels. To improve the acetoin level, a heterologous acetoin pathway was first introduced into Z. mobilis, which contained genes encoding acetolactate synthase (Als) and acetolactate decarboxylase (AldC) driven by a strong native promoter Pgap. Then a gene encoding water-forming NADH oxidase (NoxE) was introduced for NADH cofactor balance. The recombinant Z. mobilis strain containing both an artificial acetoin operon and the noxE greatly enhanced acetoin production with maximum titer reaching 8.8 g/L and the productivity of 0.34 g∙L−1∙h−1. In addition, the strategies to delete ndh gene for redox balance by native I-F CRISPR-Cas system and to redirect carbon from ethanol production to acetoin biosynthesis through a dcas12a-based CRISPRi system targeting pdc gene laid a foundation to help construct an acetoin producer in the future. This study thus provides an informative strategy and method to harness the NADH levels for biorefinery and synthetic biology studies in Z. mobilis.

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.

Relationship between lipopeptide biosurfactant and primary metabolite production by Bacillus strains in solid-state and submerged fermentation

The relationship between lipopeptide and primary metabolite production by Bacillus spp. in solid-state fermentation (SSF) and submerged fermentation (SmF) was evaluated. Four wild-type strains and one mutant strain (unable to develop biofilm) were assessed in SSF and SmF, using a defined medium and polyurethane foam as inert support for SSF. Strain ATCC 21,332 in SSF presented the highest lipopeptide production. The wild-type strains revealed higher lipopeptide and biomass production and lower synthesis of primary metabolites in SSF than in SmF. However, the mutant strain showed a slightly higher production of primary metabolites in SSF than in SmF. Carbon balance analysis showed that the carbon flux was mainly directed to lipopeptides in SSF, whereas in SmF, it was directed to the production of primary metabolites and the carbon flux to lipopeptides is inversely related to primary metabolites in both types of cultures.

Current Advances in Microbial Production of Acetoin and 2,3-Butanediol by Bacillus spp

The growing need for industrial production of bio-based acetoin and 2,3-butanediol (2,3-BD) is due to both environmental concerns, and their widespread use in the food, pharmaceutical, and chemical industries. Acetoin is a common spice added to many foods, but also a valuable reagent in many chemical syntheses. Similarly, 2,3-BD is an indispensable chemical on the platform in the production of synthetic rubber, printing inks, perfumes, antifreeze, and fuel additives. This state-of-the-art review focuses on representatives of the genus Bacillus as prospective producers of acetoin and 2,3-BD. They have the following important advantages: non-pathogenic nature, unpretentiousness to growing conditions, and the ability to utilize a huge number of substrates (glucose, sucrose, starch, cellulose, and inulin hydrolysates), sugars from the composition of lignocellulose (cellobiose, mannose, galactose, xylose, and arabinose), as well as waste glycerol. In addition, these strains can be improved by genetic engineering, and are amenable to process optimization. Bacillus spp. are among the best acetoin producers. They also synthesize 2,3-BD in titer and yield comparable to those of the pathogenic producers. However, Bacillus spp. show relatively lower productivity, which can be increased in the course of challenging future research.

iTRAQ-BASED Proteomic Analysis of the Mechanism of Fructose on Improving Fengycin Biosynthesis in Bacillus Amyloliquefaciens

Fengycin, as a lipopeptide produced by Bacillus subtilis, displays potent activity against filamentous fungi, including Aspergillus flavus and Soft-rot fungus, which exhibits a wide range of potential applications in food industries, agriculture, and medicine. To better clarify the regulatory mechanism of fructose on fengycin biosynthesis, the iTRAQ-based proteomic analysis was utilized to investigate the differentially expressed proteins of B. amyloliquefaciens fmb-60 cultivated in ML (without fructose) and MLF (with fructose) medium. The results indicated that a total of 811 proteins, including 248 proteins with differential expression levels (162 which were upregulated (fold > 2) and 86, which were downregulated (fold < 0.5) were detected, and most of the proteins are associated with cellular metabolism, biosynthesis, and biological regulation process. Moreover, the target genes’ relative expression was conducted using quantitative real-time PCR to validate the proteomic analysis results. Based on the results of proteome analysis, the supposed pathways of fructose enhancing fengycin biosynthesis in B. amyloliquefaciens fmb-60 can be summarized as improvement of the metabolic process, including cellular amino acid and amide, fatty acid biosynthesis, peptide and protein, nucleotide and nucleobase-containing compound, drug/toxin, cofactor, and vitamin; reinforcement of peptide/protein translation, modification, biological process, and response to a stimulus. In conclusion, this study represents a comprehensive and systematic investigation of the fructose mechanism on improving fengycin biosynthesis in B. amyloliquefaciens, which will provide a road map to facilitate the potential application of fengycin or its homolog in defending against filamentous fungi.

