Improved 1,3-propanediol production by engineering the 2,3-butanediol and formic acid pathways in integrative recombinant Klebsiella pneumoniae

Cofactor engineering in Thermoanaerobacterium aotearoense SCUT27 for maximizing ethanol yield and revealing an enzyme complex with high ferredoxin-NAD+ reductase activity

Thermoanaerobacterium aotearoense SCUT27 is a prominent producer of biofuels from lignocellulosic materials. To provide sufficient NAD(P)H for ethanol production, redox-related genes, including lactate dehydrogenase (ldh), redox-sensing transcriptional repressor (rex), and hydrogenase (hfsB), were knocked out. However, the growth of strain PRH (Δldh/Δrex/ΔhfsB) was suppressed due to the intracellular redox state imbalance with the increased NADH concentration. Coincidentally, when the Bcd-EtfAB (BCD) complex was overexpressed, the resulting strain PRH-B3 (Δldh/Δrex/ΔhfsB::BCD) grew rapidly and produced ethanol with a high yield. With lignocellulosic hydrolysates, PRH-BA (Δldh/Δrex/ΔhfsB::BCD::adhE) demonstrated high ethanol productivity and yield, reaching levels of 0.45-0.51 g/L/h and 0.46-0.53 g/g sugars, respectively. The study results shed light on the cofactor balance for cell stability and the high ferredoxin-NAD+ reductase activity of the BCD complex under an intracellular low redox state. They also provide an essential reference for developing strains for improved biofuel production.

Genetically encoded ATP and NAD(P)H biosensors: potential tools in metabolic engineering

To date, many metabolic engineering tools and strategies have been developed, including tools for cofactor engineering, which is a common strategy for bioproduct synthesis. Cofactor engineering is used for the regulation of pyridine nucleotides, including NADH/NAD+ and NADPH/NADP+, and adenosine triphosphate/adenosine diphosphate (ATP/ADP), which is crucial for maintaining redox and energy balance. However, the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP cannot be monitored in real time using traditional methods. Recently, many biosensors for detecting, monitoring, and regulating the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP have been developed. Although cofactor biosensors have been mainly developed for use in mammalian cells, the potential application of cofactor biosensors in metabolic engineering in bacterial and yeast cells has received recent attention. Coupling cofactor biosensors with genetic circuits is a promising strategy in metabolic engineering for optimizing the production of biochemicals. In this review, we focus on the development of biosensors for NADH/NAD+, NADPH/NADP+, and ATP/ADP and the potential application of these biosensors in metabolic engineering. We also provide critical perspectives, identify current research challenges, and provide guidance for future research in this promising field.

Enhancing 1,3-Propanediol Productivity in the Non-Model Chassis Clostridium beijerinckii through Genetic Manipulation

Biotechnological processes at biorefineries are considered one of the most attractive alternatives for valorizing biomasses by converting them into bioproducts, biofuels, and bioenergy. For example, biodiesel can be obtained from oils and grease but generates glycerol as a byproduct. Glycerol recycling has been studied in several bioprocesses, with one of them being its conversion to 1,3-propanediol (1,3-PDO) by Clostridium. Clostridium beijerinckii is particularly interesting because it can produce a range of industrially relevant chemicals, including solvents and organic acids, and it is non-pathogenic. However, while Clostridium species have many potential advantages as chassis for synthetic biology applications, there are significant limitations when considering their use, such as their limited genetic tools, slow growth rate, and oxygen sensitivity. In this work, we carried out the overexpression of the genes involved in the synthesis of 1,3-PDO in C. beijerinckii Br21, which allowed us to increase the 1,3-PDO productivity in this strain. Thus, this study contributed to a better understanding of the metabolic pathways of glycerol conversion to 1,3-PDO by a C. beijerinckii isolate. Also, it made it possible to establish a transformation method of a modular vector in this strain, therefore expanding the limited genetic tools available for this bacterium, which is highly relevant in biotechnological applications.

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.

