Simultaneous production of 3-hydroxypropionic acid and 1,3-propanediol from glycerol by a recombinant strain of Klebsiella pneumoniae

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.

Recent Advances, Challenges and Metabolic Engineering Strategies in the Biosynthesis of 3-Hydroxypropionic Acid

As an attractive and valuable platform chemical, 3-hydroxypropionic acid (3-HP) can be used to produce a variety of industrially important commodity chemicals and biodegradable polymers. Moreover, the biosynthesis of 3-HP has drawn much attention in recent years due to its sustainability and environmental friendliness. Here, we focus on recent advances, challenges and metabolic engineering strategies in the biosynthesis of 3-HP. While glucose and glycerol are major carbon sources for its production of 3-HP via microbial fermentation, other carbon sources have also been explored. To increase yield and titer, synthetic biology and metabolic engineering strategies have been explored, including modifying pathway enzymes, eliminating flux blockages due to byproduct synthesis, eliminating toxic byproducts, and optimizing via genome-scale models. This review also provides insights on future directions for 3-HP biosynthesis. This article is protected by copyright. All rights reserved.

Biochemical biorefinery: A low-cost and non-waste concept for promoting sustainable circular bioeconomy

The transition from a fossil-based linear economy to a circular bioeconomy is no longer an option but rather imperative, given worldwide concerns about the depletion of fossil resources and the demand for innovative products that are ecocompatible. As a critical component of sustainable development, this discourse has attracted wide attention at the regional and international levels. Biorefinery is an indispensable technology to implement the blueprint of the circular bioeconomy. As a low-cost, non-waste innovative concept, the biorefinery concept will spur a myriad of new economic opportunities across a wide range of sectors. Consequently, scaling up biorefinery processes is of the essence. Despite several decades of research and development channeled into upscaling biorefinery processes, the commercialization of biorefinery technology appears unrealizable. In this review, challenges limiting the commercialization of biorefinery technologies are discussed, with a particular focus on biofuels, biochemicals, and biomaterials. To counteract these challenges, various process intensification strategies such as consolidated bioprocessing, integrated biorefinery configurations, the use of highly efficient bioreactors, simultaneous saccharification and fermentation, have been explored. This study also includes an overview of biomass pretreatment-generated inhibitory compounds as platform chemicals to produce other essential biocommodities. There is a detailed examination of the technological, economic, and environmental considerations of a sustainable biorefinery. Finally, the prospects for establishing a viable circular bioeconomy in Nigeria are briefly discussed.

Biosynthesis pathways and strategies for improving 3-hydroxypropionic acid production in bacteria

3-Hydroxypropionic acid (3-HP) represents an economically important platform compound from which a panel of bulk chemicals can be derived. Compared with petroleum-dependent chemical synthesis, bioproduction of 3-HP has attracted more attention due to utilization of renewable biomass. This review outlines bacterial production of 3-HP, covering aspects of host strains (e.g., Escherichia coli and Klebsiella pneumoniae), metabolic pathways, key enzymes, and hurdles hindering high-level production. Inspired by the state-of-the-art advances in metabolic engineering and synthetic biology, we come up with protocols to overcome the hurdles constraining 3-HP production. The protocols range from rewiring of metabolic networks, alleviation of metabolite toxicity, to dynamic control of cell size and density. Especially, this review highlights the substantial contribution of microbial growth to 3-HP production, as we recognize the synchronization between cell growth and 3-HP formation. Accordingly, we summarize the following growth-promoting strategies: (i) optimization of fermentation conditions; (ii) construction of gene circuits to alleviate feedback inhibition; (iii) recruitment of RNA polymerases to overexpress key enzymes which in turn boost cell growth and 3-HP production. Lastly, we propose metabolic engineering approaches to simplify downstream separation and purification. Overall, this review aims to portray a picture of bacterial production of 3-HP.

Development of Pseudomonas asiatica as a host for the production of 3-hydroxypropionic acid from glycerol

Pseudomonas asiatica C1, which could grow on glucose and aerobically synthesize coenzyme B₁₂, was isolated and developed as a microbial cell factory for the production of 3-hydroxypropionic acid (3-HP) from glycerol. Three heterologous enzymes, glycerol dehydratase (GDHt), GDHt reactivase (GdrAB) and aldehyde dehydrogenase (ALDH), constituting the 3-HP synthesis pathway, were introduced, and three putative dehydrogenases, responsible for 3-HP degradation, were disrupted. In addition, the transcriptional repressor glpR and the glycerol kinase glpK were removed to increase glycerol import while eliminating the catabolic use of glycerol. Furthermore, the global regulatory protein encoded by crc and several putative oxidoreductases (PDORs) were disrupted. One resulting strain, when grown on glucose, could produce 3-HP at ~ 700 mM in 48 h in a fed-batch bioreactor experiment, with the molar yield > 0.99 on glycerol without much by-products. This study demonstrates that P. asiatica C1 is a promising host for production of 3-HP from glycerol.

