Atomistic molecular dynamics simulation and COSMO-SAC approach for enhanced 1,3-propanediol extraction with imidazolium-based ionic liquids

CONTEXT

1,3-Propanediol (1,3-PDO) is a key chemical in various industries, including pharmaceuticals and material sciences, and is projected to see significant market growth. However, the current challenges in its downstream processing, particularly in terms of cost and efficiency, highlight the need for innovative solutions. Our study delves into using ionic liquids (ILs) as a potential alternative, aiming to address these critical separation challenges more sustainably and efficiently. In this study, we utilized molecular dynamics (MD) simulations and the COSMO-SAC to examine 1,3-propanediol (1,3-PDO) extraction using four imidazolium-based ionic liquids with 1-butyl-3-methylimidazolium [Bmim] cation and with different anions bis(pentafluoroethanesulfonyl)imide [NPF2]-, bis(trifluoromethylsulfonyl)imide [NTF2]-, thiocyanate [SCN]-, and trifluoromethanesulfonate [TFO]-. Molecular dynamics simulations, incorporating analysis of radial distribution functions (RDF) and spatial distribution functions (SDF), revealed that [Bmim][SCN] and [Bmim][TFO] exhibit enhanced interactions with 1,3-PDO. Notably, [Bmim][SCN] formed the most hydrogen bonds, averaging 1.639 per molecule, due to its coordinating [SCN]- anion. This was in contrast to the fewer hydrogen bonds formed by non-coordinating anions in [Bmim][NPF2] and [Bmim][NTF2]. In ternary systems, [Bmim][SCN] and [Bmim][TFO] demonstrated superior selectivity for 1,3-PDO extraction compared to the other ionic liquids, with selectivity values around 29. These findings, supported by COSMO-SAC predictive modeling, highlight the potential of [Bmim][SCN] as a promising candidate for 1,3-PDO extraction, emphasizing the importance of anion selection in optimizing ionic liquid properties for this application.

METHODS

In our study, we employed MD simulations, incorporating the OPLS-AA force field, and COSMO-SAC to investigate the extraction of 1,3-PDO using imidazolium-based ionic liquids: [Bmim][NTF2], [Bmim][NPF2], [Bmim][SCN], and [Bmim][TFO]. The MD simulations were conducted using LAMMPS software, focusing on elucidating the RDF, SDF, and hydrogen bonding. Analysis of the distribution coefficient (β) and selectivity (S) for the ternary mixture was also conducted. These aspects of the simulation were analyzed using TRAVIS and VMD software. Additionally, the COSMO-SAC model was employed to determine the activity coefficients of 1,3-PDO in the ionic liquids, with molecular optimization conducted using Gaussian16 and sigma profile calculations performed using COSMO-SAC.

Co-production of 1,3-propanediol and phage phiKpS2 from the glycerol fermentation by Klebsiella pneumoniae

As an alternative to antibiotics in response to antimicrobial-resistant infections, bacteriophages (phages) are garnering renewed interest in recent years. However, the massive preparation of phage is restricted using traditional pathogens as host cells, which incurs additional costs and contamination. In this study, an opportunistic pathogen, Klebsiella pneumoniae used to convert glycerol to 1,3-propanediol (1,3-PDO), was reused to prepare phage after fermentation. The phage infection showed that the fed-batch fermentation broth containing 71.6 g/L 1,3-PDO can be directly used for preparation of phage with a titer of 1 × 108 pfu/mL. Then, the two-step salting-out extraction was adopted to remove most impurities, e.g. acetic acid (93.5%), ethanol (91.5%) and cells (99.4%) at the first step, and obtain 1,3-PDO (56.6%) in the top phase as well as phage (97.4%) in the middle phase at the second step. This integrated process provides a cheap and environment-friendly manner for coproduction of 1,3-PDO and phage.

Selective Hydrogenation of Diethyl Malonate to 1,3-Propanediol Over Ga-Promoted Cu/SiO2 Catalysts With Enhanced Activity and Stability

Cu catalysts with different compositions and different Cu and promoter contents were prepared by precipitation-gel method and studied for the selective hydrogenation of syngas or biomass-based diethyl malonate (DEM) to valuable 1,3-propanediol (1,3-PDO). The Ga-promoted 70Cu6Ga/SiO2 catalyst was found to exhibit the highest catalytic performance, achieving 100 % DEM conversion and 76.6 % 1,3-PDO selectivity under reaction conditions of 160 °C and 8 MPa H2. The 70Cu6Ga/SiO2 bimetallic catalyst also presented obviously better stability than that of the monometallic 70Cu/SiO2 catalyst in a continuous flow reactor over 180 h time-on stream. Characterization results showed that the incorporation of Ga increased the interaction between Cu and Ga species, hindered the full reduction of Cu2+ species, and thus increased the proportion of Cu+ and the number of Lewis acidic sites on the catalyst surface. The synergistic effect between Cu0 and Cu+ enhanced the adsorption and activation of ester carbonyl groups and their subsequent hydrogenation, eventually contributed to the outstanding performances of the CuGa/SiO2 bimetallic catalysts.

Kinetics-based development of two-stage continuous fermentation of 1,3-propanediol from crude glycerol by Clostridium butyricum

BACKGROUND

Glycerol, as a by-product, mainly derives from the conversion of many crops to biodiesel, ethanol, and fatty ester. Its bioconversion to 1,3-propanediol (1,3-PDO) is an environmentally friendly method. Continuous fermentation has many striking merits over fed-batch and batch fermentation, such as high product concentration with easy feeding operation, long-term high productivity without frequent seed culture, and energy-intensive sterilization. However, it is usually difficult to harvest high product concentrations.

RESULTS

In this study, a three-stage continuous fermentation was firstly designed to produce 1,3-PDO from crude glycerol by Clostridium butyricum, in which the first stage fermentation was responsible for providing the excellent cells in a robust growth state, the second stage focused on promoting 1,3-PDO production, and the third stage aimed to further boost the 1,3-PDO concentration and reduce the residual glycerol concentration as much as possible. Through the three-stage continuous fermentation, 80.05 g/L 1,3-PDO as the maximum concentration was produced while maintaining residual glycerol of 5.87 g/L, achieving a yield of 0.48 g/g and a productivity of 3.67 g/(L·h). Based on the 14 sets of experimental data from the first stage, a kinetic model was developed to describe the intricate relationships among the concentrations of 1,3-PDO, substrate, biomass, and butyrate. Subsequently, this kinetic model was used to optimize and predict the highest 1,3-PDO productivity of 11.26 g/(L·h) in the first stage fermentation, while the glycerol feeding concentration and dilution rate were determined to be 92 g/L and 0.341 h-1, separately. Additionally, to achieve a target 1,3-PDO production of 80 g/L without the third stage fermentation, the predicted minimum volume ratio of the second fermenter to the first one was 11.9. The kinetics-based two-stage continuous fermentation was experimentally verified well with the predicted results.

CONCLUSION

A novel three-stage continuous fermentation and a kinetic model were reported. Then a simpler two-stage continuous fermentation was developed based on the optimization of the kinetic model. This kinetics-based development of two-stage continuous fermentation could achieve high-level production of 1,3-PDO. Meanwhile, it provides a reference for other bio-chemicals production by applying kinetics to optimize multi-stage continuous fermentation.

A genome-scale metabolic model of the effect of dissolved oxygen on 1,3-propanediol fermentation by Klebsiella pneumoniae

Although 1,3-propanediol (1,3-PD) is usually considered an anaerobic fermentation product from glycerol by Klebsiella pneumoniae, microaerobic conditions proved to be more conducive to 1,3-PD production. In this study, a genome-scale metabolic model (GSMM) specific to K. pneumoniae KG2, a high 1.3-PD producer, was constructed. The iZY1242 model contains 2090 reactions, 1242 genes and 1433 metabolites. The model was not only able to accurately characterise cell growth, but also accurately simulate the fed-batch 1,3-PD fermentation process. Flux balance analyses by iZY1242 was performed to dissect the mechanism of stimulated 1,3-PD production under microaerobic conditions, and the maximum yield of 1,3-PD on glycerol was 0.83 mol/mol under optimal microaerobic conditions. Combined with experimental data, the iZY1242 model is a useful tool for establishing the best conditions for microaeration fermentation to produce 1,3-PD from glycerol in K. pneumoniae.