Biochemical conversion of biodiesel by-product into malic acid: A way towards sustainability

Crude glycerol, one of the ever-growing by-product of biodiesel industry and is receiving the closest review in recent times because direct disposal of crude glycerol may emerge ecological issues. The renewability, bioavailability and typical structure of glycerol, therefore, discover conceivable application in serving the role of carbon and energy source for microbial biosynthesis of high value products. This conceivable arrangement could find exploitation of crude glycerol as a renewable building block for bio-refineries as it is economically as well as environmentally profitable. In this review, we summarize the uptake and catabolism of crude glycerol by different wild and recombinant microorganism. The chemical and biochemical transformation of crude glycerol into high esteem malic acid by various microbial pathways is also additionally discussed. An extensive investigation in the synthesis of high-value malic acid production from various feed stock which finds applications in cosmeceutical and chemical industries, food and beverages, and to some extent in the field of medical science is also likewise studied. Finally, the open doors for unrefined crude glycerol in serving as a promising abundant energy source for malic acid production in near future have been highlighted.

Impact of acetolactate synthase inactivation on 1,3-propanediol fermentation by Klebsiella pneumoniae

1,3-Propanediol (1,3-PDO) is an important compound that is mainly used in industry for polymer production. Fermentation of 1,3-PDO from glycerol by Klebsiella pneumoniae is accompanied by formation of 2,3-butanediol (2,3-BDO) as one of the main byproduct. The first step in the formation of 2,3-BDO from pyruvate is catalyzed by acetolactate synthase (ALS), an enzyme that competes with 1,3-PDO oxidoreductase for the cofactor NADH. This study aimed to analyze the impact of engineering the 2,3-BDO formation pathway via inactivation of ALS on 1,3-PDO fermentation by K. pneumoniae HSL4. An ALS mutant was generated using Red recombinase assisted gene replacement. The ALS specific activities of K. pneumoniae ΔALS were notably lower than that of the wild-type strain. Fed-batch fermentation of the mutant strain resulted in a 1,3-PDO concentration, productivity and conversion of 72.04 g L^–1, 2.25 g L^–1 h^–1, and 0.41 g g^–1, increase by 4.71%, 4.65% and 1.99% compared with the parent strain. Moreover, inactivation of ALS decreased meso-2,3-BDO formation to trace amounts, significantly increased 2S,3S-BDO and lactate production, and a pronounced redistribution of intracellular metabolic flux was apparent.

Recent advances in the production of value added chemicals and lipids utilizing biodiesel industry generated crude glycerol as a substrate - Metabolic aspects, challenges and possibilities: An overview

One of the major ecological concerns associated with biodiesel production is the generation of waste/crude glycerol during the trans-esterification process. Purification of this crude glycerol is not economically viable. In this context, the development of an efficient and economically viable strategy would be biotransformation reactions converting the biodiesel derived crude glycerol into value added chemicals. Hence the process ensures the sustainability and waste management in biodiesel industry, paving a path to integrated biorefineries. This review addresses a waste to wealth approach for utilization of crude glycerol in the production of value added chemicals, current trends, challenges, future perspectives, metabolic approaches and the genetic tools developed for the improved synthesis over wild type microorganisms were described.

High tolerance to glycerol and high production of 1,3-propanediol in batch fermentations by microbial consortium from marine sludge

1,3-Propanediol (1,3-PD) is a versatile bulk chemical and widely used as a monomer to synthesis polymers, such as polyesters, polyethers and polyurethanes. 1,3-PD can be produced by microbial fermentation with the advantages of the environmental protection and sustainable development. Low substrate tolerance and wide by-product profile limit microbial production of 1,3-PD by Klebsiella pneumonia on industrial scale. In this study, microbial consortia were investigated to overcome some disadvantages of pure fermentation by single strain. Microbial consortium named DL38 from marine sludge gave the best performance. Its bacterial community composition was analyzed by 16S rRNA gene amplicon high-throughput sequencing and showed that Enterobacteriaceae was the most abundant family. Compared with three K. pneumonia strains isolated from DL38, the microbial consortium could grow well at an initial glycerol concentration of 200 g/L to produce 81.40 g/L of 1,3-PD with a yield of 0.63 mol/mol. This initial glycerol concentration is twice the highest concentration by single isolated strain and more than the critical value (188 g/L) extrapolated from the fermentation kinetics for K. pneumonia. On the other hand, a small amount of by-products were produced in batch fermentation of microbial consortium DL38,  especially no 2,3-butanediol detected. The mixed culture of strain W3, Y5 and Y1 improved the tolerance to glycerol and changed the metabolite profile of single strain W3. The batch fermentation with the natural proportion (W3: Y5: Y1 = 208: 82: 17) was superior to that with other proportions and single strain. This study showed that microbial consortium DL38 possessed excellent substrate tolerance, narrow by-product profile and attractive potential for industrial production of 1,3-PD.