Poly(3-hydroxypropionate): Biosynthesis Pathways and Malonyl-CoA Biosensor Material Properties

Many single-use non-degradable plastics are a threat to life today, and several polyhydroxyalkanoates (PHAs) biopolymers have been developed in the bioplastic industry to place petrochemical-based plastics. One of such is the novel biomaterial poly(3-hydroxypropionate) [poly(3HP)] because of its biocompatibility, biodegradability, and high yield synthesis using engineered strains. To date, many bio-polymer-based functional composites have been developed to increase the value of raw microbial-biopolymers obtained from cheap sources. This review article broadly covers poly(3HP), a comprehensive summary of critical biosynthetic production pathways comparing the yields and titers achieved in different Microbial cell Factories. This article also provides extensive knowledge and highlights recent progress on biosensors' use to optimize poly(3HP) production, some bacteria host adopted for production, chemical and physical properties, life cycle assessment for poly(3HP) production using corn oil as carbon source, and some essential medical applications of poly(3HP).

Psychrophile-based simple biocatalysts for effective coproduction of 3-hydroxypropionic acid and 1,3-propanediol

3-Hydroxypropionic acid (3-HP) and 1,3-propanediol (1,3-PDO) have tremendous potential markets in many industries. This study evaluated the simultaneous biosynthesis of the 2 compounds using the new psychrophile-based simple biocatalyst (PSCat) reaction system. The PSCat method is based on the expression of glycerol dehydratase, 1,3-propanediol dehydrogenase, and aldehyde dehydrogenase from Klebsiella pneumoniae in Shewanella livingstonensis Ac10 and Shewanella frigidimarina DSM 12253, individually. Heat treatment at 45 °C for 15 min deactivated the intracellular metabolic flux, and the production process was started after adding substrate, cofactor, and coenzyme. In the solo production process after 1 h, the maximum production of 3-HP was 62.0 m m. For 1,3-PDO, the maximum production was 25.0 m m. In the simultaneous production process, productivity was boosted, and the production of 3-HP and 1,3-PDO increased by 13.5 and 4.9 m m, respectively. Hence, the feasibility of the individual production and the simultaneous biosynthesis system were verified in the new PSCat approach.

Strengthening the TCA cycle to alleviate metabolic stress due to blocking by-products synthesis pathway in Klebsiella pneumoniae

1,3-Propanediol (1,3-PDO) is an important synthetic monomer for the production of polytrimethylene terephthalate (PTT). Here, we engineered Klebsiella pneumoniae by a multi-strategy to improve 1,3-PDO production and reduce by-products synthesis. First, the 2,3-butanediol (2,3-BDO) synthesis pathway was blocked by deleting the budB gene, resulting in a 74% decrease of 2,3-BDO titer. The synthesis of lactate was decreased by 79% via deleting the ldhA gene, leading to a 10% increase of 1,3-PDO titer. Further, reducing ethanol synthesis by deleting the aldA gene led to a 64% decrease of ethanol titer, and the 1,3-PDO titer and yield on glycerol increased by 12 and 10%, respectively. Strengthening the TCA cycle by overexpressing the mdh gene improved 1,3-PDO synthesis effectively. Under 5-L fed-batch fermentation conditions, compared to wild type strain, the production of 2,3-BDO, lactate and ethanol in the mutant strain decreased by 73, 65 and 50%, respectively. Finally, the production of 1,3-PDO was 73.5 g/L with a molar yield of 0.67 mol/mol glycerol, improved 16% and 20%, respectively. This work provides a combined strategy for improving 1,3-PDO production by strengthening the TCA cycle to relieve metabolic stress by deleting genes of by-products synthesis, which was also beneficial for the extraction and separation of downstream products.

Investigation of fermentation conditions of biodiesel by-products for high production of β-farnesene by an engineered Escherichia coli

Recently, the research on conversion of biodiesel by-products to high value-added products has received much attention, due to the adverse effects of large accumulations of biodiesel by-products caused by the rapid increase in biodiesel production. Herein, this study investigated the utilization of by-products crude glycerol (CG-1 and CG-2) from two different industrial methods of biodiesel production and the favorable fermentation conditions for the high yield of β-farnesene by an engineered Escherichia coli F4, which harbored an optimized mevalonate pathway. Through analyzing by-products' components and fermentation performance, we found that CG-2 did not contain harmful impurities such as methanol and black solid impurities, and the β-farnesene production was up to 2.7 g/L from CG-2, which was similar to that from pure glycerol (2.5 g/L) and higher than that (2.21 g/L) from CG-1. Therefore, CG-2 was more suitable for β-farnesene production than CG-1, which might provide a reference for choosing a more suitable method on practical biodiesel production. Afterward, a variety of important fermentation conditions were explored using CG-2 as a substrate in shaken flasks. Under the optimal conditions (including induced cell density 1.0, initial cell density 0.25, temperature after induction 33 °C, initial medium pH 6.5), the yield of β-farnesene from CG-2 reached 10.31 g/L in a 5-L bioreactor, which was 2.8-fold higher than initial conditions in shake flasks and was the highest yield of β-farnesene produced from biodiesel by-products by fermentation as well. The recommended fermentation conditions in this work will provide a valuable reference for the industrial production of β-farnesene utilizing biodiesel by-products.