Volumetric oxygen transfer coefficient as fermentation control parameter to manipulate the production of either acetoin or D-2,3-butanediol using bakery waste

The formation of either acetoin or D-2,3-butanediol (D-BDO) by Bacillus amyloliquefaciens cultivated on bakery waste hydrolysates has been evaluated in bioreactor cultures by varying the volumetric oxygen transfer coefficient (k_La). The highest D-BDO production (55.2 g L^-1) was attained in batch fermentations with k_La value of 64 h^-1. Batch fermentations performed at 203 h^-1 led to the highest productivity (2.16 g L^-1h^-1) and acetoin production (47.4 g L^-1). The utilization of bakery waste hydrolysate in fed-batch cultures conducted at k_La of 110 h^-1 led to combined production of acetoin, meso-BDO and D-BDO (103.9 g L^-1). Higher k_La value (200 h^-1) resulted to 65.9 g L^-1 acetoin with 1.57 g L^-1h^-1 productivity. It has been demonstrated that the k_La value may divert the bacterial metabolism towards high acetoin or D-BDO production during fermentation carried out in crude bakery waste hydrolysates.

Highly Efficient 2,3-Butanediol Production by Bacillus licheniformis via Complex Optimization of Nutritional and Technological Parameters

2,3-Butanediol (2,3-BD) is a reagent with remarkable commercial use as a platform chemical in numerous industries. The present study aims to determine the capabilities of non-pathogenic and cellulolytic Bacillus licheniformis 24 as a 2,3-BD producer. By applying the Plackett–Burman design and response surface methodology through central composite design (CCD), a complex optimization of medium and process parameters was conducted. Thus, among ten studied factors of medium content, four components were evaluated with a significant positive effect on 2,3-BD formation. Their optimal values for 2,3-BD production (yeast extract, 13.38 g/L; tryptone, 6.41 g/L; K2HPO4, 4.2 g/L; MgSO4, 0.32 g/L), as well as the optimal temperature (37.8 °C), pH (6.23) and aeration rate (3.68 vvm) were predicted by CCD experiments and validated in a series of batch processes. In optimized batch fermentation of 200 g/L of glucose 91.23 g/L of 2,3-BD was obtained, with the overall productivity of 1.94 g/L/h and yield of 0.488 g/g. To reveal the maximum 2,3-BD tolerance of B. licheniformis 24, fed-batch fermentation was carried out. The obtained 138.8 g/L of 2,3-BD with a yield of 0.479 g/g and productivity of 1.16 g/L/h ranks the strain among the best 2,3-BD producers.

Prospects on bio-based 2,3-butanediol and acetoin production: Recent progress and advances

The bio-based platform chemicals 2,3-butanediol (BDO) and acetoin have various applications in chemical, cosmetics, food, agriculture, and pharmaceutical industries, whereas the derivatives of BDO could be used as fuel additives, polymer and synthetic rubber production. This review summarizes the novel technological developments in adapting genetic and metabolic engineering strategies for selection and construction of chassis strains for BDO and acetoin production. The valorization of renewable feedstocks and bioprocess development for the upstream and downstream stages of bio-based BDO and acetoin production are discussed. The techno-economic aspects evaluating the viability and industrial potential of bio-based BDO production are presented. The commercialization of bio-based BDO and acetoin production requires the utilization of crude renewable resources, the chassis strains with high fermentation production efficiencies and development of sustainable purification or conversion technologies.