Recent advances in metabolic engineering of microorganisms for the production of monomeric C3 and C4 chemical compounds

Bio-based C3 and C4 bi-functional chemicals are useful monomers in biopolymer production. This review describes recent progresses in the biosynthesis of four such monomers as a hydroxy-carboxylic acid (3-hydroxypropionic acid), a dicarboxylic acid (succinic acid), and two diols (1,3-propanediol and 1,4-butanediol). The use of cheap carbon sources and the development of strains and processes for better product titer, rate and yield are presented. Challenges and future perspectives for (more) economical commercial production of these chemicals are also briefly discussed.

Extractive adsorption of 1,3-propanediol on a novel polystyrene macroporous resin enclosing medium and long-chain alcohols as extractant

Extractive adsorption is an integrated separation method employing a novel resin with both particle and liquid characteristics in terms of adsorption and extraction. In this study, the novel extractive adsorption polystyrene-divinylbenzene (PS-DVB) macroporous resin was synthesized by suspension polymerization, in which n-octanol (OL-PS-DVB) or mixed alcohols of n-octanol, undecyl alcohol, and tetradecyl alcohol (MA-PS-DVB) were added as porogen and enclosed in the resin skeleton after the reaction. The characterization of the two novel resins of OL-PS-DVB and MA-PS-DVB showed that they have large specific surface areas of 48.7 and 17.4 m2/g, respectively. Additionally, the two synthesized resins have much higher static adsorption capacities of 1,3-propanediol (511 and 473 mg/g) and dynamic adsorption capacities (312 and 267 mg/g) than traditional resins, because extractants enclosed in the resin can increase the adsorption capacity. Through Langmuir equation, the theoretical static maximum adsorption capacity of the mixed alcohols resin is 515 mg/g at 298 K and Gibbs free energy change of adsorption was -3781 J/mol, indicating that the adsorption process was spontaneous. In addition, the sorbent concentration effect in the resin was generated at high 1,3-propanediol (1,3-PDO) concentrations. The fitting of the Flocculation model can reveal that there is a possible relation between adsorption and flocculation. Compared to OL-PS-DVB, MA-PS-DVB showed better performance in the recovery yield of 1,3-PDO and other byproducts, the removal rates of the inorganic salt and protein, and the efficiency of recycled resin. For MA-PS-DVB, the recovery of 1,3-PDO, butyrate acid, acetic acid, and residual glycerol was 97.1%, 94.7%, 93.3%, and 90.3%, respectively. Simultaneously, the resin of MA-PS-DVB could remove 93.8% of inorganic salts and 90.9% of proteins in the concentrated fermentation broth. The two synthesized resins of OL-PS-DVB and MA-PS-DVB still had 90% or 92% of capacity for extractive adsorption of 1,3-propanediol after 10 times of recycling, which exhibited potential application in the separation of 1,3-propanediol from fermentation broth.

Production of 1,3-propanediol using enzymatic hydrolysate derived from pretreated distillers' grains

To minimize environmental pollution and waste of resources, distillers' grains (DG) was used to produce 1,3-propanediol. Biological, physical, and chemical methods were used for pretreatment. The correlation between features of pretreated samples and enzymatic digestibility was analyzed. The results showed that the glucan and xylan conversion of dilute sulfuric acid pretreated DG increased by 69.59% and 413.68%, respectively. The glucan conversion of microwave pretreated and xylan conversion of laccase pretreated DG increased by 14.22% and 34.19%, respectively. Pretreatment enhanced enzymatic digestibility through changing the dense structure and features of DG making them conductive to enzymatic hydrolysis. The production of 1,3-propanediol using enzymatic hydrolysate of pretreated DG and glycerol in shake-flask was 17 g/L. The utilization of DG not only provides plentiful raw materials replacing fossil fuels to produce biofuels and other chemicals but efficiently reduces environmental waste.

Enhanced 1,3-propanediol production with high yield from glycerol through a novel Klebsiella-Shewanella co-culture

BACKGROUND

1,3-Propanediol (1,3-PDO) is a platform compound, which has been widely used in food, pharmaceutical and cosmetic industries. Compared with chemical methods, the biological synthesis of 1,3-PDO has shown promising applications owing to its mild conditions and environmental friendliness. However, the biological synthesis of 1,3-PDO still has the problem of low titer and yield due to the shortage of reducing powers.

RESULTS

In this study, Klebsiella sp. strain YT7 was successfully isolated, which can synthesize 11.30 g/L of 1,3-PDO from glycerol in flasks. The intracellular redox regulation strategy based on the addition of electron mediators can increase the 1,3-PDO titer to 28.01 g/L. Furthermore, a co-culturing system consisting of strain YT7 and Shewanella oneidensis MR-1 was established, which can eliminate the supplementation of exogenous electron mediators and reduce the by-products accumulation. The 1,3-PDO yield reached 0.44 g/g and the final titer reached 62.90 g/L. The increased titer and yield were attributed to the increased redox levels and the consumption of by-products.

CONCLUSIONS

A two-bacterium co-culture system with Klebsiella sp. strain YT7 and S. oneidensis strain MR-1 was established, which realized the substitution of exogenous electron mediators and the reduction of by-product accumulation. Results provided theoretical basis for the high titer of 1,3-PDO production with low by-product concentration.

High-level co-production of 3-hydroxypropionic acid and 1,3-propanediol from glycerol: Metabolic engineering and process optimization

3-Hydroxypropionic acid (3-HP) and 1,3-propanediol (1,3-PDO) are value-added chemicals with versatile applications in the chemical, pharmaceutical, and food industries. Nevertheless, sustainable production of 3-HP and 1,3-PDO is often limited by the lack of efficient strains and suitable fermentation configurations. Herein, attempts have been made to improve the co-production of both metabolites through metabolic engineering of Escherichia coli and process optimization. First, the 3-HP and 1,3-PDO co-biosynthetic pathways were recruited and optimized in E. coli, followed by coupling the pathways to the transhydrogenase-mediated cofactor regeneration systems that increased cofactor availability and product synthesis. Next, pathway rebalancing and block of by-product formation significantly improved 3-HP and 1,3-PDO net titer. Subsequently, glycerol flux toward 3-HP and 1,3-PDO synthesis was maximized by removing metabolic repression and fine-tuning the glycerol oxidation pathway. Lastly, the combined fermentation process optimization and two-stage pH-controlled fed-batch fermentation co-produced 140.50 g/L 3-HP and 1,3-PDO, with 0.85 mol/mol net yield.

Genome-Scale Modeling and Systems Metabolic Engineering of Vibrio natriegens for the Production of 1,3-Propanediol

The fastest-growing bacterium Vibrio natriegens is a highly promising next-generation workhorse for molecular biology and industrial biotechnology. In this work, we described the workflows for developing genome-scale metabolic models and genome-editing protocols for engineering Vibrio natriegens. A case study for metabolic engineering of Vibrio natriegens for the production of 1,3-propanediol was also presented.

Strain evolution and novel downstream processing with integrated catalysis enable highly efficient co-production of 1,3-Propanediol and organic acid esters from crude glycerol

Bioconversion of natural microorganisms generally results in a mixture of various compounds. Downstream processing (DSP) which only targets a single product often lacks economic competitiveness due to incomplete use of raw material and high cost of waste treatment for by-products. Here, we show with the efficient microbial conversion of crude glycerol by an artificially evolved strain and how a catalytic conversion strategy can improve the total products yield and process economy of the DSP. Specifically, Clostridium pasteurianum was first adapted to increased concentration of crude glycerol in a novel automatic laboratory evolution system. At m³ scale bioreactor the strain achieved a simultaneous production of 1,3-propanediol (PDO), acetic and butyric acids at 81.21, 18.72 and 11.09 g/L within only 19 h, respectively, representing the most efficient fermentation of crude glycerol to targeted products. A heterogeneous catalytic step was developed and integrated into the DSP process to obtain high-value methyl esters from acetic and butyric acids at high yields. The co-production of the esters also greatly simplified the recovery of PDO. For example, a cosmetic grade PDO (96% PDO) was easily obtained by a simple single-stage distillation process (with an overall yield more than 77%). This integrated approach provides an industrially attractive route for the simultaneous production of three appealing products from the crude glycerol fermentation broth, which greatly improve the process economy and ecology. This article is protected by copyright. All rights reserved.

