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

Application of synthetic biology strategies to promote biosynthesis of fatty acids and their derivatives

Fatty acids and their derivatives are indispensable biomolecules in all organisms, and can be used as intermediates in the synthesis of pharmaceuticals, biofuels and pesticides, and thus their demand has increased dramatically in recent years. In addition to serving as structural components of cell membranes and metabolic energy, fatty acids and their derivatives can also be used as signal transduction and regulatory bioactive molecules to regulate cell functions. Biosynthesis of fatty acids and their derivatives through microbial catalysis provides green and alternative options to meet the goal. However, the low biosynthetic titer of fatty acids and their derivatives limits their industrial production and application. In this review, we first summarize the metabolic pathways and related enzymes of fatty acids and their derivatives biosynthesis. Then, the strategies and research progress of biosynthesis of fatty acids and derivatives through metabolic and enzyme engineering were reviewed. The biosynthesis of saturated fatty acids (medium chain fatty acids and long chain fatty acids), bioactive fatty acids (PUFAs, oxylipins, ether lipids), and their derivatives with microbial and enzymatic catalysis were respectively summarized. Finally, synthetic biology strategies to improve fatty acids and their derivatives production through enzyme rational design, carbon metabolism flux, cofactors balance, and metabolic pathways design were discussed. The review provides references and prospects for fatty acids and their derivatives biosynthesis and industrial production.

Efficient production of acetoin from lactate by engineered Escherichia coli whole-cell biocatalyst

Acetoin, an important and high-value added bio-based platform chemical, has been widely applied in fields of foods, cosmetics, chemical synthesis, and agriculture. Lactate is a significant intermediate short-chain carboxylate in the anaerobic breakdown of carbohydrates that comprise ~ 18% and ~ 70% in municipal wastewaters and some food processing wastewaters, respectively. In this work, a series of engineered Escherichia coli strains were constructed for efficient production of acetoin from cheaper and abundant lactate through heterogenous co-expression of fusion protein (α-acetolactate synthetase and α-acetolactate decarboxylase), lactate dehydrogenase and NADH oxidase, and blocking acetate synthesis pathways. After optimization of whole-cell bioconversion conditions, the engineered strain BL-11 produced 251.97 mM (22.20 g/L) acetoin with a yield of 0.434 mol/mol in shake flasks. Moreover, a titer of 648.97mM (57.18 g/L) acetoin was obtained in 30 h with a yield of 0.484 mol/mol lactic acid in a 1-L bioreactor. To the best of our knowledge, this is the first report on the production of acetoin from renewable lactate through whole-cell bioconversion with both high titer and yield, which demonstrates the economy and efficiency of acetoin production from lactate. Key Points • The lactate dehydrogenases from different organisms were expressed, purified, and assayed. • It is the first time that acetoin was produced from lactate by whole-cell biocatalysis. • The highest titer of 57.18 g/L acetoin was obtained with high theoretical yield in a 1-L bioreactor.

Enzymatic cofactor regeneration systems: A new perspective on efficiency assessment

Nowadays, the specificity of enzymatic processes makes them more and more important every year, and their usage on an industrial scale seems to be necessary. Enzymatic cofactors, however, play a crucial part in the prospective applications of enzymes, because they are indispensable for conducting highly effective biocatalytic activities. Due to the relatively high cost of these compounds and their consumption during the processes carried out, it has become crucial to develop systems for cofactor regeneration. Therefore, in this review, an attempt was made to summarize current knowledge on enzymatic regeneration methods, which are characterized by high specificity, non-toxicity and reported to be highly efficient. The regeneration of cofactors, such as nicotinamide dinucleotides, coenzyme A, adenosine 5'-triphosphate and flavin nucleotides, which are necessary for the proper functioning of a large number of enzymes, is discussed, as well as potential directions for further development of these systems are highlighted. This review discusses a range of highly effective cofactor regeneration systems along with the productive synthesis of many useful chemicals, including the simultaneous renewal of several cofactors at the same time. Additionally, the impact of the enzyme immobilization process on improving the stability and the potential for multiple uses of the developed cofactor regeneration systems was also presented. Moreover, an attempt was made to emphasize the importance of the presented research, as well as the identification of research gaps, which mainly result from the lack of available literature on this topic.