Optimization of process variables for acetoin production in a bioreactor using Taguchi orthogonal array design

Microbial production of acetoin is eco-friendly and inexpensive when compared with its synthetic methods of production. In the present findings, bioproduction of acetoin in a typical bioreactor was discussed with a view to ascertain the seemingly comparative advantage of bioreactor system over shake flask, and more importantly, to confirm that corn steep liquor can indeed adequately be used as a replacement for other organic nitrogen sources. Taguchi design was statistically used to optimized the fermentation process which resulted in a 3-fold increase in molar yield (83%) corresponding to a six-fold increase in acetoin concentration (63.43 g/L), as compared to a similar study conducted in a shake flask. Although agitation rate was observed to be the most controlling, the bioreactor may underperform at agitation rate greater than 300 rpm. The optimum parameters for acetoin production in this study were 300 rpm agitation, 1.5 slpm aeration, 2 days fermentation time, and pH 6.5. The results show that the commercial production of acetoin can be envisioned using a biological approach that may be of economic advantage.

Conversion of Xylose from Birch Hemicellulose Hydrolysate to 2,3-Butanediol with Bacillus vallismortis

Biotechnologically produced 2,3-butanediol (2,3-BDO) is a potential starting material for industrial bulk chemicals, such as butadiene or methyl ethyl ketone, which are currently produced from fossil feedstocks. So far, the highest 2,3-BDO concentrations have been obtained with risk class 2 microorganisms and pure glucose as substrate. However, as glucose stays in competition to food and feed industries, a lot of effort has been done in the last years finding efficient alternative substrates. Thereby xylose from hydrolysed wood hemicelluloses is a promising substrate for the production of 2,3-BDO. The risk class 1 microorganism Bacillus vallismortis strain was identified as a very promising 2,3-BDO producer. The strain is able to utilize xylose almost in the same manner as glucose. B. vallismortis is less prone to common inhibiting compounds in lignocellulosic extracts/hydrolysates. When using a concentrated hemicellulose fraction from birch wood hydrolysate, which was produced with ultrafiltration and after which the acetate concentration was reduced, a yield of 0.43 g g−1 was achieved and the xylose consumption and the 2,3-BDO production is basically the same as using pure xylose.

Bioreactor production of 2,3-butanediol by Pantoea agglomerans using soybean hull acid hydrolysate as substrate

Production of 2,3-butanediol (2,3-BD) by Pantoea agglomerans strain BL1 was investigated using soybean hull hydrolysate as substrate in batch reactors. The cultivation media consisted of a mixture of xylose, arabinose, and glucose, obtained from the hemicellulosic fraction of the soybean hull biomass. We evaluated the influence of oxygen supply, pH control, and media supplementation on the growth kinetics of the microorganism and on 2,3-BD production. P. agglomerans BL1 was able to simultaneously metabolize all three monosaccharides present in the broth, with average conversions of 75% after 48 h of cultivation. The influence of aeration conditions employed demonstrated the mixed acid pathway of 2,3-BD formation by enterobacteria. Under fully aerated conditions (2 vvm of air), up to 14.02 g L-1 of 2.3-BD in 12 h of cultivation were produced, corresponding to yields of 0.53 g g-1 and a productivity of 1.17 g L-1 h-1, the best results achieved. These results suggest the production potential of 2,3-BD by P. agglomerans BL1, which has been recently isolated from an environmental consortium. The present work proposes a solution for the usage of the hemicellulosic fraction of agroindustry biomasses, carbohydrates whose utilization are not commonly addressed in bioprocess.

Engineering central pathways for industrial-level (3R)-acetoin biosynthesis in Corynebacterium glutamicum

BACKGROUND

Acetoin, especially the optically pure (3S)- or (3R)-enantiomer, is a high-value-added bio-based platform chemical and important potential pharmaceutical intermediate. Over the past decades, intense efforts have been devoted to the production of acetoin through green biotechniques. However, efficient and economical methods for the production of optically pure acetoin enantiomers are rarely reported. Previously, we systematically engineered the GRAS microorganism Corynebacterium glutamicum to efficiently produce (3R)-acetoin from glucose. Nevertheless, its yield and average productivity were still unsatisfactory for industrial bioprocesses.