Systems metabolic engineering of Corynebacterium glutamicum for high-level production of 1,3-propanediol from glucose and xylose

Corynebacterium glutamicum is a versatile chassis which has been widely used to produce various amino acids and organic acids. In this study, we report the development of an efficient C. glutamicum strain to produce 1,3-propanediol (1,3-PDO) from glucose and xylose by systems metabolic engineering approaches, including (1) construction and optimization of two different glycerol synthesis modules; (2) combining glycerol and 1,3-PDO synthesis modules; (3) reducing 3-hydroxypropionate accumulation by clarifying a mechanism involving 1,3-PDO re-consumption; (4) reducing the accumulation of toxic 3-hydroxypropionaldehyde by pathway engineering; (5) engineering NADPH generation pathway and anaplerotic pathway. The final engineered strain can efficiently produce 1,3-PDO from glucose with a titer of 110.4 g/L, a yield of 0.42 g/g glucose, and a productivity of 2.30 g/L/h in fed-batch fermentation. By further introducing an optimized xylose metabolism module, the engineered strain can simultaneously utilize glucose and xylose to produce 1,3-PDO with a titer of 98.2 g/L and a yield of 0.38 g/g sugars. This result demonstrates that C. glutamicum is a potential chassis for the industrial production of 1,3-PDO from abundant lignocellulosic feedstocks.

Effective bioconversion of 1,3-propanediol from biodiesel-derived crude glycerol using organic acid resistance-enhanced Lactobacillus reuteri JH83

Organic acids produced during the fermentation of lactic acid bacteria inhibit cellular growth and the production of 1,3-propanediol (1,3-PDO). Lactobacillus reuteri JH83, which has an increase of 18.6% in organic acid resistance, was obtained through electron beam irradiation mutagenesis irrelevant to the problem of genetically modified organisms. The maximum bioconversion of 1,3-PDO in fed-batch fermentation using pure glycerol by L. reuteri JH83 was 93.2 g/L at 72 h, and the productivity was 1.29 g/L·h, which achieved an increase by 34.6%, compared to that of the wild-type strain. In addition, the result of fed-batch fermentation for the production of 1,3-PDO using crude glycerol was not significantly different from that of pure glycerol. Additionally, transcriptome analysis confirmed changes in the expression levels of sucrose phosphorylase, which is a major facilitator superfamily transporter, and muramyl ligase family proteins, which protect lactic acid bacteria from various stressors, such as organic acids.

Metabolic engineering of Lactobacillus reuteri DSM 20,016 for improved 1,3-propanediol production from glycerol

The production of 1,3-propanediol (1,3-PDO) from glycerol was studied by GRAS and native 1,3-PDO producer, Lactobacillus reuteri DSM 20016. This strain ferments glucose with production of lactate, acetate, ethanol, and converts glycerol to 1,3-PDO using NADH generated by glucose metabolism. To improve 1,3-PDO production, alcohol dehydrogenases (ADH) were disrupted and 1,3-PDO oxidoreductases (PDOR) were overexpressed. Deletion of ADH (adh2) enhanced 1,3-PDO production yield on glucose by reducing ethanol synthesis, and overexpression of PDOR (pduQ) elevated 1,3-PDO production rate and cell growth rate. The strain with simultaneous adh2 deletion, pduQ overexpression (Δadh2pduQ⁺⁺) could produce 687 mM 1,3-PDO with the yield of 1.2 ± 0.08 mol 1,3-PDO/mol glucose by fed-batch bioreactor cultivation in 48 h. However, the 1,3-PDO production rate was greatly reduced in the late period of bioreactor culture, mainly due to high lactate accumulation. This is the first report on rational metabolic engineering of L. reuteri for improved 1,3-PDO production.

Isolation and characterization of a newly identified Clostridium butyricum strain SCUT343-4 for 1,3-propanediol production

A novel 1,3-propanediol (1,3-PDO) producing strain was isolated and identified as Clostridium butyricum with respect to its morphological and physiological characteristics, as well as 16S rDNA. The results of substrates test and stress tolerance indicated that C. butyricum SCUT343-4 could produce 1,3-PDO efficiently from glycerol. The optimal fermentation conditions were determined to be 5 g/L yeast extract at 37 °C and pH 6.5. To fully evaluate its 1,3-PDO production capacity, different cultivation strategies have been implemented. The highest 1,3-PDO concentration obtained for batch and fed-batch fermentation were 51.64 and 61.30 g/L, respectively. Immobilized cell fermentation in fibrous-bed bioreactor was also performed, and the concentration of 1,3-PDO further increased to 86 g/L with a yield of 0.52 g/g. In addition, the 1,3-PDO productivity reached 4.20 g/L h, which is the highest level reported for C. butyricum, demonstrating the potential of C. butyricum SCUT343-4 for 1,3-PDO production from glycerol.

Systems metabolic engineering of Vibrio natriegens for the production of 1,3-propanediol

The economic viability of current bio-production systems is often limited by its low productivity due to slow cell growth and low substrate uptake rate. The fastest-growing bacterium Vibrio natriegens is a highly promising next-generation workhorse of the biotechnology industry which can utilize various industrially relevant carbon sources with high substrate uptake rates. Here, we demonstrate the first systematic engineering example of V. natriegens for the heterologous production of 1,3-propanediol (1,3-PDO) from glycerol. Systems metabolic engineering strategies have been applied in this study to develop a superior 1,3-PDO producer, including: (1) heterologous pathway construction and optimization; (2) engineering cellular transcriptional regulators and global transcriptomic analysis; (3) enhancing intracellular reducing power by cofactor engineering; (4) reducing the accumulation of toxic intermediate by pathway engineering; (5) systematic engineering of glycerol oxidation pathway to eliminate byproduct formation. A final engineered strain can efficiently produce 1,3-PDO with a titer of 56.2 g/L, a yield of 0.61 mol/mol, and an average productivity of 2.36 g/L/h. The strategies described in this study would be useful for engineering V. natriegens as a potential chassis for the production of other useful chemicals and biofuels.

Sustainable utilization of waste glycerol for 1,3-propanediol production over Pt/WOx/Al2O3 catalysts: Effects of catalyst pore sizes and optimization of synthesis conditions

Recycling of waste glycerol derived from biodiesel production to high value-added chemicals is essential for sustainable development of Bio-Circular-Green Economy. This work studied the conversion of glycerol to 1,3-propanediol over Pt/WO_x/Al₂O₃ catalysts, pointing out the impacts of catalyst pore sizes and operating conditions for maximizing the yield of 1,3-propanediol. The results suggested that both pore confinement effect and number of available reactive metals as well as operating conditions determined the glycerol conversion and 1,3-propanediol selectivity. The small-pore 5Pt/WO_x/S-Al₂O₃ catalyst (6.1 nm) gave a higher Pt dispersion (32.0%), a smaller Pt crystallite size (3.5 nm) and a higher number of acidity (0.47 mmol NH₃ g^-1) compared to those of the large-pore 5Pt/WO_x/L-Al₂O₃ catalyst (40.3 nm). However, glycerol conversion and 1,3-propanediol yield over the small-pore 5Pt/WO_x/S-Al₂O₃ catalyst were significantly lower than those of the large-pore Pt/WO_x/L-Al₂O₃ catalyst, suggesting that the diffusional restriction within the small-pore catalyst suppressed transportation of molecules to expose catalytic active sites, favoring the excessive hydrogenolysis of 1,3-propanediol, giving rise to undesirable products. The best 1,3-propanediol yield of 32.8% at 78% glycerol conversion were achieved over the 5Pt/WO_x/L-Al₂O₃ under optimal reaction condition of 220 °C, 6 MPa, 5 h reaction time and amount of catalyst to glycerol ratio of 0.25 g mL^-1. However, the 1,3-propanediol yield and glycerol conversion decreased to 19.6% and 51% after the 4th reaction-regeneration which were attributed to the carbonaceous deposition and the agglomeration of Pt particles.

The presence of 3-hydroxypropionate and 1,3-propanediol suggests an alternative path for conversion of glycerol to Acetyl-CoA

BACKGROUND

In our recent study using [U-13C3]glycerol, a small subset of hamsters showed an unusual profile of glycerol metabolism: negligible gluconeogenesis from glycerol plus conversion of glycerol to 1,3-propanediol (1,3PDO) and 3-hydroxypropionate (3HP) which were detected in the liver and blood. The purpose of the current study is to evaluate the association of these unusual glycerol products with other biochemical processes in the liver.