Co-conversion of lignocellulose-derived glucose, xylose, and aromatics to polyhydroxybutyrate by metabolically engineered Cupriavidus necator

Utilization of all major components of lignocellulose is essential for biomass biorefining. Glucose, xylose, and lignin-derived aromatics can be generated from cellulose, hemicellulose, and lignin of lignocellulose degradation through pretreatment and hydrolysis. In present work, Cupriavidus necator H16 was engineered to utilize glucose, xylose, p-coumaric acid, and ferulic acid simultaneously by multi-step genetic engineering. Firstly, genetic modification and adaptive laboratory evolution were performed to promote glucose transmembrane transport and metabolism. Xylose metabolism was then engineered by integrating genes xylAB (xylose isomerase and xylulokinase) and xylE (proton-coupled symporter) in the locus of ldh (lactate dehydrogenase) and ackA (acetate kinase) on the genome, respectively. Thirdly, p-coumaric acid and ferulic acid metabolism was achieved by constructing an exogenous CoA-dependent non-β-oxidation pathway. Using corn stover hydrolysates as carbon sources, the resulting engineered strain Reh06 simultaneously converted all components of glucose, xylose, p-coumaric acid, and ferulic acid to produce 11.51 g/L polyhydroxybutyrate.

Integrating Carbohydrate and C1 Utilization for Chemicals Production

In the face of increasing mobility and energy demand, as well as the mitigation of climate change, the development of sustainable and environmentally friendly alternatives to fossil fuels will be one of the most important tasks facing humankind in the coming years. In order to initiate the transition from a petroleum-based economy to a new, greener future, biofuels and synthetic fuels have great potential as they can be adapted to already common processes. Thereby, especially synthetic fuels from CO₂ and renewable energies are seen as the next big step for a sustainable and ecological life. In our study, we directly address the sustainable production of the most common biofuel, ethanol, and the highly interesting next-generation biofuel, isobutanol, from methanol and xylose, which are directly derivable from CO₂ and lignocellulosic waste streams, respectively, such integrating synthetic fuel and biofuel production. After enzyme and reaction optimization, we succeeded in producing either 3 g L^-1 ethanol or 2 g L^-1 isobutanol from 7.5 g L^-1 xylose and 1.6 g L^-1 methanol. In our cell-free enzyme system, C1-compounds are efficiently combined and fixed by the key enzyme transketolase and converted to the intermediate pyruvate. This opens the way for a hybrid production of biofuels, platform chemicals and fine chemicals from CO₂ and lignocellulosic waste streams as alternative to conventional routes depending solely either on CO₂ or sugars.

Production of acetoin and its derivative tetramethylpyrazine from okara hydrolysate with Bacillus subtilis

Okara, a renewable biomass resource, is a promising fermentative raw material for the bio-production of value-added chemicals due to its abundance and low-costs. we developed a process for the enzymatic hydrolysis of okara, and then engineered Bacillus subtilis to utilize mixed sugars to produce acetoin in okara hydrolysis without the addition of a supplemental nitrogen source. Okara was initially hydrolyzed with cellulase, β-glucosidase, and pectinase to obtain okara hydrolysate containing mixed sugars (32.78 ± 0.23 g/L glucose, 1.43 ± 0.064 g/L arabinose, 7.74 ± 0.11 g/L galactose) and amino acids. In this study, Bacillus subtilis 168 was used as the acetoin-producing strain, and the key genes bdhA and acoA of the acetoin catabolism pathway were knocked out to improve the fermentation yield of acetoin. In order to utilize the galactose in the hydrolysate, the recombinant strain BS03 (Bacillus subtilis168∆bdhA∆acoA) was used to overexpress the arabinose transporter-encoding gene (araE) drive heterologous expression of the Leloir pathway gene (galKTE). The corn dry powder concentration was optimized to 29 g/L in the reducing sugar okara hydrolysate. The results show that the recombinant bacterium BS03 could still synthesize 11.79 g/L acetoin without using corn dry powder as a nitrogen source. Finally, using okara enzymatic hydrolysate as the carbon and nitrogen source, 11.11 g/L and 29.7 g/L acetoin were obtained by batch fermentation and fed-batch fermentation, respectively, which was further converted to 5.33 g/L and 13.37 g/L tetramethylpyrazine (TTMP) by reaction with an ammonium salt.