RESULTS

In this study, cellular carbon fluxes in the acetoin producer CGR6 were further redirected toward acetoin synthesis using several metabolic engineering strategies, including blocking anaplerotic pathways, attenuating key genes of the TCA cycle and integrating additional copies of the alsSD operon into the genome. Among them, the combination of attenuation of citrate synthase and inactivation of phosphoenolpyruvate carboxylase showed a significant synergistic effect on acetoin production. Finally, the optimal engineered strain CGS11 produced a titer of 102.45 g/L acetoin with a yield of 0.419 g/g glucose at a rate of 1.86 g/L/h in a 5 L fermenter. The optical purity of the resulting (3R)-acetoin surpassed 95%.

CONCLUSION

To the best of our knowledge, this is the highest titer of highly enantiomerically enriched (3R)-acetoin, together with a competitive product yield and productivity, achieved in a simple, green processes without expensive additives or substrates. This process therefore opens the possibility to achieve easy, efficient, economical and environmentally-friendly production of (3R)-acetoin via microbial fermentation in the near future.

Metabolic Engineering of Bacillus licheniformis for Production of Acetoin

Acetoin is a potential platform compound for a variety of chemicals. Bacillus licheniformis MW3, a thermophilic and generally regarded as safe (GRAS) microorganism, can produce 2,3-butanediol with a high concentration, yield, and productivity. In this study, B. licheniformis MW3 was metabolic engineered for acetoin production. After deleting two 2,3-butanediol dehydrogenases encoding genes budC and gdh, an engineered strain B. licheniformis MW3 (ΔbudCΔgdh) was constructed. Using fed-batch fermentation of B. licheniformis MW3 (ΔbudCΔgdh), 64.2 g/L acetoin was produced at a productivity of 2.378 g/[L h] and a yield of 0.412 g/g from 156 g/L glucose in 27 h. The fermentation process exhibited rather high productivity and yield of acetoin, indicating that B. licheniformis MW3 (ΔbudCΔgdh) might be a promising acetoin producer.

Design of a high-efficiency synthetic system for l-asparaginase production in Bacillus subtilis

l-asparaginase has high application value in medicine and food industry, but the low yield limits its application. In this study, we designed a synthetic system in Bacillus subtilis to produce l-asparaginase by improving gene expression and optimizing the fermentation agitation speed. Gene expression was improved by respectively increasing transcription levels and translation speeds through screening promoters and RBS sequences. With the optimal promoter, P43, and the synthetic RBS sequence, the yield obtained in a shake flask was 371.87 U/mL, which was 2.09 times that with the original strain. To further enhance production in a 5-L fermenter, a multistage agitation speed control strategy was adopted, involving agitation at 600 rpm for the first 12 h, followed by a gradual increase in speed to 900 rpm, which resulted in the highest yield of l-asparaginase, 5321 U/mL, after 42 h of fermentation.

A Single-Plasmid Genome Editing System for Metabolic Engineering of Lactobacillus casei

Genome engineering of Lactobacillus casei, an important industrial microorganism for dairy fermented product, currently relies on inefficient and time-consuming double crossover events. In this study, we developed an easy-to-use genome engineering strategy for metabolic engineering of L. casei for acetoin production. Plasmid pMSP456-Cre, that contains prophage recombinase operon LCABL_13040-50-60 driven by the nisin-controlled inducible expression (NICE) system and the site-specific recombinase gene cre under the control of the promoter of the lactose operon from L. casei, was constructed. Using this plasmid, integration of a hicD3 gene linear donor cassette (up-lox66-cat-lox71-down) was catalyzed by the LCABL_13040-50-60 recombinase and the cat gene was excised by the Cre/lox system with an efficiency of 60%. To demonstrate this system for sequential and iterative knocking out genes in L. casei, another three genes (pflB, ldh and pdhC) related to acetoin production were deleted with the efficiencies of 60, 40, and 60%, respectively. The yielding quadruple mutant could produce a ∼18-fold higher amount of acetoin than the wild-type and converted 59.8% of glucose to acetoin in aerobic. Therefore, these results proved this simple genome engineering strategy have potential in metabolic engineering of L. casei for production of high value-added metabolites.