METHODS

Fasted hamsters received acetaminophen (400 mg/kg; n = 16) or saline (n = 10) intraperitoneally. After waiting 2 h, all the animals received [U-13C3]glycerol intraperitoneally. Liver and blood were harvested 1 h after the glycerol injection for NMR analysis and gene expression assays.

RESULTS

1,3PDO and 3HP derived from [U-13C3]glycerol were detected in the liver and plasma of eight hamsters (two controls and six hamsters with acetaminophen treatment). Glycerol metabolism in the liver of these animals differed substantially from conventional metabolic pathways. [U-13C3]glycerol was metabolized to acetyl-CoA as evidenced with downstream products detected in glutamate and β-hydroxybutyrate, yet 13C labeling in pyruvate and glucose was minimal (p < 0.001, 13C labeling difference in each metabolite). Expression of aldehyde dehydrogenases was enhanced in hamster livers with 1,3PDO and 3HP (p < 0.05).

CONCLUSION

Detection of 1,3PDO and 3HP in the hamster liver was associated with unorthodox metabolism of glycerol characterized by conversion of 3HP to acetyl-CoA followed by ketogenesis and oxidative metabolism through the TCA cycle. Additional mechanistic studies are needed to determine the causes of unusual glycerol metabolism in a subset of these hamsters.

Co-fermentation of glycerol and glucose by a co-culture system of engineered Escherichia coli strains for 1,3-propanediol production without vitamin B12 supplementation

The necessity of costly co-enzyme B₁₂ for the activity of glycerol dehydratase (GDHt) is considered as a major bottleneck in sustainable bioproduction of 1,3-propanediol (1,3-PD) from glycerol. Here, an E. coil Rosetta-dhaB1-dhaB2 strain was constructed by overexpressing a B₁₂-independent GDHt (dhaB1) and its activating factor (dhaB2) from Clostridium butyricum. Subsequently, it was used in designing a co-culture with E. coli BL21-dhaT that overexpressed 1,3-PD oxidoreductase (dhaT), to produce 1,3-PD during co-fermentation of glycerol and glucose. The optimum initial ratio of BL21-dhaT to Rosetta-dhaB1-dhaB2 strains in the co-culture was 1.5. Compared to the fermentation of glycerol alone, co-fermentation approach provided 1.3-folds higher 1,3-PD. Finally, co-fermentation was done in a 10 L bioreactor that produced 41.65 g/L 1,3-PD, which corresponded to 0.69 g/L/h productivity and 0.67 mol/mol yield of 1,3-PD. Hence, the developed co-culture could produce 1,3-PD cost-effectively without requiring vitamin B₁₂.

Metabolism, morphology and transcriptome analysis of oscillatory behavior of Clostridium butyricum during long-term continuous fermentation for 1,3-propanediol production

BACKGROUND

Oscillation is a special cell behavior in microorganisms during continuous fermentation, which poses threats to the output stability for industrial productions of biofuels and biochemicals. In previous study, a spontaneous oscillatory behavior was observed in Clostridium butyricum-intensive microbial consortium in continuous fermentation for 1,3-propanediol (1,3-PDO) production from glycerol, which led to the discovery of oscillation in species C. butyricum.

RESULTS

Spontaneous oscillations by C. butyricum tended to occur under glycerol-limited conditions at low dilution rates. At a glycerol feed concentration of 88 g/L and a dilution rate of 0.048 h^-1, the oscillatory behavior of C. butyricum was observed after continuous operation for 146 h and was sustained for over 450 h with an average oscillation period of 51 h. During oscillations, microbial glycerol metabolism exhibited dramatic periodic changes, in which productions of lactate, formate and hydrogen significantly lagged behind that of other products including biomass, 1,3-PDO and butyrate. Analysis of extracellular oxidation-reduction potential and intracellular ratio of NAD⁺/NADH indicated that microbial cells experienced distinct redox changes during oscillations, from oxidized to reduced state with decreasing of growth rate. Meanwhile, C. butyricum S3 exhibited periodic morphological changes during oscillations, with aggregates, elongated shape, spores or cell debris at the trough of biomass production. Transcriptome analysis indicated that expression levels of multiple genes were up-regulated when microbial cells were undergoing stress, including that for pyruvate metabolism, conversion of acetyl-CoA to acetaldehyde as well as stress response.

CONCLUSION

This study for the first time systematically investigated the oscillatory behavior of C. butyricum in aspect of occurrence condition, metabolism, morphology and transcriptome. Based on the experimental results, two hypotheses were put forward to explain the oscillatory behavior: disorder of pyruvate metabolism, and excessive accumulation of acetaldehyde.

Sequential fed-batch fermentation of 1,3-propanediol from glycerol by Clostridium butyricum DL07

The demand for 1,3-propanediol (1,3-PDO) has increased sharply due to its role as a monomer for the synthesis of polytrimethylene terephthalate (PTT). Although Clostridium butyricum is considered to be one of the most promising bioproducers for 1,3-PDO, its low productivity hinders its application on industrial scale because of the longer time needed for anaerobic cultivation. In this study, an excellent C. butyricum (DL07) strain was obtained with high-level titer and productivity of 1,3-PDO, i.e., 104.8 g/L and 3.38 g/(L•h) vs. 94.2 g/L and 3.04 g/(L•h) using pure or crude glycerol as substrate in fed-batch fermentation, respectively. Furthermore, a novel sequential fed-batch fermentation was investigated, in which the next bioreactor was inoculated by C. butyricum DL07 cells growing at exponential phase in the prior bioreactor. It could run steadily for at least eight cycles. The average concentration of 1,3-PDO in eight cycles was 85 g/L with the average productivity of 3.1 g/(L•h). The sequential fed-batch fermentation could achieve semi-continuous production of 1,3-PDO with higher productivity than repeated fed-batch fermentation and would greatly contribute to the industrial production of 1,3-PDO by C. butyricum. KEY POINTS: • A novel C. butyricum strain was screened to produce 104.8 g/L 1,3-PDO from glycerol. • Corn steep liquor powder was used as a cheap nitrogen source for 1,3-PDO production. • A sequential fed-batch fermentation process was established for 1,3-PDO production. • An automatic glycerol feeding strategy was applied in the production of 1,3-PDO.

Metabolic engineering of Pseudomonas denitrificans for the 1,3-propanediol production from glycerol

Bio-production of 1,3-propanediol (1,3-PDO) from glycerol was studied using Pseudomonas denitrificans as host, which aerobically synthesizes coenzyme B₁₂, an essential cofactor of glycerol dehydratase (GDHt). P. denitrificans was transformed with the 1,3-PDO synthesis pathway composed of GDHt and 1,3-PDO oxidoreductase (PDOR), and its putative 3-hydroxypropionaldehyde (3-HPA) dehydrogenase(s), leading to the production of 3-hydroxypropioninc acid form the intermediary 3-HPA, was identified and deleted. In addition, to improve the availability of NADH for PDOR, oxidation of NADH in the electron transport chain was disturbed by deletion of the nuo operon and/or ndh gene. Finally, acetate formation pathway was eliminated. One resulting strain could produce 68.95 mM 1,3-PDO with the yield of 0.92 mol 1,3-PDO/mol glycerol on flask scale and 440 mM with the yield of 0.89 mol 1,3-PDO/mol glycerol in a fed-batch bioreactor experiment. This study demonstrates that P. denitrificans is a promising recombinant host for the production of 1,3-PDO from glycerol.

Random mutagenesis of Clostridium butyricum strain and optimization of biosynthesis process for enhanced production of 1,3-propanediol

The aim of this work was to study the random mutagenesis of Clostridium butyricum strain. A high 1,3-PD tolerant mutant strain, designated as C. butyricum YP855, was developed from the wild strain C. butyricum XYB11, using combined chemical (NTG, N-methyl-N'-nitro-N-nitrosoguanidine,) and plasma-based mutagenesis (ARTP, atmospheric and room temperature plasma). The YP855 showed a maximum tolerance of 85 g/L to 1,3-PD (up to 30.8% increase) when compared with the tolerance exhibited by the wild strain. Under the optimum conditions as established by the response surface methodology (RSM), the mutant strain produced 37.20 g/L of 1,3-PD, which is 29.48% higher than the concentration obtained from the wild strain (28.73 g/L). This research would offer information for further development of the biosynthesis of 1,3-PD by the mutant strain of C. butyricum.