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.

Effects of culture conditions on the kinetic behavior of 1,3-propanediol fermentation by Clostridium butyricum with a kinetic model

The effects of culture conditions on the kinetic behavior of 1,3-propanediol (PD) fermentation were investigated with a kinetic model. First, with initial glycerol concentration (S0) increasing, μmax and PD inhibition increased. Glycerol assimilation was harder and a little glycerol was consumed on cell maintenance at high S0. Second, with yeast extract concentration increasing, PD inhibition decreased. However, μmax decreased and glycerol assimilation became harder. It seems that the stimulus effect of yeast extract resulted from decreased PD inhibition. Glycerol amount consumed on cell maintenance also decreased. Third, with temperature decreasing, μmax and PD inhibition decreased. Glycerol assimilation was harder and a little more glycerol was consumed on cell maintenance at low temperature. Fourth, with pH increasing, μmax and PD inhibition decreased. Glycerol assimilation was harder and much more glycerol was consumed on cell maintenance at pH 6.5 and 7.5 than 7.0. This work facilitates further fermentation process optimization.

Metabolic engineering of Bacillus subtilis for redistributing the carbon flux to 2,3-butanediol by manipulating NADH levels

BACKGROUND

Acetoin reductase (Acr) catalyzes the conversion of acetoin to 2,3-butanediol (2,3-BD) with concomitant oxidation of NADH to NAD(+). Therefore, intracellular 2,3-BD production is likely governed by the quantities of rate-limiting factor(s) Acr and/or NADH. Previously, we showed that a high level of Acr was beneficial for 2,3-BD accumulation.

RESULTS

Metabolic engineering strategies were proposed to redistribute carbon flux to 2,3-BD by manipulating NADH levels. The disruption of NADH oxidase (YodC, encoded by yodC) by insertion of a formate dehydrogenase gene in Bacillus subtilis was more efficient for enhancing 2,3-BD production and decreasing acetoin formation than the disruption of YodC by the insertion of a Cat expression cassette. This was because the former resulted in the recombinant strain AFY in which an extra NADH regeneration system was introduced and NADH oxidase was disrupted simultaneously. On fermentation by strain AFY, the highest 2,3-BD concentration increased by 19.9 % while the acetoin titer decreased by 71.9 %, relative to the parental strain. However, the concentration of lactate, the main byproduct, increased by 47.2 %. To further improve carbon flux and NADH to 2,3-BD, the pathway to lactate was blocked using the insertional mutation technique to disrupt the lactate dehydrogenase gene ldhA. The resultant engineered strain B. subtilis AFYL could efficiently convert glucose into 2,3-BD with little acetoin and lactate accumulation.

CONCLUSIONS

Through increasing the availability of NADH and decreasing the concentration of unwanted byproducts, this work demonstrates an important strategy in the metabolic engineering of 2,3-BD production by integrative recombinant hosts.

Control of ATP concentration in Escherichia coli using synthetic small regulatory RNAs for enhanced S-adenosylmethionine production

ATP is the limiting precursor and driving force for S-adenosylmethionine (SAM) biosynthesis in Escherichia coli. In contrast to traditional optimization of fermentation processes, the synthetic sRNA-based repression strategy, which was developed as a highly efficient gene knockdown approach, has been applied for the regulation of the intracellular ATP concentration in order to enhance SAM production. In this work, proB, glnA and argB, all involved in the synthesis of ATP-dependent by-products in the S-adenosylmethionine production were selected as candidates for repression. The results show that the S-adenosylmethionine titer and yield in the recombinant strain were doubled compared with the control. The best-performing strain, Anti-argB, produced the highest SAM titer (1.21 mg L(-1)), and strain Anti-glnA gave the highest yield (0.13 mg g(-1), 12 h). Both the concentration of ATP and the ratio of ATP to ADP were shown to have a positive effect on the S-adenosylmethionine synthesis. Overall, the synthetic sRNA-based downregulation strategy has a high potential for cofactor regulation and will be useful for industrial ATP-driven bioprocesses.