Biosynthesis of value-added bioproducts from hemicellulose of biomass through microbial metabolic engineering

Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed. The bioprocess for degradation and conversion of natural lignocellulose to monosaccharides and organic acids using anaerobic thermophilic bacteria and thermostable glycoside hydrolases were summarized. Xylose transmembrane transporting systems in natural microorganisms and the latest strategies for promoting the transporting capacity by metabolic engineering were summarized. The carbon catabolite repression effect restricting xylose utilization in microorganisms, and metabolic engineering strategies developed for co-utilization of glucose and xylose were discussed. Secondly, the metabolic pathways of xylose catabolism in microorganisms were comparatively analyzed. Microbial metabolic engineering for converting xylose to value-added bioproducts based on redox pathways, non-redox pathways, pentose phosphate pathway, and improving inhibitors resistance were summarized. Thirdly, strategies for degrading lignocellulosic polysaccharides and fully converting hemicellulose to value-added bioproducts through microbial metabolic engineering were proposed.

•

Hemicellulose is the main carbohydrate of biomass and has valuable applications.

•

Hemicellulose is underutilized in conventional biomass refinery and pretreatment.

•

Microbial and enzymatic catalysis were applied for hemicellulose utilization.

•

Xylose is converted to value-added bioproducts by metabolic engineering.

Advances in biological production of acetoin: a comprehensive overview

Acetoin, a high-value-added bio-based platform chemical, is widely used in foods, cosmetics, agriculture, and the chemical industry. It is an important precursor for the synthesis of: 2,3-butanediol, liquid hydrocarbon fuels and heterocyclic compounds. Since the fossil resources are becoming increasingly scarce, biological production of acetoin has received increasing attention as an alternative to chemical synthesis. Although there are excellent reviews on the: application, catabolism and fermentative production of acetoin, little attention has been paid to acetoin production via: electrode-assisted fermentation, whole-cell biocatalysis, and in vitro/cell-free biocatalysis. In this review, acetoin biosynthesis pathways and relevant key enzymes are firstly reviewed. In addition, various strategies for biological acetoin production are summarized including: cell-free biocatalysis, whole-cell biocatalysis, microbial fermentation, and electrode-assisted fermentation. The advantages and disadvantages of the different approaches are discussed and weighed, illustrating the increasing progress toward economical, green and efficient production of acetoin. Additionally, recent advances in acetoin extraction and recovery in downstream processing are also briefly reviewed. Moreover, the current issues and future prospects of diverse strategies for biological acetoin production are discussed, with the hope of realizing the promises of industrial acetoin biomanufacturing in the near future.

Getting the Most Out of Enzyme Cascades: Strategies to Optimize In Vitro Multi-Enzymatic Reactions

In vitro enzyme cascades possess great benefits, such as their synthetic capabilities for complex molecules, no need for intermediate isolation, and the shift of unfavorable equilibria towards the products. Their performance, however, can be impaired by, for example, destabilizing or inhibitory interactions between the cascade components or incongruous reaction conditions. The optimization of such systems is therefore often inevitable but not an easy task. Many parameters such as the design of the synthesis route, the choice of enzymes, reaction conditions, or process design can alter the performance of an in vitro enzymatic cascade. Many strategies to tackle this complex task exist, ranging from experimental to in silico approaches and combinations of both. This review collates examples of various optimization strategies and their success. The feasibility of optimization goals, the influence of certain parameters and the usage of algorithm-based optimizations are discussed.