Production of 1,3-propanediol from pure and crude glycerol using a UASB reactor with attached biomass in silicone support

The 1,3-propanediol (1,3-PDO) yield and productivity from glycerol were studied over a 155-day period. A UASB reactor that also contained silicone support for biomass attachment was used to evaluate the optimal operational conditions and microbiota development. The highest average 1,3-PDO yield was 0.54 and 0.48 mol.mol-gly^-1 when reactor pH was 5.0-5.5 and the applied loading rate was 18 and 20 g-gly.L^-1.d^-1 using the pure and crude substrate, respectively. The productivity was close to 7.5 g.L^-1.d^-1 for both substrates; therefore, the direct use of crude glycerol can be valorized in practice. Clostridium was the predominant genus for 1,3-PDO production and C. pasteurianum was dominant in the biofilm. Using crude glycerol, C. beijerinckii dropped strongly; some Clostridium population was then replaced by Klebsiella pneumoniae and Lactobacillus spp. The good process performance and the advances in the microbiota knowledge are steps forward to obtain a more cost-effective system in practice.

Two-stage microbial conversion of crude glycerol to 1,3-propanediol and polyhydroxyalkanoates after pretreatment

With increasing demand for biodiesel, crude glycerol as a by-product in biodiesel production has been generated and oversupplied. This study, therefore, explored the pretreatment and a subsequent two-stage microbial system to convert crude glycerol into high value-added products: 1,3-propanediol (1,3-PDO) and polyhydroxyalkanoates (PHAs). After pretreatment, long chain fatty acids (LCFAs) could be effectively removed from crude glycerol to eliminate the inhibition effects on subsequent microbial process. In the anaerobic fermentation, when fed treated crude glycerol increased from 20 g/L to 100 g/L, 1,3-PDO yield decreased from 0.438 g/g to 0.345 g/g and accompanied carboxylic acids shifted from acetate and lactate dominant to lactate overwhelmingly dominant. Meanwhile, the relative abundance of Clostridiales sustained around 50% but Enterobacteriales increased from 19% to 53%. Further fed glycerol increase to 140 g/L resulted in severe substrate inhibition, which could be relieved by intermittent feeding. In aerobic process, glycerol anaerobic digestion effluent (ADE) was fed to the consortium of Bacillus megaterium and Corynebacterium hydrocarbooxydans for selectively consumption of carboxylic acids and residual glycerol from 1,3-PDO to produce PHAs as a secondary high value-added product. The consortium accumulated maximum 8.0 g/L poly (3-hydroxybutyrate) (PHB), and 1,3-PDO purity increased from initial 27.7% to almost 100% when fed with 100 g/L glycerol ADE. Overall, this study provided comprehensive and insightful information on microbial conversion of crude glycerol to high value-added products after pretreatment.

Improving the production of isoprene and 1,3-propanediol by metabolically engineered Escherichia coli through recycling redox cofactor between the dual pathways

The biosynthesis of isoprene by microorganisms is a promising green route. However, the yield of isoprene is limited due to the generation of excess NAD(P)H via the mevalonate (MVA) pathway, which converts more glucose into CO₂ or undesired reduced by-products. The production of 1,3-propanediol (1,3-PDO) from glycerol is a typical NAD(P)H-consuming process, which restricts 1,3-PDO yield to ~ 0.7 mol/mol. In this study, we propose a strategy of redox cofactor balance by coupling the production of isoprene with 1,3-PDO fermentation. With the introduction and optimization of the dual pathways in an engineered Escherichia coli, ~ 85.2% of the excess NADPH from isoprene pathway was recycled for 1,3-PDO production. The best strain G05 simultaneously produced 665.2 mg/L isoprene and 2532.1 mg/L 1,3-PDO under flask fermentation conditions. The yields were 0.3 mol/mol glucose and 1.0 mol/mol glycerol, respectively, showing 3.3- and 4.3-fold improvements relative to either pathway independently. Since isoprene is a volatile organic compound (VOC) whereas 1,3-PDO is separated from the fermentation broth, their coproduction process does not increase the complexity or cost for the separation from each other. Hence, the presented strategy will be especially useful for developing efficient biocatalysts for other biofuels and biochemicals, which are driven by cofactor concentrations.

Metabolic engineering of Escherichia coli for 1,3-propanediol biosynthesis from glycerol

In this study, the engineered E. coli was constructed for efficient transformation of glycerol to 1,3-propanediol (1,3-PDO). To regenerate NADPH, the key bottleneck in 1,3-PDO production, heterologous NADP⁺-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDN, encoded by gapN) pathway was introduced, and the gapN expression level was fine-tuned with specific 5'-untranslated regions (5'-UTR) to balance the carbon flux distribution between the metabolic pathways of NADPH regeneration and 1,3-PDO biosynthesis. Additionally, glucose was added to the medium to promote glycerol utilization and cell growth. To elevate the utilization of glycerol in the presence of glucose, E. coli JA11 was constructed through destroying PEP-dependent glucose transport system while strengthening the ATP-dependent transport system. Subsequent optimization of nitrogen sources further improved 1,3-PDO production. Finally, under the optimal fermentation condition, E. coli JA11 produced 13.47 g/L 1,3-PDO, with a yield of 0.64 mol/mol, increased by 325% and 100% compared with the original engineered E. coli JA03, respectively.

Dynamic flux balance analysis for microbial conversion of glycerol into 1,3-propanediol by Klebsiella pneumoniae

To investigate the relationship between the yield of 1,3-propanediol (1,3-PD) and the flux variation in metabolic pathways of Klebsiella pneumoniae, an optimized calculation method was constructed on basis of dynamic flux balance analysis by combining genome-scale flux balance analysis with a kinetic model of extracellular metabolites. Through optimizing calculations, a more completely expanded metabolic pathway was obtained, which includes the previously reported metabolic pathway and additional three pathways or site: a pentose phosphate pathway (PPP) elicited at the dihydroxyacetone (DHA) node to provide more reducing equivalents; a branch of synthetic amino acids at the 3-phosphoglycerate (3PG) node; and the α-ketoglutarate site in the tricarboxylic acid (TCA) cycle leading to anabolic pathways for glutamate and other amino acids. On this basis, the relationships between the dynamic flux distribution of the important nodes in the metabolic pathway and the yield of 1,3-propanediol were analyzed. First, dynamic flux change from DHA to the PPP is positively correlated with the yield. Second, variation in flux in the TCA cycle is also positively correlated with the yield of 1,3-propanediol. In addition, the influence of the feedback loop formed by the cofactor tetrahydrofolate on the flux change of TCA in the amino acid anabolic pathway was examined. These results are of important reference value and have guiding significance for the extension of the glycerol metabolism pathway in K. pneumoniae, the rational transformation of genetic engineering in bacteria, and the optimization of metabolic pathways for industrial production.

Optimized 1,3-propanediol production from crude glycerol using mixed cultures in batch and continuous reactors

The production of 1,3-propanediol from crude glycerol and mixed anaerobic sludge was investigated in batch experiments and continuous reactors. Using a 2³ complete factorial design, the effects of the concentration of glycerol (22-30 g L^-1), KH₂PO₄ (1.50-2.00 g L^-1), and vitamin B12 (7-8 mg L^-1) were examined in batch reactors. As an evaluated response, the highest 1,3-PD yields occurred for high concentrations of vitamin B12 and low levels of KH₂PO₄, reaching 0.57 g g^-1 glycerol consumed. The variable glycerol concentration was not significant in the studied range. In addition, the condition that provided the best 1,3-PD yield was applied to an anaerobic fluidized bed reactor fed with crude glycerol (26.0 g L^-1), which was monitored as the hydraulic retention time (HRT) decreased from 36 to 12 h. The greatest 1,3-PD yield, of 0.31 g g^-1 glycerol, was obtained with an HRT of 28 h.