Analysis of the Growth and Metabolites of a Pyruvate Dehydrogenase Complex- Deficient Klebsiella pneumoniae Mutant in a Glycerol-Based Medium

To determine the role of pyruvate dehydrogenase complex (PDHC) in Klebsiella pneumoniae, the growth and metabolism of PDHC-deficient mutant in glycerol-based medium were analyzed and compared with those of other strains. Under aerobic conditions, the PDHC activity was fourfold higher than that of pyruvate formate lyase (PFL), and blocking of PDHC caused severe growth defect and pyruvate accumulation, indicating that the carbon flux through pyruvate to acetyl coenzyme A mainly depended on PDHC. Under anaerobic conditions, although the PDHC activity was only 50% of that of PFL, blocking of PDHC resulted in more growth defect than blocking of PFL. Subsequently, combined with the requirement of CO2 and intracellular redox status, it was presumed that the critical role of PDHC was to provide NADH for the anaerobic growth of K. pneumoniae. This presumption was confirmed in the PDHC-deficient mutant by further blocking one of the formate dehydrogenases, FdnGHI. Besides, based on our data, it can also be suggested that an improvement in the carbon flux in the PFL-deficient mutant could be an effective strategy to construct highyielding 1,3-propanediol-producing K. pneumoniae strain.

High-level production of 3-hydroxypropionic acid from glycerol as a sole carbon source using metabolically engineered Escherichia coli

As climate change is an important environmental issue, the conventional petrochemical-based processes to produce valuable chemicals are being shifted toward eco-friendly biological-based processes. In this study, 3-hydroxypropionic acid (3-HP), an industrially important three carbon (C3) chemical, was overproduced by metabolically engineered Escherichia coli using glycerol as a sole carbon source. As the first step to construct a glycerol-dependent 3-HP biosynthetic pathway, the dhaB1234 and gdrAB genes from Klebsiella pneumoniae encoding glycerol dehydratase and glycerol reactivase, respectively, were introduced into E. coli to convert glycerol into 3-hydroxypropionaldehyde (3-HPA). In addition, the ydcW gene from K. pneumoniae encoding γ-aminobutyraldehyde dehydrogenase, among five aldehyde dehydrogenases examined, was selected to further convert 3-HPA to 3-HP. Increasing the expression level of the ydcW gene enhanced 3-HP production titer and reduced 1,3-propanediol production. To enhance 3-HP production, fed-batch fermentation conditions were optimized by controlling dissolved oxygen (DO) level and employing different feeding strategies including intermittent feeding, pH-stat feeding, and continuous feeding strategies. Fed-batch culture of the final engineered E. coli strain with DO control and continuous feeding strategy produced 76.2 g/L of 3-HP with the yield and productivity of 0.457 g/g glycerol and 1.89 g·L^-1 ·h^-1 , respectively. To the best of our knowledge, this is the highest 3-HP productivity achieved by any microorganism reported to date.

Metabolic engineering of type II methanotroph, Methylosinus trichosporium OB3b, for production of 3-hydroxypropionic acid from methane via a malonyl-CoA reductase-dependent pathway

We engineered a type II methanotroph, Methylosinus trichosporium OB3b, for 3-hydroxypropionic acid (3HP) production by reconstructing malonyl-CoA pathway through heterologous expression of Chloroflexus aurantiacus malonyl-CoA reductase (MCR), a bifunctional enzyme. Two strategies were designed and implemented to increase the malonyl-CoA pool and thus, increase in 3HP production. First, we engineered the supply of malonyl-CoA precursors by overexpressing endogenous acetyl-CoA carboxylase (ACC), substantially enhancing the production of 3HP. Overexpression of biotin protein ligase (BPL) and malic enzyme (NADP⁺-ME) led to a ∼22.7% and ∼34.5% increase, respectively, in 3HP titer in ACC-overexpressing cells. Also, the acetyl-CoA carboxylation bypass route was reconstructed to improve 3HP productivity. Co-expression of methylmalonyl-CoA carboxyltransferase (MMC) of Propionibacterium freudenreichii and phosphoenolpyruvate carboxylase (PEPC), which provides the MMC precursor, further improved the 3HP titer. The highest 3HP production of 49 mg/L in the OB3b-MCRMP strain overexpressing MCR, MMC and PEPC resulted in a 2.4-fold improvement of titer compared with that in the only MCR-overexpressing strain. Finally, we could obtain 60.59 mg/L of 3HP in 42 h using the OB3b-MCRMP strain through bioreactor operation, with a 6.36-fold increase of volumetric productivity compared than that in the flask cultures. This work demonstrates metabolic engineering of type II methanotrophs, opening the door for using type II methanotrophs as cell factories for biochemical production along with mitigation of greenhouse gases.