Production of acetoin from hydrothermally pretreated oil mesocarp fiber using metabolically engineered Escherichia coli in a bioreactor system

Acetoin is used in the biochemical, chemical and pharmaceutical industries. Several effective methods for acetoin production from petroleum-based substrates have been developed, but they all have an environmental impact and do not meet sustainability criteria. Here we describe a simple and efficient method for acetoin production from oil palm mesocarp fiber hydrolysate using engineered Escherichia coli. An optimization of culture conditions for acetoin production was carried out using reagent-grade chemicals. The final concentration reached 29.9gL^-1 with a theoretical yield of 79%. The optimal pretreatment conditions for preparing hydrolysate with higher sugar yields were then determined. When acetoin was produced using hydrolysate fortified with yeast extract, the theoretical yield reached 97% with an acetoin concentration of 15.5gL^-1. The acetoin productivity was 10-fold higher than that obtained using reagent-grade sugars. This approach makes use of a compromise strategy for effective utilization of oil palm biomass towards industrial application.

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.

Rational design of Meso-2,3-butanediol dehydrogenase by molecular dynamics simulation and experimental evaluations

Meso-2,3-butanediol dehydrogenase (meso-2,3-BDH) catalyzes NAD⁺ -dependent conversion of meso-2,3-butanediol to acetoin, a crucial external energy storage molecule in fermentive bacteria. In this study, the active tunnel of meso-2,3-BDH was identified. The two short α helixes positioned away from the α4-helix possibly expose the hydrophobic ligand-binding cavity, gating the exit of product and cofactor from the activity pocket. Further MM/GBSA-binding free energy analysis shows that Phe212 and Asn146 function as the key product-release sites. Site-directed mutagenesis experiments targeted to the sites show that the k_cat of Phe212Tyr is enhanced up to (4-8)-fold. The original activity of Asn146Gln is retained, but the activity of Asn146Ala mutation is lost. These results could provide helpful guidance on rational design of short-chain dehydrogenases/reductases.

Screening of novel bacteria for the 2,3-butanediol production

Biotechnologically produced 2,3-butanediol (2,3-BDO) is a potential starting material for industrial bulk chemicals such as butadiene or methyl ethyl ketone which are currently produced from fossil feedstocks. So far, the highest 2,3-BDO concentrations have been obtained with risk group 2 microorganisms. In this study, three risk group 1 microorganisms are presented that are so far unknown for an efficient production of 2,3-BDO. The strains Bacillus atrophaeus NRS-213, Bacillus mojavensis B-14698, and Bacillus vallismortis B-14891 were evaluated regarding their ability to produce high 2,3-BDO concentrations with a broad range of different carbon sources. A maximum 2,3-BDO concentration of 60.4 g/L was reached with the strain B. vallismortis B-14891 with an initial glucose concentration of 200 g/L within 55 h in a batch cultivation. Besides glucose, B. vallismortis B-14891 converts 14 different substrates that can be obtained from residual biomass sources to 2,3-BDO. Therefore B. vallismortis B-14891 is a promising candidate for the large-scale production of 2,3-BDO with low-cost substrates.

Production of Acetoin through Simultaneous Utilization of Glucose, Xylose, and Arabinose by Engineered Bacillus subtilis

Glucose, xylose and arabinose are the three most abundant monosaccharide found in lignocellulosic biomass. Effectively and simultaneously utilization of these sugars by microorganisms for production of the biofuels and bio-chemicals is essential toward directly fermentation of the lignocellulosic biomass. In our previous study, the recombinant Bacillus subtilis 168ARSRCPΔacoAΔbdhA strain was already shown to efficiently utilize xylose for production of acetoin, with a yield of 0.36 g/g xylose. In the current study, the Bacillus subtilis168ARSRCPΔacoAΔbdhA strain was further engineered to produce acetoin from a glucose, xylose, and arabinose mixtures. To accomplish this, the endogenous xylose transport protein AraE, the exogenous xylose isomerase gene xylA and the xylulokinase gene xylB from E. coli were co-overexpressed in the Bacillus subtilis 168ARSRCPΔacoAΔbdhA strain, which enabled the resulting strain, denoted ZB02, to simultaneously utilize glucose and xylose. Unexpectedly, the ZB02 strain could simultaneously utilize glucose and arabinose also. Further results indicated that the transcriptional inhibition of the arabinose transport protein gene araE was the main limiting factor for arabinose utilization in the presence of glucose. Additionally, the arabinose operon in B. subtilis could be activated by the addition of arabinose, even in the presence of glucose. Through fed-batch fermentation, strain ZB02 could simultaneously utilize glucose, xylose, and arabinose, with an average sugar consumption rate of 3.00 g/l/h and an average production of 62.2 g/l acetoin at a rate of 0.864 g/l/h. Finally, the strain produced 11.2 g/l acetoin from lignocellulosic hydrolysate (containing 20.6g/l glucose, 12.1 g/l xylose and 0.45 g/l arabinose) in flask cultivation, with an acetoin yield of 0.34 g/g total sugar. The result demonstrates that this strain has good potential for the utilization of lignocellulosic hydrolysate for production of acetoin.

