Microbial production of short chain diols

Next-generation feedstocks methanol and ethylene glycol and their potential in industrial biotechnology

Microbial fermentation processes are expected to play an important role in reducing dependence on fossil-based raw materials for the production of everyday chemicals. In order to meet the growing demand for biotechnological products in the future, alternative carbon sources that do not compete with human nutrition must be exploited. The chemical conversion of the industrially emitted greenhouse gas CO2 into microbially utilizable platform chemicals such as methanol represents a sustainable strategy for the utilization of an abundant carbon source and has attracted enormous scientific interest in recent years. A relatively new approach is the microbial synthesis of products from the C2-compound ethylene glycol, which can also be synthesized from CO2 and non-edible biomass and, in addition, can be recovered from plastic waste. Here we summarize the main chemical routes for the synthesis of methanol and ethylene glycol from sustainable resources and give an overview of recent metabolic engineering work for establishing natural and synthetic microbial assimilation pathways. The different metabolic routes for C1 and C2 alcohol-dependent bioconversions were compared in terms of their theoretical maximum yields and their oxygen requirements for a wide range of value-added products. Assessment of the process engineering challenges for methanol and ethylene glycol-based fermentations underscores the theoretical advantages of new synthetic metabolic routes and advocates greater consideration of ethylene glycol, a C2 substrate that has received comparatively little attention to date.

Biorefineries: Achievements and challenges for a bio-based economy

Climate change, socioeconomical pressures, and new policy and legislation are driving a decarbonization process across industries, with a critical shift from a fossil-based economy toward a biomass-based one. This new paradigm implies not only a gradual phasing out of fossil fuels as a source of energy but also a move away from crude oil as a source of platform chemicals, polymers, drugs, solvents and many other critical materials, and consumer goods that are ubiquitous in our everyday life. If we are to achieve the United Nations' Sustainable Development Goals, crude oil must be substituted by renewable sources, and in this evolution, biorefineries arise as the critical alternative to traditional refineries for producing fuels, chemical building blocks, and materials out of non-edible biomass and biomass waste. State-of-the-art biorefineries already produce cost-competitive chemicals and materials, but other products remain challenging from the economic point of view, or their scaled-up production processes are still not sufficiently developed. In particular, lignin's depolymerization is a required milestone for the success of integrated biorefineries, and better catalysts and processes must be improved to prepare bio-based aromatic simple molecules. This review summarizes current challenges in biorefinery systems, while it suggests possible directions and goals for sustainable development in the years to come.

Cell-Free Biosynthesis of ω-Hydroxy Acids Boosted by a Synergistic Combination of Alcohol Dehydrogenases

The activity orchestration of an unprecedented cell-free enzyme system with self-sufficient cofactor recycling enables the stepwise transformation of aliphatic diols into ω-hydroxy acids at the expense of molecular oxygen as electron acceptor. The efficiency of the biosynthetic route was maximized when two compatible alcohol dehydrogenases were selected as specialist biocatalysts for each one of the oxidative steps required for the oxidative lactonization of diols. The cell-free system reached up to 100 % conversion using 100 mM of linear C₅ diols and performed the desymmetrization of prochiral branched diols into the corresponding ω-hydroxy acids with an exquisite enantioselectivity (ee>99 %). Green metrics demonstrate superior sustainability of this system compared to traditional metal catalysts and even to whole cells for the synthesis of 5-hydroxypetanoic acid. Finally, the cell-free system was assembled into a consortium of heterogeneous biocatalysts that allowed the enzyme reutilization. This cascade illustrates the potential of systems biocatalysis to access new heterofunctional molecules such as ω-hydroxy acids.