Understanding D-xylonic acid accumulation: a cornerstone for better metabolic engineering approaches

The xylose oxidative pathway (XOP) has been engineered in microorganisms for the production of a wide range of industrially relevant compounds. However, the performance of metabolically engineered XOP-utilizing microorganisms is typically hindered by D-xylonic acid accumulation. It acidifies the media and perturbs cell growth due to toxicity, thus curtailing enzymatic activity and target product formation. Fortunately, from the growing portfolio of genetic tools, several strategies that can be adapted for the generation of efficient microbial cell factories have been implemented to address D-xylonic acid accumulation. This review centers its discussion on the causes of D-xylonic acid accumulation and how to address it through different engineering and synthetic biology techniques with emphasis given on bacterial strains. In the first part of this review, the ability of certain microorganisms to produce and tolerate D-xylonic acid is also tackled as an important aspect in developing efficient microbial cell factories. Overall, this review could shed some insights and clarity to those working on XOP in bacteria and its engineering for the development of industrially applicable product-specialist strains. KEY POINTS: D-Xylonic acid accumulation is attributed to the overexpression of xylose dehydrogenase concomitant with basal or inefficient expression of enzymes involved in D-xylonic acid assimilation. Redox imbalance and insufficient cofactors contribute to D-xylonic acid accumulation. Overcoming D-xylonic acid accumulation can increase product formation among engineered strains. Engineering strategies involving enzyme engineering, evolutionary engineering, coutilization of different sugar substrates, and synergy of different pathways could potentially address D-xylonic acid accumulation.

Production of Ethylene Glycol from Glycerol Using an In Vitro Enzymatic Cascade

Glycerol is a readily available and inexpensive substance that is mostly generated during biofuel production processes. In order to ensure the viability of the biofuel industry, it is essential to develop complementing technologies for the resource utilization of glycerol. Ethylene glycol is a two-carbon organic chemical with multiple applications and a huge market. In this study, an artificial enzymatic cascade comprised alditol oxidase, catalase, glyoxylate/hydroxypyruvate reductase, pyruvate decarboxylase and lactaldehyde:propanediol oxidoreductase was developed for the production of ethylene glycol from glycerol. The reduced nicotinamide adenine dinucleotide (NADH) generated during the dehydrogenation of the glycerol oxidation product d-glycerate can be as the reductant to support the ethylene glycol production. Using this in vitro synthetic system with self-sufficient NADH recycling, 7.64 ± 0.15 mM ethylene glycol was produced from 10 mM glycerol in 10 h, with a high yield of 0.515 ± 0.1 g/g. The in vitro enzymatic cascade is not only a promising alternative for the generation of ethylene glycol but also a successful example of the value-added utilization of glycerol.

One-pot efficient biosynthesis of (3R)-acetoin from pyruvate by a two-enzyme cascade

Opening the possibility of sustainable industrial (3R)-acetoin biomanufacturing in vitro.

Combined cross-linked enzyme aggregates of glycerol dehydrogenase and NADH oxidase for high efficiency in situ NAD+ regeneration

Cofactor regeneration is an important method to avoid the consumption of large quantities of oxidized cofactor NAD⁺ in enzyme-catalyzed reactions. Herein, glycerol dehydrogenase (GDH) and NADH oxidase preparations by aggregating enzymes with ammonium sulphate followed by cross-linking formed aggregates for effective regeneration of NAD⁺. After optimization, the activity of combi-CLEAs and separate CLEAs mixtures were 950 and 580 U/g, respectively. And the catalytic stability of combi-CLEAs against pH and temperature was superior to the free enzyme mixture. After ten cycles of reuse, the catalytic efficiency could still retain 63.3% of its initial activity, indicating that the constructed combi-CLEAs system had excellent reusability. Also, the conversion of glycerol to 1,3-dihydroxyacetone (DHA) was improved by the constructed NAD⁺ regeneration system, resulting in 4.6%, which was 2.5 times of the free enzyme system. Thus, wide applications of this co-immobilization method in the production of various chiral chemicals could be expected in the industry for its high efficiency at a low cost.