Enhancement of 1,3-propanediol production from industrial by-product by Lactobacillus reuteri CH53

Background

1,3-propanediol (1,3-PDO) is the most widely studied value-added product that can be produced by feeding glycerol to bacteria, including Lactobacillus sp. However, previous research reported that L. reuteri only produced small amounts and had low productivity of 1,3-PDO. It is urgent to develop procedures that improve the production and productivity of 1,3-PDO.

Results

We identified a novel L. reuteri CH53 isolate that efficiently converted glycerol into 1,3-PDO, and performed batch co-fermentation with glycerol and glucose to evaluate its production of 1,3-PDO and other products. We optimized the fermentation conditions and nitrogen sources to increase the productivity. Fed-batch fermentation using corn steep liquor (CSL) as a replacement for beef extract led to 1,3-PDO production (68.32 ± 0.84 g/L) and productivity (1.27 ± 0.02 g/L/h) at optimized conditions (unaerated and 100 rpm). When CSL was used as an alternative nitrogen source, the activity of the vitamin B12-dependent glycerol dehydratase (dhaB) and 1,3-propanediol oxidoreductase (dhaT) increased. Also, the productivity and yield of 1,3-PDO increased as well. These results showed the highest productivity in Lactobacillus species. In addition, hurdle to 1,3-PDO production in this strain were identified via analysis of the half-maximal inhibitory concentration for growth (IC50) of numerous substrates and metabolites.

Conclusions

We used CSL as a low-cost nitrogen source to replace beef extract for 1,3-PDO production in L. reuteri CH53. These cells efficiently utilized crude glycerol and CSL to produce 1,3-PDO. This strain has great promise for the production of 1,3-PDO because it is generally recognized as safe (GRAS) and non-pathogenic. Also, this strain has high productivity and high conversion yield.

Regulation of Pyruvate Formate Lyase-Deficient Klebsiella pneumoniae for Efficient 1,3-Propanediol Bioproduction

Anaerobic growth defect of pyruvate formate lyase (PFL)-deficient Klebsiella pneumoniae limits its industrial application, and the reason for this growth defect was analyzed in this study. The obtained evidences, combined with normal intracellular redox status and no further inhibition by adhE deletion, strongly suggested that growth defect in PFL-deficient K. pneumoniae was probably caused by lack of carbon flux from pyruvate to acetyl-CoA (AcCoA). Correspondingly, the anaerobic growth of PFL-deficient K. pneumoniae was promoted by deletion of pdhR, a negative transcriptional regulator gene for AcCoA generation. Through the regulation of pdhR deletion, the PFL-deficient K. pneumoniae exhibited highly efficient 1,3-propanediol production. Besides, in a 2-L fed-batch fermentation process, the cell growth of PFL-deficient K. pneumoniae strain almost recovered, when compared with that of the normal strain, and the 1,3-propanediol yield increased by 14%, while the byproducts acetate and 2,3-butanediol contents decreased by 29% and 24%, respectively.

Screening, identification, and low-energy ion modified breeding of a yeast strain producing high level of 3-hydroxypropionic acid

3-Hydroxypropionic acid (3HP) is an important platform chemical with a wide range of applications. The biological preparation of this compound is safe and low cost. In this study, orchard soil and human waste were used as raw materials to screen microbial strains that could produce 3HP in selective medium containing varying amounts of propionic acid. A yeast strain that can use propionic acid as substrate and produce 48.96 g/L 3HP was screened. Morphological observation, physiological and biochemical identification, and 26s rDNA sequencing identified the IS451 strain as Debaryomyces hansenii. The low-energy ion N⁺ , with the energy of 10 keV and a dose of 70 × 2.6 × 10¹³  ions/cm² , was implanted into the IS451 strain. The mutant strain WT39, whose 3HP titer reached 62.42 g/L, was obtained. The strain exhibited genetic stability and tolerance to high concentrations of propionic acid and was considered to have broad application prospects.

Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria

3-hydroxypropanoic acid (3-HP) is a valuable platform chemical with a high demand in the global market. 3-HP can be produced from various renewable resources. It is used as a precursor in industrial production of a number of chemicals, such as acrylic acid and its many derivatives. In its polymerized form, 3-HP can be used in bioplastic production. Several microbes naturally possess the biosynthetic pathways for production of 3-HP, and a number of these pathways have been introduced in some widely used cell factories, such as Escherichia coli and Saccharomyces cerevisiae. Latest advances in the field of metabolic engineering and synthetic biology have led to more efficient methods for bio-production of 3-HP. These include new approaches for introducing heterologous pathways, precise control of gene expression, rational enzyme engineering, redirecting the carbon flux based on in silico predictions using genome scale metabolic models, as well as optimizing fermentation conditions. Despite the fact that the production of 3-HP has been extensively explored in established industrially relevant cell factories, the current production processes have not yet reached the levels required for industrial exploitation. In this review, we explore the state of the art in 3-HP bio-production, comparing the yields and titers achieved in different microbial cell factories and we discuss possible methodologies that could make the final step toward industrially relevant cell factories.

