Modular design of metabolic network for robust production of n-butanol from galactose-glucose mixtures

Engineering Escherichia coli for D-allulose biosynthesis from glycerol

D-allulose, a naturally occurring monosaccharide, is present in small quantities in nature. It is considered a valuable low-calorie sweetener due to its low absorption in the digestive tract and zero energy for growth. Most of the recent efforts to produce D-allulose have focused on in vitro enzyme catalysis. However, microbial fermentation is emerging as a promising alternative that offers the advantage of combining enzyme manufacturing and product synthesis within a single bioreactor. Here, a novel approach was proposed for the efficient biosynthesis of D-allulose from glycerol using metabolically engineered Escherichia coli. FbaA, Fbp, AlsE, and A6PP were used to construct the D-allulose synthesis pathway. Subsequently, PfkA, PfkB, and Pgi were disrupted to block the entry of the intermediate fructose-6-phosphate (F6P) into the Embden-Meyerhof-Parnas (EMP) and pentose phosphate (PP) pathways. Additionally, GalE and FryA were inactivated to reduce D-allulose consumption by the cells. Finally, a fed-batch fermentation process was implemented to optimize the performance of the cell factory. As a result, the titer of D-allulose reached 7.02 g/L with a maximum yield of 0.287 g/g.

Feasibility study on heterotrophic utilization of galactose by Chlorella sorokiniana and promotion of galactose utilization through mixed carbon sources culture

BACKGROUND

The development of alternative carbon sources is important for reducing the cost of heterotrophic microalgae cultivation. Among cheap feedstocks, galactose is one of the most abundant sugars and can be easily obtained from many natural biomasses. However, it is generally difficult to be utilized by microalgae. In addition, the mechanism of its low utilization efficiency in heterotrophic cultivation is still unknown.

RESULTS

Among seven tested carbon sources, only glucose and acetate could be efficiently utilized by C. sorokiniana in heterotrophic cultivation while there were no apparent signs of utilization of other carbohydrates, including galactose, in regular heterotrophic cultivation. However, galactose could be utilized in cultures with high inoculation sizes. This confirmed that C. sorokiniana has a complete pathway for transporting and assimilating galactose under dark conditions, but the rate of galactose utilization is quite low. In addition, the galactose utilization was greatly enhanced in mixotrophic cultures, which indicated that galactose utilization could be enhanced by additional pathways that can enhance cell growth. Based on above results, a mixed carbon source culture strategy was proposed to improve the utilization rate of galactose, and a significant synergistic effect on cell growth was achieved in cultures using a mixture of galactose and acetate.

CONCLUSIONS

This study indicated that the galactose metabolism pathway may not be inherently deficient in Chlorophyta. However, its utilization rate was too low to be detected in regular heterotrophic cultivation. Mixed carbon source culture strategy was confirmed effective to improve the utilization rate of galactose. This study contributes to a deeper understanding of the utilization ability of difficultly utilized substrates in the heterotrophic cultivation of microalgae, which is of great significance for reducing the cost of heterotrophic cultivation of microalgae.

Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals

Although strain tolerance to high product concentrations is a barrier to the economically viable biomanufacturing of industrial chemicals, chemical tolerance mechanisms are often unknown. To reveal tolerance mechanisms, an automated platform was utilized to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals (1,2-propanediol, 2,3-butanediol, glutarate, adipate, putrescine, hexamethylenediamine, butanol, isobutyrate, coumarate, octanoate, hexanoate), reaching tolerance at concentrations 60%-400% higher than initial toxic levels. Sequencing genomes of 223 isolates from 89 populations, reverse engineering, and cross-compound tolerance profiling were employed to uncover tolerance mechanisms. We show that: 1) cells are tolerized via frequent mutation of membrane transporters or cell wall-associated proteins (e.g., ProV, KgtP, SapB, NagA, NagC, MreB), transcription and translation machineries (e.g., RpoA, RpoB, RpoC, RpsA, RpsG, NusA, Rho), stress signaling proteins (e.g., RelA, SspA, SpoT, YobF), and for certain chemicals, regulators and enzymes in metabolism (e.g., MetJ, NadR, GudD, PurT); 2) osmotic stress plays a significant role in tolerance when chemical concentrations exceed a general threshold and mutated genes frequently overlap with those enabling chemical tolerance in membrane transporters and cell wall-associated proteins; 3) tolerization to a specific chemical generally improves tolerance to structurally similar compounds whereas a tradeoff can occur on dissimilar chemicals, and 4) using pre-tolerized starting isolates can hugely enhance the subsequent production of chemicals when a production pathway is inserted in many, but not all, evolved tolerized host strains, underpinning the need for evolving multiple parallel populations. Taken as a whole, this study provides a comprehensive genotype-phenotype map based on identified mutations and growth phenotypes for 223 chemical tolerant isolates.

Biosensor-Assisted Adaptive Laboratory Evolution for Violacein Production

Violacein is a naturally occurring purple pigment, widely used in cosmetics and has potent antibacterial and antiviral properties. Violacein can be produced from tryptophan, consequently sufficient tryptophan biosynthesis is the key to violacein production. However, the complicated biosynthetic pathways and regulatory mechanisms often make the tryptophan overproduction challenging in Escherichia coli. In this study, we used the adaptive laboratory evolution (ALE) strategy to improve violacein production using galactose as a carbon source. During the ALE, a tryptophan-responsive biosensor was employed to provide selection pressure to enrich tryptophan-producing cells. From the biosensor-assisted ALE, we obtained an evolved population of cells capable of effectively catabolizing galactose to tryptophan and subsequently used the population to obtain the best violacein producer. In addition, whole-genome sequencing of the evolved strain identified point mutations beneficial to the overproduction. Overall, we demonstrated that the biosensor-assisted ALE strategy could be used to rapidly and selectively evolve the producers to yield high violacein production.

Vibrio sp. dhg as a platform for the biorefinery of brown macroalgae

Although brown macroalgae holds potential as an alternative feedstock, its utilization by conventional microbial platforms has been limited due to the inability to metabolize one of the principal sugars, alginate. Here, we isolate Vibrio sp. dhg, a fast-growing bacterium that can efficiently assimilate alginate. Based on systematic characterization of the genomic information of Vibrio sp. dhg, we establish a genetic toolbox for its engineering. We also demonstrate its ability to rapidly produce ethanol, 2,3-butanediol, and lycopene from brown macroalgae sugar mixture with high productivities and yields. Collectively, Vibrio sp. dhg can be used as a platform for the efficient conversion of brown macroalgae sugars into diverse value-added biochemicals.

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

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

Metagenomics Investigation of Agarlytic Genes and Genomes in Mangrove Sediments in China: A Potential Repertory for Carbohydrate-Active Enzymes

Monosaccharides and oligosaccharides produced by agarose degradation exhibit potential in the fields of bioenergy, medicine, and cosmetics. Mangrove sediments (MGSs) provide a special environment to enrich enzymes for agarose degradation. However, representative investigations of the agarlytic genes in MGSs have been rarely reported. In this study, agarlytic genes in MGSs were researched in detail from the aspects of diversity, abundance, activity, and location through deep metagenomics sequencing. Functional genes in MGSs were usually incomplete but were shown as results, which could cause virtually high number of results in previous studies because multiple fragmented sequences could originate from the same genes. In our work, only complete and nonredundant (CNR) genes were analyzed to avoid virtually high amount of the results. The number of CNR agarlytic genes in our datasets was significantly higher than that in the datasets of previous studies. Twenty-one recombinant agarases with agarose-degrading activity were detected using heterologous expression based on numerous complete open-reading frames, which are rarely obtained in metagenomics sequencing of samples with complex microbial communities, such as MGSs. Aga2, which had the highest crude enzyme activity among the 21 recombinant agarases, was further purified and subjected to enzymatic characterization. With its high agarose-degrading activity, resistance to temperature changes and chemical agents, Aga2 could be a suitable option for industrial production. The agarase ratio with signal peptides to that without signal peptides in our MGS datasets was lower than that of other reported agarases. Six draft genomes, namely, Clusters 1-6, were recovered from the datasets. The taxonomic annotation of these genomes revealed that Clusters 1, 3, 5, and 6 were annotated as Desulfuromonas sp., Treponema sp., Ignavibacteriales spp., and Polyangiaceae spp., respectively. Meanwhile, Clusters 2 and 4 were potential new species. All these genomes were first reported and found to have abilities of degrading various important polysaccharides. The metabolic pathway of agarose in Cluster 4 was also speculated. Our results showed the capacity and activity of agarases in the MGS microbiome, and MGSs exert potential as a repertory for mining not only agarlytic genes but also almost all genes of the carbohydrate-active enzyme family.