Efficient production of 1,3-propanediol from crude glycerol by repeated fed-batch fermentation strategy of a lactate and 2,3-butanediol deficient mutant of Klebsiella pneumoniae

BACKGROUND

1,3-Propanediol (1,3-PDO) is important building blocks for the bio-based chemical industry, Klebsiella pneumoniae can be an attractive candidate for their production. However, 1,3-PDO production is high but productivity is generally low by K. pneumoniae. In this study, repeated fed-batch cultivation by a lactate and 2,3-butanediol (2,3-BDO) deficient mutant of K. pneumoniae were investigated for efficient 1,3-PDO production from industrial by-products such as crude glycerol.

RESULTS

First, optimal conditions for repeated fed-batch fermentation of a ΔldhA mutant defective for lactate formation due to deletion of the lactate dehydrogenase gene (ldhA) were determined. Maximal 1,3-PDO production level and productivity obtained by repeated fed-batch fermentation under optimized conditions were 81.1 g/L and 3.38 g/L/h, respectively, and these values were successfully maintained for five cycles of fermentation without any loss of fermentation capacity. This results were much higher than that of the normal fed-batch fermentation. The levels of 2,3-BDO, which is a major by-product, reaching up to ~ 50% of the level of 1,3-PDO, were reduced using a mutant strain [Δ(ldhA als)] containing an additional mutation in the biosynthetic pathway of 2,3-BDO (deletion of the acetolactate synthase gene). The levels of 2,3-BDO were reduced to about 20% of 1,3-PDO levels by repeated fed-batch fermentation of Δ(ldhA als), although maximal 1,3-PDO production and productivity also decreased owing to a defect in the growth of the 2,3-BDO-defective mutant strain.

CONCLUSION

This repeated fed-batch fermentation may be useful for reducing the cost of 1,3-PDO production and may be promising industrialization prospect for the 1,3-PDO production.

Combined polyhydroxyalkanoates (PHA) and 1,3-propanediol production from crude glycerol: Selective conversion of volatile fatty acids into PHA by mixed microbial consortia

Crude glycerol is an important by-product of the biodiesel industry, which can be converted into volatile fatty acids (VFA) and/or 1,3-propanediol (1,3-PDO) by fermentation. In this study, a selective conversion of VFA to polyhydroxyalkanoates (PHA) was attained while leaving 1,3-PDO in the supernatant by means of mixed microbial consortia selection strategies. The process showed highly reproducible results in terms of PHA yield, 0.99 ± 0.07 C_mol PHA/C_mol S (0.84 g COD PHA/g COD S), PHA content (76 ± 3.1 g PHA/100 g TSS) and 1,3-PDO recovery (99 ± 2.1%). The combined process had an ultimate yield from crude glycerol of 0.19 g COD PHA and 0.42 g COD 1,3-PDO per g of input COD. The novel enrichment strategy applied for selectively transforming fermentation by-products into a high value product (PHA) demonstrates the significance of the enrichment process for targeting specific bio-transformations and could potentially prove valuable for other biotechnological applications as well.

An efficient aqueous two phase systems using dual inorganic electrolytes to separate 1,3-propanediol from the fermented broth

An aqueous two phase extraction using K₂CO₃:K₂HPO₄/Isoproponal was investigated for the recovery of 1,3-propanediol from the fermented broth. Initially, the concentration of K₂CO₃ on phase formation, the partition co-efficient and recovery of 1,3-PDO was evaluated with a optimum salt concentration of 60%. Later the partition co-efficient was improved using dual inorganic salts, K₂CO₃ and K₂HPO₄ with an optimum concentration of 45% and 15% respectively. Using Central Composite Design, pH and temperature on partition and recovery of 1,3-PDO was evaluated. With the optimized physical conditions and inorganic salts concentration, ATPS extraction was carried out in synthetic solution as well as fermented broth resulting in maximum 1,3-PDO partition co-efficient value of 42.46 and 56.93 and recovery yield of 97.69 and 98.27% respectively. A fair partition was observed with organic acids and 1,3-PDO, with removal of lactic acid and acetic acid up to 93.29 and 90.42% respectively.

Xylan supplement improves 1,3-propanediol fermentation by Clostridium butyricum

Lignocellulosic biomass as co-substrate enhances the 1,3-propanediol (1,3-PD) production of anaerobic fermenters by increasing their conversion yield from glycerol. To improve 1,3-propanediol (1,3-PD) production by this efficient approach, Clostridium butyricum I5-42 was supplemented with lignocellulosic biomasses (starch free fiber (CPF) from cassava pulp and xylan) as co-substrates. The 1,3-PD production and growth of C. butyricum were considerably higher in glycerol plus CPF and xylan than in glycerol alone, whereas another major polysaccharide (cellulose co-substrate) failed to improve the 1,3-PD production. C. butyricum I5-42 showed no degradation ability on cellulose powder, and only weak activity and slight growth on xylan. However CPF supplemented with xylan strongly enhanced the transcription levels of the major enzymes of 1,3-PD production (glycerol dehydratase, 1,3-propanediol dehydrogenase, and glycerol dehydrogenase). The intracellular redox reactions maintained equal balance in the supplemented media, suggesting that CPF plus xylan promotes 1,3-PD production in the reductive pathway. This promotion is probably mediated by NADH, which is effectively regenerated by small amounts of released oligosaccharides and subsequent activation of the glycerol oxidative pathway. Both supplements also improved the 1,3-PD production at high glycerol concentration. Therefore, supplementation with lignocellulolytic polysaccharides such as xylan can improve the production and productivity of 1,3-PD from glycerol in C. butyricum. Direct supplementation of CPF with xylan in 1,3-PD production has not been previously reported.

Non-capsulated mutants of a chemical-producing Klebsiella pneumoniae strain

OBJECTIVES

To investigate the outcomes of capsule lost on cell transformation efficiency and chemicals (1,3-propanediol, 2,3-butanediol, and 2-ketogluconic acid) production by Klebsiella pneumoniae.

RESULTS

The cps gene cluster showed low sequence homology with pathogenic strains. The wza is a highly conserved gene in the cps cluster that encodes an outer membrane protein. A non-capsulated mutant was constructed by deletion of wza. Phenotype studies demonstrated that non-capsulated cells were less buoyant and easy to sediment. The transformation efficiency of the non-capsulated mutant reached 6.4 × 10⁵ CFU μg^-1 DNA, which is 10 times higher than that of the wild strain. 52.2 g 1,3-propanediol L^-1, 30.7 g 2,3-butanediol L^-1, and 175.9 g 2-ketogluconic acid L^-1 were produced by non-capsulated mutants, which were 10-40% lower compared to wild strain. Furthermore, viscosities of the three fermentation broths decreased to approximately 1.3 cP from the range of 1.8-2.2 cP.

CONCLUSIONS

Non-capsulated K. pneumoniae mutants should allay concerns regarding biological safety, improve transformation efficiency, lower viscosity, and subsequently ameliorate the financial burden of the downstream process of chemicals production.

Characterization of a novel lytic bacteriophage from an industrial Escherichia coli fermentation process and elimination of virulence using a heterologous CRISPR-Cas9 system

Bacterial–bacteriophage interactions are a well-studied and ecologically-important aspect of microbiology. Many commercial fermentation processes are susceptible to bacteriophage infections due to the use of high-density, clonal cell populations. Lytic infections of bacterial cells in these fermentations are especially problematic due to their negative impacts on product quality, asset utilization, and fouling of downstream equipment. Here, we report the isolation and characterization of a novel lytic bacteriophage, referred to as bacteriophage DTL that is capable of rapid lytic infections of an Escherichia coli K12 strain used for commercial production of 1,3-propanediol (PDO). The bacteriophage genome was sequenced and annotated, which identified 67 potential open-reading frames (ORF). The tail fiber ORF, the largest in the genome, was most closely related to bacteriophage RTP, a T1-like bacteriophage reported from a commercial E. coli fermentation process in Germany. To eliminate virulence, both a fully functional Streptococcus thermophilus CRISPR3 plasmid and a customized S. thermophilus CRISPR3 plasmid with disabled spacer acquisition elements and seven spacers targeting the bacteriophage DTL genome were constructed. Both plasmids were separately integrated into a PDO production strain, which was subsequently infected with bacteriophage DTL. The native S. thermophilus CRISPR3 operon was shown to decrease phage susceptibility by approximately 96%, while the customized CRISPR3 operon provided complete resistance to bacteriophage DTL. The results indicate that the heterologous bacteriophage-resistance system described herein is useful in eliminating lytic infections of bacteriophage DTL, which was prevalent in environment surrounding the manufacturing facility.