Engineering an aldehyde dehydrogenase toward its substrates, 3-hydroxypropanal and NAD+, for enhancing the production of 3-hydroxypropionic acid

3-Hydroxypropionic acid (3-HP) can be produced via the biological route involving two enzymatic reactions: dehydration of glycerol to 3-hydroxypropanal (3-HPA) and then oxidation to 3-HP. However, commercial production of 3-HP using recombinant microorganisms has been hampered with several problems, some of which are associated with the toxicity of 3-HPA and the efficiency of NAD⁺ regeneration. We engineered α-ketoglutaric semialdehyde dehydrogenase (KGSADH) from Azospirillum brasilense for the second reaction to address these issues. The residues in the binding sites for the substrates, 3-HPA and NAD⁺, were randomized, and the resulting libraries were screened for higher activity. Isolated KGSADH variants had significantly lower K_m values for both the substrates. The enzymes also showed higher substrate specificities for aldehyde and NAD⁺, less inhibition by NADH, and greater resistance to inactivation by 3-HPA than the wild-type enzyme. A recombinant Pseudomonas denitrificans strain with one of the engineered KGSADH variants exhibited less accumulation of 3-HPA, decreased levels of inactivation of the enzymes, and higher cell growth than that with the wild-type KGSADH. The flask culture of the P. denitrificans strain with the mutant KGSADH resulted in about 40% increase of 3-HP titer (53 mM) compared with that using the wild-type enzyme (37 mM).

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.

Cloning of D-lactate dehydrogenase genes of Lactobacillus delbrueckii subsp. bulgaricus and their roles in D-lactic acid production

Lactobacillus delbrueckii subsp. bulgaricus is a heterogenous lactic acid bacterium that converts pyruvate mainly to D-lactic acid using D-lactate dehydrogenases (D-LDHs), whose functional properties remain poorly characterized. Here, the D-LDHs genes (ldb0101, ldb0813, ldb1010, ldb1147 and ldb2021) were cloned and overexpressed in Escherichia coli JM109 from an inducible pUC18 vector, respectively, and the resulting strains were compared in terms of D-lactic acid production. The strain expressing ldb0101 and ldb1010 gene individually produced more D-lactate than other three strains. Further study revealed that Ldb0101 activity was down-regulated by the oxygen and, therefore, achieved a highest titer of D-lactate (1.94 g/L) under anaerobic condition, and introduction of ldb1010 gene enhanced D-lactate formation (0.94 and 0.85 g/L, respectively) both in aerobic and anaerobic conditions due to a relatively stable q _d-lactate. Our results suggested that the enzyme Ldb0101 and Ldb1010 played a role of more importance in D-lactate formation. To the best of our knowledge, we demonstrate for the first time the roles of different D-LDH homologs from L. bulgaricus in D-lactic acid production.

3-Hydroxypropionic acid production by recombinant Escherichia coli ZJU-3HP01 using glycerol-glucose dual-substrate fermentative strategy

3-Hydroxypropionic acid (3-HP) is an important platform synthesis block for sets of chemicals, but the relatively low production of 3-HP from biological sources presented major barriers for its industrial applications. In this study, a dual-substrate fermentative strategy by glycerol and glucose was proposed, and the aim was to evaluate the effect of different substrate addition strategies on the fermentation process. The results indicated that the optimal cosubstrate was glucose (20 g/L), and the enzymatic activity of aldehyde dehydrogenase (AldH) could be improved 3.5-fold as compared with no glucose addition. Continuous fed-batch fermentation at a constant speed displayed better 3-HP production of 17.20 g/L and highest specific 3-HP productivity of 1.79 mmol/(g cell·H) than the other fed-batch mode. The addition of glucose could greatly reduce the imbalance of the activity between glycerol dehydratase and AldH and provide a feasible method for improving 3-HP production. These results would be helpful in developing the 3-HP fermentation process.

Production of 3-hydroxypropionic acid via the malonyl-CoA pathway using recombinant fission yeast strains

3-Hydroxypropionic acid (3-HP) can be converted into derivatives such as acrylic acid, a source for producing super absorbent polymers. Although Escherichia coli has often been used for 3-HP production, it exhibits low tolerance to 3-HP. To circumvent this problem, we selected the fission yeast Schizosaccharomyces pombe as this microorganism has higher tolerance to 3-HP than E. coli. Therefore, we constructed S. pombe transformants overexpressing two genes, one encoding the S. pombe acetyl-CoA carboxylase (Cut6p) and the other encoding the malonyl-CoA reductase derived from Chloroflexus aurantiacus (CaMCR). To prevent the degradation of these expressed proteins, we employed an S. pombe protease-deficient strain. Moreover, to increase the cytosolic concentration of acetyl-CoA, we supplemented acetate to the medium, which improved 3-HP production. To further produce 3-HP by overexpressing Cut6p and CaMCR, we exploited the highly expressing S. pombe hsp9 promoter. Finally, culturing in high-density reached 3-HP production to 7.6 g/L at 31 h.