Rediscovering Acetate Metabolism: Its Potential Sources and Utilization for Biobased Transformation into Value-Added Chemicals

One of the great advantages of microbial fermentation is the capacity to convert various carbon compounds into value-added chemicals. In this regard, there have been many efforts to engineer microorganisms to facilitate utilization of abundant carbon sources. Recently, the potential of acetate as a feedstock has been discovered; efforts have been made to produce various biochemicals from acetate based on understanding of its metabolism. In this review, we discuss the potential sources of acetate and summarized the recent progress to improve acetate utilization with microorganisms. Furthermore, we also describe representative studies that engineered microorganisms for the production of biochemicals from acetate.

Genome-scale biological models for industrial microbial systems

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Retooling microorganisms for the fermentative production of alcohols

Bioengineering and synthetic biology approaches have revolutionised the field of biotechnology, enabling the introduction of non-native and de novo pathways for biofuels production. This 'retooling' of microorganisms is also applied to the utilisation of mixed carbon components derived from lignocellulosic biomass, a major technical barrier for the development of economically viable fermentations. This review will discuss recent advances in microorganism engineering for efficient production of alcohols from waste biomass. These advances span the introduction of new pathways to alcohols, host modifications for more cost-effective utilisation of lignocellulosic waste and modifications of existing pathways for generating new fuel additives.

Controlling Citrate Synthase Expression by CRISPR/Cas9 Genome Editing for n-Butanol Production in Escherichia coli

Genome editing using CRISPR/Cas9 was successfully demonstrated in Esherichia coli to effectively produce n-butanol in a defined medium under microaerobic condition. The butanol synthetic pathway genes including those encoding oxygen-tolerant alcohol dehydrogenase were overexpressed in metabolically engineered E. coli, resulting in 0.82 g/L butanol production. To increase butanol production, carbon flux from acetyl-CoA to citric acid cycle should be redirected to acetoacetyl-CoA. For this purpose, the 5'-untranslated region sequence of gltA encoding citrate synthase was designed using an expression prediction program, UTR designer, and modified using the CRISPR/Cas9 genome editing method to reduce its expression level. E. coli strains with decreased citrate synthase expression produced more butanol and the citrate synthase activity was correlated with butanol production. These results demonstrate that redistributing carbon flux using genome editing is an efficient engineering tool for metabolite overproduction.

Synthetic redesign of Escherichia coli for cadaverine production from galactose

BACKGROUND

With increasing concerns over the environment, biological production of cadaverine has been suggested as an alternative route to replace polyamides generated from the petroleum-based process. For an ideal bioprocess, cadaverine should be produced with high yield and productivity from various sugars abundant in biomass. However, most microorganisms are not able to efficiently metabolize other biomass-derived sugars as fast as glucose. This results in reduced growth rate and low carbon flux toward the production of desired bio-chemicals. Thus, redesign of microorganisms is necessary for utilizing those carbon sources with enhanced carbon flux and product formation.