Mixed bacterial culture mediated direct conversion of bio-glycerol to diols

Direct and economic transformation of biodiesel derived crude glycerol is gaining more significance. During screening of bacterial cultures Klebsiella pneumoniae and Enterobacter aerogenes were able to convert crude bio-glycerol to 2,3-butanediol (2,3-BDO) and 1,3-propanediol (1,3-PDO), as major compounds, ethanol and acetoin as minor compounds, with a conversion of 69% and 79% respectively. Process optimization could achieve maximum conversion at pH 7.0, 37 °C, 30-40 g/L glycerol and 1.5 g of inoculum until 120 h. Mixed cultures led to complete glycerol conversion with optimal yield and productivity. An innovative approach of using crude glycerol for sustained growth and tolerance of bacteria as source of carbon and energy makes this study more significant. In addition to this, a mixed culture concept introduced here is expected to make impact in process economics for industrial scale synthesis for direct transformation of glycerol into C3 and specifically, C4 diols.

Potential and limitations of Klebsiella pneumoniae as a microbial cell factory utilizing glycerol as the carbon source

Klebsiella pneumoniae is a Gram-negative facultative anaerobe that metabolizes glycerol efficiently under both aerobic and anaerobic conditions. This microbe is considered an outstanding biocatalyst for transforming glycerol into a variety of value-added products. Crude glycerol is a cheap carbon source and can be converted by K. pneumoniae into useful compounds such as lactic acid, 3-hydroxypropionic acid, ethanol, 1,3-propanediol, 2,3-butanediol, and succinic acid. This review summarizes glycerol metabolism in K. pneumoniae and its potential as a microbial cell factory for the production of commercially important acids and alcohols. Although many challenges remain, K. pneumoniae is a promising workhorse when glycerol is used as the carbon source.

Polyhydroxyalkanoates (PHA) production from fermented crude glycerol: Study on the conversion of 1,3-propanediol to PHA in mixed microbial consortia

Crude glycerol, a by-product from the biodiesel industry, can be converted by mixed microbial consortia into 1,3-propanediol (1,3-PDO) and volatile fatty acids. In this study, further conversion of these main products into polyhydroxyalkanoates (PHA) was investigated with the focus on 1,3-PDO. Two different approaches for the enrichment of PHA accumulating microbial consortia using an aerobic dynamic feeding strategy were applied. With the first approach, where nitrogen was present during the whole cycle, no net production of PHA from 1,3-PDO was observed in the fermented effluent, not even in a nitrogen-limited PHA accumulation assay. Nevertheless, experiments in synthetic substrates revealed that the conversion of 1,3-PDO to PHA was possible under nitrogen limiting conditions. Thus, a different enrichment strategy was formulated where nitrogen was limited during the feast phase to stimulate the storage response. Nitrogen was still supplied during the famine phase. With the latter strategy, a net production of PHA from 1,3-PDO was observed at a yield of 0.24 C_mol PHA/C_mol 1,3-PDO. The overall yield from the fermented effluent was 0.42 C_mol PHA/C_mol substrate. Overall, the PHA yield from 1,3-PDO seemed to be limited, similarly to when using glycerol as a substrate, by a decarboxylation step and accumulation of other storage polymers such as glycogen, and possibly, lipid inclusions.

Environmentally-friendly strategy for separation of 1,3-propanediol using biocatalytic conversion

Glycerol waste from the biodiesel production can be used as a carbon source in the production of 1,3-propanediol (1,3-PD) through microbial fermentation. However, downstream processing is a major bottleneck that restricts its biological production. Here, we investigated an environmentally-friendly method to enzymatically separate 1,3-PD. The transformation of 1,3-PD to an ester was achieved by exploiting the esterification reaction with fatty acids under lipase catalysis. The reaction efficiency was optimized using different poly-alcohols that were existed in the fermentation broth reacted with a fatty acid. Whereas the 1,3-PD conversion reached 62%, only a 0.06% and 0.08% conversion was reached for 2,3-butanediol and glycerol, illustrating the former's more efficient separation. The recovery efficiency of 1,3-PD was 96%. Finally, 1,3-PD was obtained by lipase-directed ester hydrolysis. Taken together, the bio-catalyzed separation process presented here is a novel and promising method for recovering 1,3-PD.

Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution

Background

Production directly from carbon dioxide by engineered cyanobacteria is one of the promising technologies for sustainable future. Previously, we have successfully achieved 1,3-propanediol (1,3-PDO) production using Synechococcus elongatus PCC 7942 with a synthetic metabolic pathway. The strain into which the synthetic metabolic pathway was introduced produced 3.48 mM (0.265 g/L) 1,3-PDO and 14.3 mM (1.32 g/L) glycerol during 20 days of incubation. In this study, the productivities of 1,3-PDO were improved by gene disruption selected by screening with in silico simulation.

Methods

First, a stoichiometric metabolic model was applied to prediction of cellular metabolic flux distribution in a 1,3-PDO-producing strain of S. elongatus PCC 7942. A genome-scale model of S. elongatus PCC 7942 constructed by Knoop was modified by the addition of a synthetic metabolic pathway for 1,3-PDO production. Next, the metabolic flux distribution predicted by metabolic flux balance analysis (FBA) was used for in silico simulation of gene disruption. As a result of gene disruption simulation, NADPH dehydrogenase 1 (NDH-1) complexes were found by screening to be the most promising candidates for disruption to improve 1,3-PDO production. The effect of disruption of the gene encoding a subunit of the NDH-1 complex was evaluated in the 1,3-PDO-producing strain.

Results and Conclusions

During 20 days of incubation, the ndhF1-null 1,3-PDO-producing strain showed the highest titers: 4.44 mM (0.338 g/L) 1,3-PDO and 30.3 mM (2.79 g/L) glycerol. In this study, we successfully improved 1,3-PDO productivity on the basis of in silico simulation of gene disruption.

Electronic supplementary material

The online version of this article (10.1186/s12934-017-0824-4) contains supplementary material, which is available to authorized users.

Metabolic engineering of Klebsiella pneumoniae J2B for co-production of 3-hydroxypropionic acid and 1,3-propanediol from glycerol: Reduction of acetate and other by-products

Production of 3-hydroxypropionic acid (3-HP) or 1,3-propanediol (1,3-PDO) production from glycerol is challenging due to the problems associated with cofactor regeneration, coenzyme B₁₂ synthesis, and the instability of pathway enzymes. To address these complications, simultaneous production of 3-HP and 1,3-PDO, instead of individual production of each compound, was attempted. With over-expression of an aldehyde dehydrogenase, recombinant Klebsiella pneumoniae could co-produce 3-HP and 1,3-PDO successfully. However, the production level was unsatisfactory due to excessive accumulation of many by-products, especially acetate. To reduce acetate production, we attempted; (i) reduction of glycerol assimilation through the glycolytic pathway, (ii) increase of glycerol flow towards co-production, and (iii) variation of aeration rate. These efforts were partially beneficial in reducing acetate and improving co-production: 21g/L of 1,3-PDO and 43g/L of 3-HP were obtained. Excessive acetate (>150mM) was still produced at the end of bioreactor runs, and limited co-production efficiency.

Preeminent productivity of 1,3-propanediol by Clostridium butyricum JKT37 and the role of using calcium carbonate as pH neutraliser in glycerol fermentation

Calcium carbonate was evaluated as a replacement for the base during the fermentation of glycerol by a highly productive strain of 1,3-propanediol (PDO), viz., Clostridium butyricum JKT37. Due to its high specific growth rate (µ_max=0.53h^-1), 40g/L of glycerol was completely converted into 19.6g/L of PDO in merely 7h of batch fermentation, leaving only acetate and butyrate as the by-products. The accumulation of these volatile fatty acids was circumvented with the addition of calcium carbonate as the pH neutraliser before the fermentation was inoculated. An optimal amount of 15g/L of calcium carbonate was statistically determined from screening with various glycerol concentrations (20-120g/L). By substituting potassium hydroxide with calcium carbonate as the pH neutraliser for fermentation in a bioreactor, a similar yield (Y_PDO/glycerol=0.6mol/mol) with a constant pH was achieved at the end of the fermentation.