Efficient anaerobic production of succinate from glycerol in engineered Escherichia coli by using dual carbon sources and limiting oxygen supply in preceding aerobic culture

Glycerol is an important resource for production of value-added bioproducts due to its large availability from the biodiesel industry as a by-product. In this study, two metabolic regulation strategies were applied in the aerobic stage of a two-stage fermentation to achieve high metabolic capacities of the pflB ldhA double mutant Escherichia coli strain overexpressing phosphoenolpyruvate carboxykinase (PCK) in the subsequent anaerobic stage: use of acetate as a co-carbon source of glycerol and restriction of oxygen supply in the PCK induction period. The succinate concentration achieved 926.7mM with a yield of 0.91mol/mol during the anaerobic stage of fermentation in a 1.5-L reactor. qRT-PCR indicated that the two strategies enhanced transcription of genes related with glycerol metabolism and succinate production. Our results showed this metabolically engineered E. coli strain has a great potential in producing succinate using glycerol as carbon source.

Conversion of Glycerol to 3-Hydroxypropanoic Acid by Genetically Engineered Bacillus subtilis

3-Hydroxypropanoic acid (3-HP) is an important biomass-derivable platform chemical that can be converted into a number of industrially relevant compounds. There have been several attempts to produce 3-HP from renewable sources in cell factories, focusing mainly on Escherichia coli, Klebsiella pneumoniae, and Saccharomyces cerevisiae. Despite the significant progress made in this field, commercially exploitable large-scale production of 3-HP in microbial strains has still not been achieved. In this study, we investigated the potential of Bacillus subtilis as a microbial platform for bioconversion of glycerol into 3-HP. Our recombinant B. subtilis strains overexpress the two-step heterologous pathway containing glycerol dehydratase and aldehyde dehydrogenase from K. pneumoniae. Genetic engineering, driven by in silico optimization, and optimization of cultivation conditions resulted in a 3-HP titer of 10 g/L, in a standard batch cultivation. Our findings provide the first report of successful introduction of the biosynthetic pathway for conversion of glycerol into 3-HP in B. subtilis. With this relatively high titer in batch, and the robustness of B. subtilis in high density fermentation conditions, we expect that our production strains may constitute a solid basis for commercial production of 3-HP.

Anodic electro-fermentation of 3-hydroxypropionic acid from glycerol by recombinant Klebsiella pneumoniae L17 in a bioelectrochemical system

BACKGROUND

3-Hydroxypropionic acid (3-HP) is an important platform chemical which can be produced biologically from glycerol. Klebsiella pneumoniae is an ideal biocatalyst for 3-HP because it can grow well on glycerol and naturally synthesize the essential coenzyme B₁₂. On the other hand, if higher yields and titers of 3-HP are to be achieved, the sustained regeneration of NAD⁺ under anaerobic conditions, where coenzyme B₁₂ is synthesized sustainably, is required.

RESULTS

In this study, recombinant K. pneumoniae L17 overexpressing aldehyde dehydrogenase (AldH) was developed and cultured in a bioelectrochemical system (BES) with the application of an electrical potential to the anode using a chronoamperometric method (+0.5 V vs. Ag/AgCl). The BES operation resulted in 1.7-fold enhancement of 3-HP production compared to the control without the applied potential. The intracellular NADH/NAD⁺ ratio was significantly lower when the L17 cells were grown under an electric potential. The interaction between the electrode and overexpressed AldH was enhanced by electron shuttling mediated by HNQ (2-hydroxy-1,4-naphthoquinone).

CONCLUSIONS

Enhanced 3-HP production by the BES was achieved using recombinant K. pneumoniae L17. The quinone-based electron transference between the electrode and L17 was investigated by respiratory uncoupler experiments. This study provides a novel strategy to control the intracellular redox states to enhance the yield and titer of 3-HP production as well as other bioconversion processes.

The Role of the Pyruvate Acetyl-CoA Switch in the Production of 1,3-Propanediol by Klebsiella pneumoniae

Pyruvate dehydrogenase-complex (AcoABCD) and pyruvate formate-lyase (PFL) are two pathways responsible for synthesis of acetyl-CoA from pyruvate (pyruvate acetyl-CoA switch). The two pathways were individually deleted in Klebsiella pneumoniae, and the role of the pyruvate acetyl-CoA switch in 1,3-propanediol production was investigated. Fermentation results showed that the two pathways were both active in the wild-type strain. Acetyl-CoA formation between the two pathways was equal in the wild-type strain. The pflB mutant produced high level of lactic acid, and deletion of ldhA eliminated lactic acid synthesis. The conversion ratio of glycerol to 1,3-propanediol in the pflB-ldhA mutant reached 0.541 g/g, which was 9.4 % higher than that of the wild-type strain. However, the productivity of 1,3-propanediol was decreased in the pflB-ldhA mutant. In contrast, the productivity of 1,3-propanediol was increased by 19 % in the acoABCD mutant, with the disadvantage of lower substrate conversion ratio. Regulating the pyruvate acetyl-CoA switch presents a novel way to improve the conversion ratio or productivity of 1,3-propanediol produced by K. pneumoniae.