Metabolic Engineering of Escherichia coli for High-Yield Production of (R)-1,3-Butanediol

1,3-Butanediol (1,3-BDO) is an important C4 platform chemical widely used as a solvent in cosmetics and a key intermediate for the synthesis of fragrances, pheromones, and pharmaceuticals. The development of sustainable bioprocesses to produce enantiopure 1,3-BDO from renewable bioresources by fermentation is a promising alternative to conventional chemical routes and has aroused great interest in recent years. Although two metabolic pathways have been previously established for the biosynthesis of (R)-1,3-PDO, the reported titer and yield are too low for cost-competitive production. In this study, we report the combination of different metabolic engineering strategies to improve the production of (R)-1,3-BDO by Escherichia coli, including (1) screening of key pathway enzymes; (2) increasing NADPH supply by cofactor engineering; (3) optimization of fermentation conditions to divert more flux into 1,3-BDO pathway; (4) reduction of byproducts formation by pathway engineering. With these efforts, the best engineered E. coli strain can efficiently produce (R)-1,3-BDO with a yield of 0.6 mol/mol glucose, corresponding to 60% of the theoretical yield. Besides, we also showed the feasibility of aerobically producing 1,3-BDO via a new pathway using 3-hydroxybutyrate as an intermediate.

Thermal Behavior and Morphology of Thermoplastic Polyurethane Derived from Different Chain Extenders of 1,3- and 1,4-Butanediol

In this study, when deriving thermoplastic polyurethane (TPU), the researchers replaced 1,4-butanediol (1,4-BDO) with 1,3-butanediol (1,3-BDO) as a chain extender and examined how the structure of the chain extender affected the final polymers. Regarding the raw materials for polymerization, three types of commercial polyols with the same molecular weight (Mn = 1000 g/mol), namely, poly (butyl acrylate) (PBA), poly (tetramethylene ether) glycol (PTMG), and polycarbonate diol (PCDL) were used. These polyols were used in conjunction with butanediol and 4,4’-methylene diphenyl diisocyanate. Three groups of TPUs were successfully synthesized using one-shot solvent-free bulk polymerization. Compared with TPUs polymerized using 1,4-BDO, materials polymerized using 1,3-BDO are more transparent and viscous. Structural analysis revealed that no substantial differences between the final structures of the TPUs were present when different chain extenders were used. Thermal analysis indicated that compared with TPUs polymerized using 1,4-BDO, the glass transition temperature of those with 1,3-BDO was 15 °C higher. Examination of microphase separation in the structure by using morphological analysis revealed that compared with TPUs synthesized using 1,4-BDO, PBA, and PTMG synthesized using 1,3-BDO were relatively separated. PCDL synthesized using 1,3-BDO exhibited no morphological difference. Rheological analysis indicated PCDL synthesized using either 1,4-BDO or 1,3-BDO did not exhibit any obvious differences. In conclusion, TPUs synthesized using PCDL and 1,3-BDO exhibited thermal plasticity at room temperature (15–20 °C). Their basic application could be extended to the development of smart materials. In terms of further application, they could be used in shape memory and temperature-sensitive high molecular polymers.

Dehydration of Biomass-Derived Butanediols over Rare Earth Zirconate Catalysts

The aim of this work is to develop an effective catalyst for the conversion of butanediols, which is derivable from biomass, to valuable chemicals such as unsaturated alcohols. The dehydration of 1,4-, 1,3-, and 2,3-butanediol to form unsaturated alcohols such as 3-buten-1-ol, 2-buten-1-ol, and 3-buten-2-ol was studied in a vapor-phase flow reactor over sixteen rare earth zirconate catalysts at 325 °C. Rare earth zirconates with high crystallinity and high specific surface area were prepared in a hydrothermal treatment of co-precipitated hydroxide. Zirconates with heavy rare earth metals, especially Y2Zr2O7 with an oxygen-defected fluorite structure, showed high catalytic performance of selective dehydration of 1,4-butanediol to 3-buten-1-ol and also of 1,3-butanediol to form 3-buten-2-ol and 2-buten-1-ol, while the zirconate catalysts were less active in the dehydration of 2,3-butanediol. The calcination of Y2Zr2O7 significantly affected the catalytic activity of the dehydration of 1,4-butanediol: a calcination temperature of Y2Zr2O7 at 900 °C or higher was efficient for selective formation of unsaturated alcohols. Y2Zr2O7 with high crystallinity exhibits the highest productivity of 3-buten-1-ol from 1,4-butanediol at 325 °C.