Regulation of the NADH pool and NADH/NADPH ratio redistributes acetoin and 2,3-butanediol proportion in Bacillus subtilis

Bacillus subtilis produces acetoin as a major product along with several NADH-dependent byproducts, especially 2,3-butanediol. In this study, the down-regulation of the NADH pool and the redistribution of NADH/NADPH were targeted using external and genetic processes, as a means by which to redistribute the metabolic flux in favor of acetoin synthesis. First, it was found that the use of carbon sources of different oxidation states resulted in very different intracellular NADH/NAD(+) ratios that dictated the total process yield of acetoin. A mixture of glucose and gluconate as substrate produced a relatively low NADH/NAD(+) ratio, and resulted in an increase in acetoin production while byproducts significantly decreased. Metabolic engineering methods using glucose as a substrate could yield a similar effect. Acetoin production was significantly enhanced by overexpression of the oxidative pentose phosphate pathway: increased expression of glucose-6-phosphate dehydrogenase resulted in a decrease in the intracellular NADH/NADPH ratio (1.9-fold) and NADH/NAD(+) ratio (1.7-fold). In fed-batch culture the engineered strain yielded an acetoin concentration of 43.3 g L(-1) , while the production of 2,3-butanediol was only 1.7 g L(-1) . The concept of the manipulation of cofactor levels to redistribute carbon flux by external and genetic means as explored in this paper provides a novel strategy for improving industrial acetoin fermentation.

Engineering Bacillus licheniformis for the production of meso-2,3-butanediol

BACKGROUND

2,3-Butanediol (2,3-BD) can be used as a liquid fuel additive to replace petroleum oil, and as an important platform chemical in the pharmaceutical and plastic industries. Microbial production of 2,3-BD by Bacillus licheniformis presents potential advantages due to its GRAS status, but previous attempts to use this microorganism as a chassis strain resulted in the production of a mix of D-2,3-BD and meso-2,3-BD isomers.

RESULTS

The aim of this work was to develop an engineered strain of B. licheniformis suited to produce the high titers of the pure meso-2,3-BD isomer. Glycerol dehydrogenase (Gdh) was identified as the catalyst for D-2,3-BD biosynthesis from its precursor acetoin in B. licheniformis. The gdh gene was, therefore, deleted from the wild-type strain WX-02 to inhibit the flux of acetoin to D-2,3-BD biosynthesis. The acoR gene involved in acetoin degradation through AoDH ES was also deleted to provide adequate flux from acetoin towards meso-2,3-BD. By re-directing the carbon flux distribution, the double-deletion mutant WX-02ΔgdhΔacoR produced 28.2 g/L of meso-2,3-BD isomer with >99 % purity. The titer was 50 % higher than that of the wide type. A bench-scale fermentation by the double-deletion mutant was developed to further improve meso-2,3-BD production. In a fed-batch fermentation, meso-2,3-BD titer reached 98.0 g/L with a purity of >99.0 % and a productivity of 0.94 g/L-h.

CONCLUSIONS

This work demonstrates the potential of producing meso-2,3-BD with high titer and purity through metabolic engineering of B. licheniformis.