Enhanced succinate production from glycerol by engineered Escherichia coli strains

In this study, an engineered strain Escherichia coli MLB (ldhA(-)pflB(-)) was constructed for production of succinate from glycerol. The succinate yield was 0.37mol/mol in anaerobic culture, however, the growth and glycerol consumption rates were very slow, resulting in a low succinate level. Two-stage fermentation was performed in flasks, and the succinate yield reached 0.93mol/mol, but the succinate titer was still low. Hence, overexpression of malate dehydrogenase, malic enzyme, phosphoenolpyruvate (PEP) carboxylase and PEP carboxykinase (PCK) from E. coli, and pyruvate carboxylase from Corynebacterium glutamicum in MLB was investigated for improving succinate production. Overexpression of PCK resulted in remarkable enhancement of glycerol consumption and succinate production. In flask experiments, the succinate concentration reached 118.1mM, and in a 1.5-L bioreactor the succinate concentration further increased to 360.2mM. The highest succinate yield achieved 0.93mol/mol, which was 93% of the theoretical yield, in the anaerobic stage.

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.

Synthesis of chemicals by metabolic engineering of microbes

Metabolic engineering is a powerful tool for the sustainable production of chemicals. Over the years, the exploration of microbial, animal and plant metabolism has generated a wealth of valuable genetic information. The prudent application of this knowledge on cellular metabolism and biochemistry has enabled the construction of novel metabolic pathways that do not exist in nature or enhance existing ones. The hand in hand development of computational technology, protein science and genetic manipulation tools has formed the basis of powerful emerging technologies that make the production of green chemicals and fuels a reality. Microbial production of chemicals is more feasible compared to plant and animal systems, due to simpler genetic make-up and amenable growth rates. Here, we summarize the recent progress in the synthesis of biofuels, value added chemicals, pharmaceuticals and nutraceuticals via metabolic engineering of microbes.

Activation of glycerol metabolic pathway by evolutionary engineering of Rhizopus oryzae to strengthen the fumaric acid biosynthesis from crude glycerol

Rhizopus oryzae is strictly inhibited by biodiesel-based by-product crude glycerol, which results in low fumaric acid production. In this study, evolutionary engineering was employed to activate the glycerol utilization pathway for fumaric acid production. An evolved strain G80 was selected, which could tolerate and utilize high concentrations of crude glycerol to produce 14.9g/L fumaric acid with a yield of 0.248g/g glycerol. Key enzymes activity analysis revealed that the evolved strain displayed a significant upregulation in glycerol dissimilation, pyruvate consumption and reductive tricarboxylic acid pathways, compared with the parent strain. Subsequently, intracellular metabolic profiling analysis showed that amino acid biosynthesis, tricarboxylic acid cycle, fatty acid and stress response metabolites accounted for metabolic difference between two strains. Moreover, a glycerol fed-batch strategy was optimized to obtain the highest fumaric acid production of 25.5g/L, significantly increased by 20.9-fold than that of the parent strain of 1.2g/L.

An S188V mutation alters substrate specificity of non-stereospecific α-haloalkanoic acid dehalogenase E (DehE)

The non-stereospecific α-haloalkanoic acid dehalogenase E (DehE) degrades many halogenated compounds but is ineffective against β-halogenated compounds such as 3-chloropropionic acid (3CP). Using molecular dynamics (MD) simulations and site-directed mutagenesis we show here that introducing the mutation S188V into DehE improves substrate specificity towards 3CP. MD simulations showed that residues W34, F37, and S188 of DehE were crucial for substrate binding. DehE showed strong binding ability for D-2-chloropropionic acid (D-2CP) and L-2-chloropropionic acid (L-2CP) but less affinity for 3CP. This reduced affinity was attributed to weak hydrogen bonding between 3CP and residue S188, as the carboxylate of 3CP forms rapidly interconverting hydrogen bonds with the backbone amide and side chain hydroxyl group of S188. By replacing S188 with a valine residue, we reduced the inter-molecular distance and stabilised bonding of the carboxylate of 3CP to hydrogens of the substrate-binding residues. Therefore, the S188V can act on 3CP, although its affinity is less strong than for D-2CP and L-2CP as assessed by K_m. This successful alteration of DehE substrate specificity may promote the application of protein engineering strategies to other dehalogenases, thereby generating valuable tools for future bioremediation technologies.

1,3-Propanediol production by Klebsiella oxytoca NRRL-B199 from glycerol. Medium composition and operational conditions

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1,3-Propanediol is produced from glycerol using Klebsiella oxytoca NRRL-B199.