Lignocellulosic bio-refinery approach for microbial 2,3-Butanediol production

Bio-refinery approach using agricultural and industrial waste material as feedstock is becoming a preferred area of interest in biotechnology in the current decades. The reasons for this trend are mainly because of the declining petroleum resources, greenhouse gas emission risks and fluctuating market price of crude oil. Most chemicals synthesized petro chemically, can be produced using microbial biocatalysts. 2,3-Butanediol (BDO) is such an important platform bulk chemical with numerous industrial applications including as a fuel additive. Although microbial production of BDO is well studied, strategies that could successfully upgrade the current lab-scale researches to an industrial level have to be developed. This review presents an overview of the recent trends and developments in the microbial production of BDO from different lignocellulose biomass.

Exploring Dual-Substrate Cultivation Strategy of 1,3-Propanediol Production Using Klebsiella pneumoniae

1,3-Propanediol (1,3-PDO) has numerous industrial applications in the synthesis of the monomer of the widely used fiber polytrimethylene terephthalate. In this work, the production of 1,3-PDO by Klebsiella pneumoniae is increased by dual-substrate cultivation and fed-batch fermentation. Experimental results indicate that the production of 1,3-PDO can be elevated to 16.09 g/L using a dual substrate ratio (of glucose to crude glycerol) of 1/30 and to 20.73 g/L using an optimized dual-substrate ratio of 1/20. Ultimately, the optimal dual-substrate feeding for a 5 L scale fed-batch fermenter that maximizes 1,3-PDO production (29.69 g/L) is determined. This production yield is better than that reported in most related studies. Eventually, the molecular weight and chemical structure of 1,3-PDO were obtained by FAB-MS, ¹H-NMR, and ¹³C-NMR. Also, in demonstrating the effectiveness of the fermentation strategy in increasing the production and production yield of 1,3-PDO, experimental results indicate that the fermentation of 1,3-PDO is highly promising for commercialization.

Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol

Carbon-carbon bond formation is one of the most important reactions in biocatalysis and organic chemistry. In nature, aldolases catalyze the reversible stereoselective aldol addition between two carbonyl compounds, making them attractive catalysts for the synthesis of various chemicals. In this work, we identified several 2-deoxyribose-5-phosphate aldolases (DERAs) having acetaldehyde condensation activity, which can be used for the biosynthesis of (R)-1,3-butanediol (1,3BDO) in combination with aldo-keto reductases (AKRs). Enzymatic screening of 20 purified DERAs revealed the presence of significant acetaldehyde condensation activity in 12 of the enzymes, with the highest activities in BH1352 from Bacillus halodurans, TM1559 from Thermotoga maritima, and DeoC from Escherichia coli The crystal structures of BH1352 and TM1559 at 1.40-2.50 Å resolution are the first full-length DERA structures revealing the presence of the C-terminal Tyr (Tyr²²⁴ in BH1352). The results from structure-based site-directed mutagenesis of BH1352 indicated a key role for the catalytic Lys¹⁵⁵ and other active-site residues in the 2-deoxyribose-5-phosphate cleavage and acetaldehyde condensation reactions. These experiments also revealed a 2.5-fold increase in acetaldehyde transformation to 1,3BDO (in combination with AKR) in the BH1352 F160Y and F160Y/M173I variants. The replacement of the WT BH1352 by the F160Y or F160Y/M173I variants in E. coli cells expressing the DERA + AKR pathway increased the production of 1,3BDO from glucose five and six times, respectively. Thus, our work provides detailed insights into the molecular mechanisms of substrate selectivity and activity of DERAs and identifies two DERA variants with enhanced activity for in vitro and in vivo 1,3BDO biosynthesis.