Regulation of extracellular oxidoreduction potential enhanced (R,R)-2,3-butanediol production by Paenibacillus polymyxa CJX518

Cellular redox status and oxygen availability influence the product formation. Herein, decreasing agitation speed or adding vitamin C (Vc) achieved the 2,3-BDL yield of 0.40 g g(-1) or 0.39 g g(-1)glucose under batch fermentation, respectively. To our knowledge, this is the highest 2,3-BDL yield reported so far for Paenibacillus polymyxa without adding acetic acid. The NADH/NAD(+) ratio and 2,3-BDL titer could be increased significantly by reducing the agitation speed or adding Vc, indicating that the enhancement of 2,3-BDL is closely associated with the adjustment of NADH/NAD(+) ratio. Especially, Vc addition elevated the 2,3-BDL titer from 43.66 g L(-1) to 71.71 g L(-1) within 54 h under fed-batch fermentation. This is the highest titer of 2,3-BDL so far reported for P. polymyxa from glucose fermentation. This work provides a new strategy to improve 2,3-BDL production and helps us to understand the responses of P. polymyxa to extracellular oxidoreduction potential.

Efficient whole-cell biocatalyst for acetoin production with NAD+ regeneration system through homologous co-expression of 2,3-butanediol dehydrogenase and NADH oxidase in engineered Bacillus subtilis

Acetoin (3-hydroxy-2-butanone), an extensively-used food spice and bio-based platform chemical, is usually produced by chemical synthesis methods. With increasingly requirement of food security and environmental protection, bio-fermentation of acetoin by microorganisms has a great promising market. However, through metabolic engineering strategies, the mixed acid-butanediol fermentation metabolizes a certain portion of substrate to the by-products of organic acids such as lactic acid and acetic acid, which causes energy cost and increases the difficulty of product purification in downstream processes. In this work, due to the high efficiency of enzymatic reaction and excellent selectivity, a strategy for efficiently converting 2,3-butandiol to acetoin using whole-cell biocatalyst by engineered Bacillus subtilis is proposed. In this process, NAD⁺ plays a significant role on 2,3-butanediol and acetoin distribution, so the NADH oxidase and 2,3-butanediol dehydrogenase both from B. subtilis are co-expressed in B. subtilis 168 to construct an NAD⁺ regeneration system, which forces dramatic decrease of the intracellular NADH concentration (1.6 fold) and NADH/NAD⁺ ratio (2.2 fold). By optimization of the enzymatic reaction and applying repeated batch conversion, the whole-cell biocatalyst efficiently produced 91.8 g/L acetoin with a productivity of 2.30 g/(L·h), which was the highest record ever reported by biocatalysis. This work indicated that manipulation of the intracellular cofactor levels was more effective than the strategy of enhancing enzyme activity, and the bioprocess for NAD⁺ regeneration may also be a useful way for improving the productivity of NAD⁺-dependent chemistry-based products.

Characterization of acetoin production in a budC gene disrupted mutant of Serratia marcescens G12

The 2,3-butanediol (2,3-BD) dehydrogenase gene budC of Serratia marcescens G12 was disrupted to construct the acetoin (AC) producing strain G12M. In shake-flask cultures, AC production was enhanced by increased concentrations of glucose or sodium acetate in G12M. In fed-batch fermentation, G12M produced 47.5 g/L AC along with 9.8 g/L 2,3-BD. The expression of the key enzymes for AC synthesis was further investigated. Alpha-acetolactate synthase gene budB decreased its expression significantly in G12M compared with G12. This probably explained the moderate AC production in G12M cultures. Additionally, overexpression of budB gene and α-acetolactate decarboxylase gene budA was conducted in G12M and no significant increase of AC was observed. The results suggested that intracellular AC accumulation might inhibit the expression of budB and budA gene and induce budC gene expression in G12M. Our analyses offered the bases for further genetic manipulations in improving AC production in microbial fermentations.

Enhancement of acetoin production in Candida glabrata by in silico-aided metabolic engineering

BACKGROUND

Acetoin is a promising chemical compound that can potentially serve as a high value-added platform for a broad range of applications. Many industrial biotechnological processes are moving towards the use of yeast as a platform. The multi-auxotrophic yeast, Candida glabrata, can accumulate a large amount of pyruvate, but produces only trace amounts of acetoin. Here, we attempted to engineer C. glabrata to redirect the carbon flux of pyruvate to increase acetoin production.

