Fermentation approach for enhancing 1-butanol production using engineered butanologenic Escherichia coli

Construction of an Antibiotic-Free Vector and its Application in the Metabolic Engineering of Escherichia Coli for Polyhydroxybutyrate Production

An antibiotic- and inducer-free culture condition was proposed for polyhydroxybutyrate (PHB) production in recombinant Escherichia coli. First, antibiotic-free vectors were constructed by installing the plasmid maintenance system, alp7, hok/sok, and the hok/sok and alp7 combination into the pUC19 vector. The plasmid stability test showed that pVEC02, the pUC19 vector containing the hok/sok system, was the most effective in achieving antibiotic-free cultivation in the E. coli B strain but not in the K strain. Second, the putative phaCAB operon derived from Caldimonas manganoxidans was inserted into pVEC02 to yield pPHB01 for PHB production in E. coli BL21 (DE3). The putative phaCAB operon was first shown function properly for PHB production and thus, inducer-free conditions were achieved. However, the maintenance of pPHB01 in E. coli requires antibiotics supplementation. Finally, an efficient E. coli ρ factor-independent terminator, thrLABC (ECK120033737), was inserted between the phaCAB operon and the hok/sok system to avoid possible transcriptional carry-over. The newly constructed plasmid pPHB01-1 facilitates an antibiotic- and inducer-free culture condition and induces the production of PHB with a concentration of 3.0 on0.2 g/L, yield of 0.26 /L0.07 g/g-glucose, and content of 44 /g3%. The PHB production using E. coli BL21 (DE3)/pPHB01-1 has been shown to last 84 and 96 h in the liquid and solid cultures.

The Physiological Responses of Escherichia coli Triggered by Phosphoribulokinase (PrkA) and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco)

Phosphoribulokinase (PrkA) and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been proposed to create a heterologous Rubisco-based engineered pathway in Escherichia coli for in situ CO₂ recycling. While the feasibility of a Rubisco-based engineered pathway has been shown, heterologous expressions of PrkA and Rubisco also induced physiological responses in E. coli that may compete with CO₂ recycling. In this study, the metabolic shifts caused by PrkA and Rubisco were investigated in recombinant strains where ppc and pta genes (encodes phosphoenolpyruvate carboxylase and phosphate acetyltransferase, respectively) were deleted from E. coli MZLF (E. coli BL21(DE3) Δzwf, ΔldhA, Δfrd). It has been shown that the demand for ATP created by the expression of PrkA significantly enhanced the glucose consumptions of E. coli CC (MZLF Δppc) and E. coli CA (MZLF Δppc, Δpta). The accompanying metabolic shift is suggested to be the mgsA route (the methylglyoxal pathway) which results in the lactate production for reaching the redox balance. The overexpression of Rubisco not only enhanced glucose consumption but also bacterial growth. Instead of the mgsA route, the overproduction of the reducing power was balanced by the ethanol production. It is suggested that Rubisco induces a high demand for acetyl-CoA which is subsequently used by the glyoxylate shunt. Therefore, Rubisco can enhance bacterial growth. This study suggests that responses induced by the expression of PrkA and Rubisco will reach a new energy balance profile inside the cell. The new profile results in a new distribution of the carbon flow and thus carbons cannot be majorly directed to the Rubisco-based engineered pathway.

Manipulating ATP supply improves in situ CO2 recycling by reductive TCA cycle in engineered Escherichia coli

The reductive tricarboxylic acid (rTCA) cycle was reconstructed in Escherichia coli by introducing pGETS118KAFS, where kor (encodes α-ketoglutarate:ferredoxin oxidoreductase), acl (encodes ATP-dependent citrate lyase), frd (encodes fumarate reductase), and sdh (encodes succinate dehydrogenase) were tandemly conjugated by the ordered gene assembly in Bacillus subtilis (OGAB). E. coli MZLF (E. coli BL21(DE3) Δzwf, Δldh, Δfrd) was employed so that the C-2/C-1 [(ethanol + acetate)/(formate + CO₂)] ratio can be used to investigate the effectiveness of the recombinant rTCA for in situ CO₂ recycling. It has been shown that supplying ATP through the energy pump (the EP), where formate donates electron to nitrate to form ATP, elevates the C-2/C-1 ratio from 1.03 ± 0.00 to 1.49 ± 0.02. Similarly, when ATP production is increased by the introduction of the heterologous ethanol production pathway (pLOI295), the C-2/C-1 ratio further increased to 1.79 ± 0.02. In summary, the ATP supply is a rate-limiting step for in situ CO₂ recycling by the recombinant rTCA cycle. The decrease in C-1 is significant, but the destination of those recycled C-1 is yet to be determined.