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The medium composition was optimized by an orthogonal experimental design.

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Scale-up form shaken bottles to STBR was studied.

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Operating conditions, agitation and temperature, were optimized.

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Under these conditions, 13.5 g/L of propanediol (selectivity = 86% with respect to glycerol) can be obtained.

Production of 1,3-propanediol from glycerol using Klebsiella oxytoca NRRL-B199 has been studied. Medium composition has been optimized by means of a statistical design based on the Taguchi method. Strong influences of glycerol and phosphate concentrations have been detected on biomass and product yields. Other factors, such as magnesium concentration and K:Na ratio, have shown a small influence on both responses, biomass and product concentrations. An optimized medium composition has been proposed, leading to a final 1,3-propanediol concentration of 12.4 g/L with a selectivity of 72% with respect to glycerol consumed at shaken bottle-scale. Once the medium composition had been optimized, the scale-up from shaken bottles to STBR was conducted. Several experiments in a 2 L STBR have been conducted in order to determine the best operating conditions concerning temperature and agitation.

Under the best operating conditions, i.e., a programmed variable stirring rate ranging from 50 to 100 rpm and a temperature of 37 °C, a final concentration of 13.5 g/L of 1,3-propanediol with a selectivity of 86% with respect to the glycerol consumed was obtained.

A novel biocatalyst for efficient production of 2-oxo-carboxylates using glycerol as the cost-effective carbon source

BACKGROUND

The surplus of glycerol has increased remarkably as a main byproduct during the biofuel's production. Exploiting an alternative route for glycerol utilization is significantly important for sustainability of biofuels.

RESULTS

A novel biocatalyst that could be prepared from glycerol for producing 2-oxo-carboxylates was developed. First, Pseudomonas putida KT2440 was reconstructed by deleting lldR to develop a mutant expressing the NAD-independent lactate dehydrogenases (iLDHs) constitutively. Then, the Vitreoscilla hemoglobin (VHb) was heterologously expressed to further improve the biotransformation activity. The reconstructed strain, P. putida KT2440 (ΔlldR)/pBSPPcGm-vgb, exhibited high activities of iLDHs when cultured with glycerol as the carbon source. This cost-effective biocatalyst could efficiently produce pyruvate and 2-oxobutyrate from dl-lactate and dl-2-hydroxybutyrate with high molar conversion rates of 91.9 and 99.8 %, respectively.

CONCLUSIONS

The process would not only be a promising alternative for the production of 2-oxo-carboxylates, but also be an example for preparation of efficient biocatalysts for the value-added utilization of glycerol.

Gas Chromatographic Method for the Analysis of Organic Acids in the Bio-Catalytic Conversion Process

An analytical method for the quantification of acrylic acid (AA), 1,3-propanediol (1,3-PD) and 3-hydroxypropionic acid (3-HP) in the bio-catalytic conversion process has been developed by gas chromatography. A simple liquid-liquid extraction (LLE) procedure was used in the sample preparation. Organic acid additives such as trifluoroacetic acid were used to improve the extraction efficiency in the LLE procedure. Under optimum analysis conditions, all analytes were satisfactorily separated with no interference. In standard calibration, all correlation coefficients (r(2)) were better than or equal to 0.994. In culture media, the intra-batch precision (% relative standard deviation) and recovery (%) as the average value of the quality control samples were 2.3 and 102.4%, respectively. In addition, the inter-batch precision and recovery as the average value of the quality control samples were 5.0 and 104.0%, respectively. In phosphate buffer, the intra-batch precision and recovery as the average value of the quality control samples were 2.7 and 101.6%, respectively. In addition, the inter-batch precision and recovery as the average value of the quality control samples were 2.9 and 101.7%, respectively. The limit of detection (S/N ratio: 3) and limit of quantification (S/N ratio: 10) were 1.0 and 3.5 µg/mL, 3.0 and 10.0 µg/mL, and 9.0 and 30.0 µg/mL, respectively, for AA, 1,3-PD and 3-HP. Consequently, this method was demonstrated to be acceptable for the quantitative analysis of AA, 1,3-PD and 3-HP in culture media and phosphate buffer.

Production of optically pure d-lactate from glycerol by engineered Klebsiella pneumoniae strain

In this study, glycerol was used to produce optically pure d-lactate by engineered Klebsiella pneumoniae strain. In the recombinant strain, d-lactate dehydrogenase LdhA was overexpressed, and two genes, dhaT and yqhD for biosynthesis of main byproduct 1,3-propanediol, were knocked out. To further improve d-lactate production, the culture condition was optimized and the results demonstrated that aeration rate played an important role in d-lactate production. In microaerobic fed-batch fermentation, the engineered strain accumulated 142.1g/L optically pure d-lactate with a yield of 0.82g/g glycerol, which represented the highest d-lactate production from glycerol so far. This study showed that K. pneumoniae strain has high efficiency to convert glycerol into d-lactate and high potentiality in utilization of crude glycerol from biodiesel industry.