RESULTS

In this study, we engineered Escherichia coli to produce cadaverine with rapid assimilation of galactose, a promising future feedstock. To achieve this, genes related to the metabolic pathway were maximally expressed to amplify the flux toward cadaverine production via synthetic expression cassettes consisting of predictive and quantitative genetic parts (promoters, 5'-untranslated regions, and terminators). Furthermore, the feedback inhibition of metabolic enzymes and degradation/re-uptake pathways was inactivated to robustly produce cadaverine. Finally, the resultant strain, DHK4, produced 8.80 g/L cadaverine with high yield (0.170 g/g) and productivity (0.293 g/L/h) during fed-batch fermentation, which was similar to or better than the previous glucose fermentation.

CONCLUSIONS

Taken together, synthetic redesign of a microorganism with predictive and quantitative genetic parts is a prerequisite for converting sugars from abundant biomass into desired platform chemicals. This is the first report to produce cadaverine from galactose. Moreover, the yield (0.170 g/g) was the highest among engineered E. coli systems.

Optimization of industrial microorganisms: recent advances in synthetic dynamic regulators

Production of biochemicals by industrial fermentation using microorganisms requires maintaining cellular production capacity, because maximal productivity is economically important. High-productivity microbial strains can be developed using static engineering, but these may not maintain maximal productivity throughout the culture period as culture conditions and cell states change dynamically. Additionally, economic reasons limit heterologous protein expression using inducible promoters to prevent metabolic burden for commodity chemical and biofuel production. Recently, synthetic and systems biology has been used to design genetic circuits, precisely controlling gene expression or influencing genetic behavior toward a desired phenotype. Development of dynamic regulators can maintain cellular phenotype in a maximum production state in response to factors including cell concentration, oxygen, temperature, pH, and metabolites. Herein, we introduce dynamic regulators of industrial microorganism optimization and discuss metabolic flux fine control by dynamic regulators in response to metabolites or extracellular stimuli, robust production systems, and auto-induction systems using quorum sensing.

A simple method to control glycolytic flux for the design of an optimal cell factory

BACKGROUND

A microbial cell factory with high yield and productivity are prerequisites for an economically feasible bio-based chemical industry. However, cell factories that show a kinetic imbalance between glycolysis and product formation pathways are not optimal. Glycolysis activity is highly robust for survival in nature, but is not optimized for chemical production.

RESULTS

Here, we propose a novel approach to balance glycolytic activity with the product formation capacity by precisely controlling expression level of ptsG (encoded glucose transporter) through UTR engineering. For various heterologous pathways with different maximum production rates, e.g., n-butanol, butyrate, and 2,3-butanediol, glycolytic fluxes could be successfully modulated to maximize yield and productivity, while minimizing by-product formation in Escherichia coli.

CONCLUSIONS

These results support the application of this simple method to explore the maximum yield and productivity when designing optimal cell factories for value-added products in the fields of metabolic engineering and synthetic biology.

Optimum Rebalancing of the 3-Hydroxypropionic Acid Production Pathway from Glycerol in Escherichia coli

3-Hydroxypropionic acid (3-HP) can be biologically produced from glycerol by two consecutive enzymatic reactions, dehydration of glycerol to 3-hydroxypropionaldehyde (3-HPA) and oxidation of 3-HPA. The pathway has been proved efficient, but imbalance between the rates of the two enzymatic reactions often results in the accumulation of the toxic 3-HPA, which severely reduces cell viability and 3-HP production. In this study, we used UTR engineering to maximally increase the activities of glycerol dehydratase (GDHt) and aldehyde dehydrogenase (ALDH) for the high conversion of glycerol to 3-HP. Thereafter, the activity of GDHt was precisely controlled to avoid the accumulation of 3-HPA by varying expression of dhaB1, a gene encoding a main subunit of GDHt. The optimally balanced E. coli HGL_DBK4 showed a substantially enhanced 3-HP titer and productivity compared with the parental strain. The yield on glycerol, 0.97 g 3-HP/g glycerol, in a fed-batch experiment, was the highest ever reported.

Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle

Covering: 2000 to 2016Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages of the biological engineering cycle. In this review we illustrate how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted.

Self-regulated 1-butanol production in Escherichia coli based on the endogenous fermentative control

BACKGROUND

As a natural fermentation product secreted by Clostridium species, bio-based 1-butanol has attracted great attention for its potential as alternative fuel and chemical feedstock. Feasibility of microbial 1-butanol production has also been demonstrated in various recombinant hosts.

RESULTS

In this work, we constructed a self-regulated 1-butanol production system in Escherichia coli by borrowing its endogenous fermentation regulatory elements (FRE) to automatically drive the 1-butanol biosynthetic genes in response to its natural fermentation need. Four different cassette of 5' upstream transcription and translation regulatory regions controlling the expression of the major fermentative genes ldhA, frdABCD, adhE, and ackA were cloned individually to drive the 1-butanol pathway genes distributed among three plasmids, resulting in 64 combinations that were tested for 1-butanol production efficiency. Fermentation of 1-butanol was triggered by anaerobicity in all cases. In the growth-decoupled production screening, only combinations with formate dehydrogenase (Fdh) overexpressed under FRE _adhE demonstrated higher titer of 1-butanol anaerobically. In vitro assay revealed that 1-butanol productivity was directly correlated with Fdh activity under such condition. Switching cells to oxygen-limiting condition prior to significant accumulation of biomass appeared to be crucial for the induction of enzyme synthesis and the efficiency of 1-butanol fermentation. With the selection pressure of anaerobic NADH balance, the engineered strain demonstrated stable production of 1-butanol anaerobically without the addition of inducer or antibiotics, reaching a titer of 10 g/L in 24 h and a yield of 0.25 g/g glucose under high-density fermentation.

CONCLUSIONS

Here, we successfully engineered a self-regulated 1-butanol fermentation system in E. coli based on the natural regulation of fermentation reactions. This work also demonstrated the effectiveness of selection pressure based on redox balance anaerobically. Results obtained from this study may help enhance the industrial relevance of 1-butanol synthesis using E. coli and solidifies the possibility of strain improvement by directed evolution.

Systematic engineering of the central metabolism in Escherichia coli for effective production of n-butanol

BACKGROUND

Microbes have been extensively explored for production of environment-friendly fuels and chemicals. The microbial fermentation pathways leading to these commodities usually involve many redox reactions. This makes the fermentative production of highly reduced products challenging, because there is a limited NADH output from glucose catabolism. Microbial production of n-butanol apparently represents one typical example.

RESULTS

In this study, we addressed the issue by adjustment of the intracellular redox state in Escherichia coli. This was initiated with strain BuT-8 which carries the clostridial CoA-dependent synthetic pathway. Three metabolite nodes in the central metabolism of the strain were targeted for engineering. First, the pyruvate node was manipulated by enhancement of pyruvate decarboxylation in the oxidative pathway. Subsequently, the pentose phosphate (PP) pathway was amplified at the glucose-6-phosphate (G6P) node. The pathway for G6P isomerization was further blocked to force the glycolytic flux through the PP pathway. It resulted in a growth defect, and the cell growth was later recovered by limiting the tricarboxylic acid cycle at the acetyl-CoA node. Finally, the resulting strain exhibited a high NADH level and enabled production of 6.1 g/L n-butanol with a yield of 0.31 g/g-glucose and a productivity of 0.21 g/L/h.

CONCLUSIONS

The production efficiency of fermentative products in microbes strongly depends on the intracellular redox state. This work illustrates the flexibility of pyruvate, G6P, and acetyl-CoA nodes at the junction of the central metabolism for engineering. In principle, high production of reduced products of interest can be achieved by individual or coordinated modulation of these metabolite nodes.