Utilization of excess NADH in 2,3-butanediol-deficient Klebsiella pneumoniae for 1,3-propanediol production

AIMS

To utilize excess NADH for 1,3-propanediol production by 2,3-butanediol-deficient mutants, the effect of dhaT overexpression in two distinct 2,3-butanediol-deficient mutants was investigated.

METHODS AND RESULTS

Two 2,3-butanediol-deficient mutants, KG1-3 (blocking of the 2,3-butanediol pathway only) and KG1-5 (blocking of both of 2,3-butanediol and lactate pathways) were constructed. Our results showed that although the intracellular redox balance (NADH/NAD(+)) was extremely high at the end of fermentation for both mutants, the status of intracellular redox in KG1-5 was maintained at a normal level following the first stage of fermentation. Analysis of cell growth and metabolite formation confirmed the inhibition of excess lactate in 2,3-butanediol pathway-deficient mutants. Furthermore, dhaT was overexpressed in two 2,3-butanediol-deficient mutants (KG1-3T and KG1-5T). In KG1-5T, the intracellular redox balance was restored to normal and 1,3-propanediol production increased. The yield of 1,3-propanediol from glycerol in KG1-5T was also restored to a normal level of 0·6.

CONCLUSIONS

The excess NADH in both the 2,3-butanediol- and lactate-deficient mutants can be used by overexpresstion of dhaT.

SIGNIFICANCE AND IMPACT OF STUDY

The metabolic flux tended to increase lactate production by the abolishment of the 2,3-butanediol pathway in Klebsiella pneumoniae, and the high accumulation of lactate prevented the cell from using excess NADH, thereby inhibiting cell growth and 1,3-propanediol production.

The effects of dissolved oxygen level on the distribution of 1,3-propanediol and 2,3-butanediol produced from glycerol by an isolated indigenous Klebsiella sp. Ana-WS5

The rapid accumulation of glycerol during biodiesel synthesis has attracted much interest on the potential usage. One of the promising applications is the conversion of glycerol to 1,3-propanediol (PDO), as well 2,3-butanediol (BDO), by using Klebsiella pneumonia. The results of this study indicate that the dissolved oxygen level (DO) is a determining factor in the distribution of PDO and BDO. The batch with a low DO could achieve a much higher PDO/BDO ratio than the high DO batch, with results of 9.9 and 0.2, respectively. The enzyme activity of glycerol dehydratase (GDHt) in the low DO batch was about three times that of the high DO batch, and this might be the cause of the enhanced PDO production. In conclusion, the results of this work show that high DO was beneficial to the production of BDO when using glycerol as the carbon source, while low DO could enhance PDO production.

Glycerol dehydrogenase plays a dual role in glycerol metabolism and 2,3-butanediol formation in Klebsiella pneumoniae

Glycerol dehydrogenase (GDH) is an important polyol dehydrogenase for glycerol metabolism in diverse microorganisms and for value-added utilization of glycerol in the industry. Two GDHs from Klebsiella pneumoniae, DhaD and GldA, were expressed in Escherichia coli, purified and characterized for substrate specificity and kinetic parameters. Both DhaD and GldA could catalyze the interconversion of (3R)-acetoin/(2R,3R)-2,3-butanediol or (3S)-acetoin/meso-2,3-butanediol, in addition to glycerol oxidation. Although purified GldA appeared more active than DhaD, in vivo inactivation and quantitation of their respective mRNAs indicate that dhaD is highly induced by glycerol and plays a dual role in glycerol metabolism and 2,3-butanediol formation. Complementation in K. pneumoniae further confirmed the dual role of DhaD. Promiscuity of DhaD may have vital physiological consequences for K. pneumoniae growing on glycerol, which include balancing the intracellular NADH/NAD(+) ratio, preventing acidification, and storing carbon and energy. According to the kinetic response of DhaD to modified NADH concentrations, DhaD appears to show positive homotropic interaction with NADH, suggesting that the physiological role could be regulated by intracellular NADH levels. The co-existence of two functional GDH enzymes might be due to a gene duplication event. We propose that whereas DhaD is specialized for glycerol utilization, GldA plays a role in backup compensation and can turn into a more proficient catalyst to promote a survival advantage to the organism. Revelation of the dual role of DhaD could further the understanding of mechanisms responsible for enzyme evolution through promiscuity, and guide metabolic engineering methods of glycerol metabolism.