1,3-Propanediol production by a newly isolated strain, Clostridium perfringens GYL

1,3-Propanediol (1,3-PD), a valuable bulk industrial material, has attracted increasing interest in recent years. A novel strain GYL isolated from soil samples could efficiently convert glycerol to 1,3-PD anaerobically. The physiological and biochemical characteristics of strain GYL were determined, indicating that strain GYL is a member of Clostridium perfringens with the neighbor-joining method of 16S rRNA gene sequences. The fermentation properties of strain GYL were also investigated systematically, which showed that the strain has a fast growth speed and high tolerance to 200g/L glycerol. Batch fermentation was carried out at a high glycerol concentration of 100g/L, and strain GYL produced 36.7g/L 1,3-PD. In fed-batch fermentation, strain GYL showed a maximum productivity of 2.0g/(L·h), and produced 40.0g/L 1,3-PD, with a high yield of 0.68mol 1,3-PD/mol glycerol. This study shows that the newly isolated strain GYL may have potential for 1,3-PD production from glycerol.

Value-adding conversion and volume reduction of sewage sludge by anaerobic co-digestion with crude glycerol

In this study, conversion of sewage sludge to biogas by anaerobic co-digestion with crude glycerol was examined. When 0.126g/L crude glycerol was added to the reactor, only methane was produced. Upon addition of 5.04g/L crude glycerol, hydrogen production occurred, and a significant amount of 1,3-propanediol (1,3-PDO) was generated in the liquid phase. On day 6, the dry weight was largely composed of organic acids (48%) and 1,3-PDO (17%), which are water-soluble. Degradation of 1,3-PDO was very slow, which is advantageous for recovery. Crude glycerol, which contains alkaline substances, promoted organic matter degradation by microorganisms, which possibly affected biogas and 1,3-PDO production. Addition of 0.630-2.52g/L glycerol initially led to hydrogen production, followed by methane production a few days later, which stabilized within 1week. In conclusion, adjustment of the crude glycerol concentration allows controllable conversion to value-added products for co-digestion.

Metabolic and proteomic analyses of product selectivity and redox regulation in Clostridium pasteurianum grown on glycerol under varied iron availability

BACKGROUND

Clostridium pasteurianum as an emerging new microbial cell factory can produce both n-butanol (BuOH) and 1,3-propanediol (1,3-PDO), and the pattern of product formation changes significantly with the composition of the culture medium. Among others iron content in the medium was shown to strongly affect the products selectivity. However, the mechanism behind this metabolic regulation is still unclear. For a better understanding of such metabolic regulation and for process optimization, we carried out fermentation experiments under either iron excess or iron limitation conditions, and performed metabolic, stoichiometric and proteomic analyses.

RESULTS

1,3-PDO is most effectively produced under iron limited condition (Fe-), whereas 1,3-PDO and BuOH were both produced under iron rich condition (Fe+). With increased iron availability the BuOH/1,3-PDO ratio increased significantly from 0.27 mol/mol (at Fe-) to 1.4 mol/mol (at Fe+). Additionally, hydrogen production was enhanced significantly under Fe+ condition. Proteomic analysis revealed differentiated expression of many proteins including several ones of the central carbon metabolic pathway. Among others, pyruvate: ferredoxin oxidoreductase, hydrogenases, and several electron transfer flavoproteins was found to be strongly up-regulated under Fe+ condition, pointing to their strong involvement in the regeneration of the oxidized form of ferredoxin, and consequently their influences on the product selectivity in C. pasteurianum. Of particular significance is the finding that H2 formation in C. pasteurianum is coupled to the ferredoxin-dependent butyryl-CoA dehydrogenase catalyzed reaction, which significantly affects the redox balance and thus the product selectivity.

CONCLUSIONS

The metabolic, stoichiometric and proteomic results clearly show the key roles of hydrogenases and ferredoxins dependent reactions in determining the internal redox balance and hence product selectivity. Not only the NADH pool but also the regulation of the ferredoxin pool could explain such product variation under different iron conditions.

Coordination of metabolic pathways: Enhanced carbon conservation in 1,3-propanediol production by coupling with optically pure lactate biosynthesis

Metabolic engineering has emerged as a powerful tool for bioproduction of both fine and bulk chemicals. The natural coordination among different metabolic pathways contributes to the complexity of metabolic modification, which hampers the development of biorefineries. Herein, the coordination between the oxidative and reductive branches of glycerol metabolism was rearranged in Klebsiella oxytoca to improve the 1,3-propanediol production. After deliberating on the product value, carbon conservation, redox balance, biological compatibility and downstream processing, the lactate-producing pathway was chosen for coupling with the 1,3-propanediol-producing pathway. Then, the other pathways of 2,3-butanediol, ethanol, acetate, and succinate were blocked in sequence, leading to improved d-lactate biosynthesis, which as return drove the 1,3-propanediol production. Meanwhile, efficient co-production of 1,3-propanediol and l-lactate was also achieved by replacing ldhD with ldhL from Bacillus coagulans. The engineered strains PDL-5 and PLL co-produced over 70g/L 1,3-propanediol and over 100g/L optically pure d-lactate and l-lactate, respectively, with high conversion yields of over 0.95mol/mol from glycerol.

Multi-modular engineering of 1,3-propanediol biosynthesis system in Klebsiella pneumoniae from co-substrate

1,3-Propanediol (1,3-PDO) is a monomer for the synthesis of various polyesters. It is widely used in industries including cosmetics, solvents, and lubricants. Here, the multi-modular engineering was used to improve the concentration and tolerance of 1,3-PDO in Klebsiella pneumoniae. Firstly, the concentration of 1,3-PDO was increased by 25 %, while the concentrations of by-products were reduced considerably through one-step evolution which focused on the glycerol pathway. In addition, the 1,3-PDO tolerance was improved to 150 g L^-1. Secondly, co-substrate transport system was regulated, and the 1,3-PDO concentration, yield, and productivity of the mutant were improved to 76.4 g L^-1, 0.53 mol mol^-1, and 2.55 g L^-1 h^-1, respectively. Finally, NADH regeneration was introduced and the recombinant strain was successfully achieved with a high productivity of 2.69 g L^-1 h^-1. The concentration and yield of 1,3-PDO were also improved to 86 g L^-1 and 0.59 mol mol^-1. This strategy described here provides an approach of achieving a superior strain which is able to produce 1,3-PDO with high productivity and yield.

Effects of mutation of 2,3-butanediol formation pathway on glycerol metabolism and 1,3-propanediol production by Klebsiella pneumoniae J2B

The current study investigates the impact of mutation of 2,3-butanediol (BDO) formation pathway on glycerol metabolism and 1,3-propanediol (PDO) production by lactate dehydrogenase deficient mutant of Klebsiella pneumoniae J2B. To this end, BDO pathway genes, budA, budB, budC and budO (whole-bud operon), were deleted from K. pneumoniae J2B ΔldhA and the mutants were studied for glycerol metabolism and alcohols (PDO, BDO) production. ΔbudO-mutant-only could completely abolish BDO production, but with reductions in cell growth and PDO production. By modifying the culture medium, the ΔbudO mutant could recover its performance on the flask scale. However, in bioreactor experiments, the ΔbudO mutant accumulated a significant amount of pyruvate (>73mM) in the late phase and PDO production stopped concomitantly. Glycolytic intermediates of glycerol, especially glyceraldehyde-3-phosphate (G3P) was highly inhibitory to glycerol dehydratase (GDHt); its accumulation, followed by pyruvate accumulation, was assumed to be responsible for the ΔbudO mutant's low PDO production.

Biological valorization of pure and crude glycerol into 1,3-propanediol using a novel isolate Lactobacillus brevis N1E9.3.3

The aim of the study was to evaluate a novel onsite enrichment approach to isolate a crude glycerol utilizing facultative anaerobic bacteria. An onsite enrichment in natural conditions resulted an isolate, Lactobacillus brevis N1E9.3.3, that can utilize glycerol and produce 1,3-propanediol with a yield of 0.89g1,3-PDO/gGlycerol and productivity of 0.78g1,3-PDO/l/h at pH-8.5 under anaerobic conditions. Batch fermentation experiments with glycerol-glucose co-fermentation strategy was carried out to evaluate the production of 1,3-propanediol and other byproducts. The effect of other carbon sources as co-substrate was also evaluated. At the optimized condition, 18.6g/l 1,3-propanediol was monitored when biodiesel industry generated crude glycerol and 2.5% glucose were used as the substrate.