Catalytically active inclusion bodies of L-lysine decarboxylase from E. coli for 1,5-diaminopentane production

Sustainable and eco-efficient alternatives for the production of platform chemicals, fuels and chemical building blocks require the development of stable, reusable and recyclable biocatalysts. Here we present a novel concept for the biocatalytic production of 1,5-diaminopentane (DAP, trivial name: cadaverine) using catalytically active inclusion bodies (CatIBs) of the constitutive L-lysine decarboxylase from E. coli (EcLDCc-CatIBs) to process L-lysine-containing culture supernatants from Corynebacterium glutamicum. EcLDCc-CatIBs can easily be produced in E. coli followed by a simple purification protocol yielding up to 43% dry CatIBs per dry cell weight. The stability and recyclability of EcLDCc-CatIBs was demonstrated in (repetitive) batch experiments starting from L-lysine concentrations of 0.1 M and 1 M. EcLDC-CatIBs exhibited great stability under reaction conditions with an estimated half-life of about 54 h. High conversions to DAP of 87-100% were obtained in 30-60 ml batch reactions using approx. 180-300 mg EcLDCc-CatIBs, respectively. This resulted in DAP titres of up to 88.4 g l^-1 and space-time yields of up to 660 g_DAP l^-1 d^-1 per gram dry EcLDCc-CatIBs. The new process for DAP production can therefore compete with the currently best fermentative process as described in the literature.

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

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

Novel Aldo-Keto Reductases for the Biocatalytic Conversion of 3-Hydroxybutanal to 1,3-Butanediol: Structural and Biochemical Studies

The nonnatural alcohol 1,3-butanediol (1,3-BDO) is a valuable building block for the synthesis of various polymers. One of the potential pathways for the biosynthesis of 1,3-BDO includes the biotransformation of acetaldehyde to 1,3-BDO via 3-hydroxybutanal (3-HB) using aldolases and aldo-keto reductases (AKRs). This pathway requires an AKR selective for 3-HB, but inactive toward acetaldehyde, so it can be used for one-pot synthesis. In this work, we screened more than 20 purified uncharacterized AKRs for 3-HB reduction and identified 10 enzymes with significant activity and nine proteins with detectable activity. PA1127 from Pseudomonas aeruginosa showed the highest activity and was selected for comparative studies with STM2406 from Salmonella enterica serovar Typhimurium, for which we have determined the crystal structure. Both AKRs used NADPH as a cofactor, reduced a broad range of aldehydes, and showed low activities toward acetaldehyde. The crystal structures of STM2406 in complex with cacodylate or NADPH revealed the active site with bound molecules of a substrate mimic or cofactor. Site-directed mutagenesis of STM2406 and PA1127 identified the key residues important for the activity against 3-HB and aromatic aldehydes, which include the residues of the substrate-binding pocket and C-terminal loop. Our results revealed that the replacement of the STM2406 Asn65 by Met enhanced the activity and the affinity of this protein toward 3-HB, resulting in a 7-fold increase in k_cat/K_m Our work provides further insights into the molecular mechanisms of the substrate selectivity of AKRs and for the rational design of these enzymes toward new substrates.IMPORTANCE In this study, we identified several aldo-keto reductases with significant activity in reducing 3-hydroxybutanal to 1,3-butanediol (1,3-BDO), an important commodity chemical. Biochemical and structural studies of these enzymes revealed the key catalytic and substrate-binding residues, including the two structural determinants necessary for high activity in the biosynthesis of 1,3-BDO. This work expands our understanding of the molecular mechanisms of the substrate selectivity of aldo-keto reductases and demonstrates the potential for protein engineering of these enzymes for applications in the biocatalytic production of 1,3-BDO and other valuable chemicals.

Production of C2-C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies

C2-C4 diols classically derived from fossil resource are very important bulk chemicals which have been used in a wide range of areas, including solvents, fuels, polymers, cosmetics, and pharmaceuticals. Production of C2-C4 diols from renewable resources has received significant interest in consideration of the reducing fossil resource and the increasing environmental issues. While bioproduction of certain diols like 1,3-propanediol has been commercialized in recent years, biosynthesis of many other important C2-C4 diol isomers is highly challenging due to the lack of natural synthesis pathways. Recent advances in synthetic biology have enabled the de novo design of completely new pathways to non-natural molecules from renewable feedstocks. In this study, we review recent advances in bioproduction of C2-C4 diols, focusing on new metabolic pathways and metabolic engineering strategies being developed. We also discuss the challenges and future trends toward the development of economically competitive processes for bio-based diol production.