RESULTS

Based on an in silico strategy, a synthetic, composite metabolic pathway involving two distinct enzymes, acetolactate synthase (ALS) and acetolactate decarboxylase (ALDC), was constructed, leading to the accumulation of acetoin in C. glabrata. Further genetic modifications were introduced to increase the carbon flux of the heterologous pathway, increasing the production of acetoin to 2.08 g/L. Additionally, nicotinic acid was employed to regulate the intracellular NADH level, and a higher production of acetoin (3.67 g/L) was obtained at the expense of 2,3-butanediol production under conditions of a lower NADH/NAD+ ratio.

CONCLUSION

With the aid of in silico metabolic engineering and cofactor engineering, C. glabrata was designed and constructed to improve acetoin production.

Metabolic engineering of Candida glabrata for diacetyl production

In this study, Candida glabrata, an efficient pyruvate-producing strain, was metabolically engineered for the production of the food ingredient diacetyl. A diacetyl biosynthetic pathway was reconstructed based on genetic modifications and medium optimization. The former included (i) channeling carbon flux into the diacetyl biosynthetic pathway by amplification of acetolactate synthase, (ii) elimination of the branched pathway of α-acetolactate by deleting the ILV5 gene, and (iii) restriction of diacetyl degradation by deleting the BDH gene. The resultant strain showed an almost 1∶1 co-production of α-acetolactate and diacetyl (0.95 g L(-1)). Furthermore, addition of Fe3+ to the medium enhanced the conversion of α-acetolactate to diacetyl and resulted in a two-fold increase in diacetyl production (2.1 g L(-1)). In addition, increased carbon flux was further channeled into diacetyl biosynthetic pathway and a titer of 4.7 g L(-1) of diacetyl was achieved by altering the vitamin level in the flask culture. Thus, this study illustrates that C. glabrata could be tailored as an attractive platform for enhanced biosynthesis of beneficial products from pyruvate by metabolic engineering strategies.

Two-stage pH control strategy based on the pH preference of acetoin reductase regulates acetoin and 2,3-butanediol distribution in Bacillus subtilis

Acetoin reductase/2,3-butanediol dehydrogenase (AR/BDH), which catalyzes the interconversion between acetoin and 2,3-butanediol, plays an important role in distribution of the products pools. This work characterized the Bacillus subtilis AR/BDH for the first time. The enzyme showed very different pH preferences of pH 6.5 for reduction and pH 8.5 for oxidation. Based on these above results, a two-stage pH control strategy was optimized for acetoin production, in which the pH was controlled at 6.5 for quickly converting glucose to acetoin and 2,3-butanediol, and then 8.0 for reversely transforming 2,3-butanediol to acetoin. By over-expression of AR/BDH in the wild-type B. subtilis JNA 3-10 and applying fed-batch fermentation based on the two-stage pH control strategy, acetoin yield of B. subtilis was improved to a new record of 73.6 g/l, with the productivity of 0.77 g/(l·h). The molar yield of acetoin was improved from 57.5% to 83.5% and the ratio of acetoin/2,3-butanediol was switched from 2.7∶1 to 18.0∶1.

Engineering of carboligase activity reaction in Candida glabrata for acetoin production

Utilization of Candida glabrata overproducing pyruvate is a promising strategy for high-level acetoin production. Based on the known regulatory and metabolic information, acetaldehyde and thiamine were fed to identify the key nodes of carboligase activity reaction (CAR) pathway and provide a direction for engineering C. glabrata. Accordingly, alcohol dehydrogenase, acetaldehyde dehydrogenase, pyruvate decarboxylase, and butanediol dehydrogenase were selected to be manipulated for strengthening the CAR pathway. Following the rational metabolic engineering, the engineered strain exhibited increased acetoin biosynthesis (2.24 g/L). In addition, through in silico simulation and redox balance analysis, NADH was identified as the key factor restricting higher acetoin production. Correspondingly, after introduction of NADH oxidase, the final acetoin production was further increased to 7.33 g/L. By combining the rational metabolic engineering and cofactor engineering, the acetoin-producing C. glabrata was improved stepwise, opening a novel pathway for rational development of microorganisms for bioproduction.