High-specificity synthesis of novel monomers by remodeled alcohol hydroxylase

BACKGROUND

Diols are important monomers for the production of plastics and polyurethanes, which are widely used in our daily life. The medium-chain diols with one hydroxyl group at its subterminal end are able to confer more flexibility upon the synthesized materials. But unfortunately, this type of diols has not been synthesized so far. The strong need for advanced materials impelled us to develop a new strategy for the production of these novel diols. In this study, we use the remodeled P450BM3 for high-specificity production of 1,7-decanediol.

RESULTS

The native P450BM3 was capable of converting medium-chain alcohols into corresponding α, ω1-, α, ω2- and α, ω3-diols, with each of them accounting for about one third of the total diols, but it exhibited a little or no activity on the short-chain alcohols. Greatly improved regiospecificity of alcohol hydroxylation was obtained by laboratory evolution of P450BM3. After substitution of 12 amino acid residues (J2-F87A), the ratio of 1,7-decanediol (ω-3 hydroxylation) to total decanediols increased to 86.8 % from 34.0 %. Structure modeling and site-directed mutagenesis demonstrated that the heme end residues such as Ala(78), Phe(87) and Arg(255) play a key role in controlling the regioselectivity of the alcohol hydroxylation, while the residues at the mouth of substrate binding site is not responsible for the regioselectivity.

CONCLUSIONS

Herein we employ an engineered P450BM3 for the first time to enable the high-specificity biosynthesis of 1,7-decanediol, which is a promising monomer for the development of advanced materials. Several key amino acid residues that control the regioselectivity of alcohol hydroxylation were identified, providing some new insights into how to improve the regiospecificity of alcohol hydroxylation. This report not only provides a good strategy for the biosynthesis of 1,7-decanediol, but also gives a promising approach for the production of other useful diols.

Biorefinery for Glycerol Rich Biodiesel Industry Waste

The biodiesel industry has the potential to meet the fuel requirements in the future. A few inherent lacunae of this bioprocess are the effluent, which is 10 % of the actual product, and the fact that it is 85 % glycerol along with a few impurities. Biological treatments of wastes have been known as a dependable and economical direction of overseeing them and bring some value added products as well. A novel eco-biotechnological strategy employs metabolically diverse bacteria, which ensures higher reproducibility and economics. In this article, we have opined, which organisms and what bioproducts should be the focus, while exploiting glycerol as feed.

Scaling up of renewable chemicals

The transition of promising technologies for production of renewable chemicals from a laboratory scale to commercial scale is often difficult and expensive. As a result the timeframe estimated for commercialization is typically underestimated resulting in much slower penetration of these promising new methods and products into the chemical industries. The theme of 'sugar is the next oil' connects biological, chemical, and thermochemical conversions of renewable feedstocks to products that are drop-in replacements for petroleum derived chemicals or are new to market chemicals/materials. The latter typically offer a functionality advantage and can command higher prices that result in less severe scale-up challenges. However, for drop-in replacements, price is of paramount importance and competitive capital and operating expenditures are a prerequisite for success. Hence, scale-up of relevant technologies must be interfaced with effective and efficient management of both cell and steel factories. Details involved in all aspects of manufacturing, such as utilities, sterility, product recovery and purification, regulatory requirements, and emissions must be managed successfully.

Bioconversion technologies of crude glycerol to value added industrial products

Crude glycerol that is produced as the by-product from biodiesel, has to be effectively utilized to contribute to the viability of biodiesel. Crude glycerol in large amounts can pose a threat to the environment. Therefore, there is a need to convert this crude glycerol into valued added products using biotechnological processes, which brings new revenue to biodiesel producers. Crude glycerol can serve as a feedstock for biopolymers, poly unsaturated fatty acids, ethanol, hydrogen and n-butanol production and as a raw material for different value added industrial products. Hence, in this review we have presented different bioconversion technologies of glycerol to value added industrial products.