Exceeding the theoretical fermentation yield in mixotrophic Rubisco-based engineered Escherichia coli

Rubisco-based engineered Escherichia coli MZLFB (E. coli BL21(DE3) Δzwf, Δldh, Δfrd) containing heterologous phosphoribulokinase (Prk) and Ribulose-1,5- bisphosphate carboxylase/oxygenase (Rubisco) was constructed for the mixotrophic growth. However, in situ CO₂ recycling was hindered by clogs of pyruvate during glucose metabolism, which consequently resulted in an insufficient regeneration of NAD⁺ through the pflB-mediated ethanol production. Recombinant plasmid pLOI295 (encodes pyruvate decarboxylase and alcohol dehydrogenase II, referred to as the Pdc-based carbon tap valve (CTV) for convenience) was introduced into E. coli MZLFB + CTV to bypass the pflB-mediated ethanol production. Results show that while the C-2/C-1 ratio (i.e., the molar ratio of ethanol and acetate to formate and total CO₂) for parental strain MZLFB was 1.0 ± 0.1, the C-2/C-1 for MZLFB + CTV increased to 1.6 ± 0.1. This indicates that the Pdc-based CTV enhanced the performance of in situ CO₂ recycling. By simultaneously utilizing glucose and CO₂, the fermentation product yield of MZLFB + CTV exceeded the normal theoretical yield and reached 2.2 ± 0.0 (mol/mol). In silico analysis shows that 61% of the glucose consumption went through the Rubisco-based engineered pathway when the CTV was equipped. Also shown are the average CO₂ consumption rate of 55.3 mg L^-1·h^-1 and an average ethanol production rate of 144.8 mg L^-1·h^-1. The conversion of CO₂ to ethanol through the Rubisco-based engineered pathway and the Pdc-based carbon tap valve is important for mixotrophic growth, since these two modules serve as the energy sink to achieve intracellular energy balance. Also, during mixotrophic growth, ATP production from a certain percentage (39% in this study) of the EMP pathway activity is needed for mixotrophic growth.

The significance of proline and glutamate on butanol chaotropic stress in Bacillus subtilis 168

BACKGROUND

Butanol is an intensively used industrial solvent and an attractive alternative biofuel, but the bioproduction suffers from its high toxicity. Among the native butanol producers and heterologous butanol-producing hosts, Bacillus subtilis 168 exhibited relatively higher butanol tolerance. Nevertheless, organic solvent tolerance mechanisms in Bacilli and Gram-positive bacteria have relatively less information. Thus, this study aimed to elucidate butanol stress responses that may involve in unique tolerance of B. subtilis 168 to butanol and other alcohol biocommodities.

RESULTS

Using comparative proteomics approach and molecular analysis of butanol-challenged B. subtilis 168, 108 butanol-responsive proteins were revealed, and classified into seven groups according to their biological functions. While parts of them may be similar to the proteins reportedly involved in solvent stress response in other Gram-positive bacteria, significant role of proline in the proline-glutamate-arginine metabolism was substantiated. Detection of intracellular proline and glutamate accumulation, as well as glutamate transient conversion during butanol exposure confirmed their necessity, especially proline, for cellular butanol tolerance. Disruption of the particular genes in proline biosynthesis pathways clarified the essential role of the anabolic ProB-ProA-ProI system over the osmoadaptive ProH-ProA-ProJ system for cellular protection in response to butanol exposure. Molecular modifications to increase gene dosage for proline biosynthesis as well as for glutamate acquisition enhanced butanol tolerance of B. subtilis 168 up to 1.8% (vol/vol) under the conditions tested.

CONCLUSION

This work revealed the important role of proline as an effective compatible solute that is required to protect cells against butanol chaotropic effect and to maintain cellular functions in B. subtilis 168 during butanol exposure. Nevertheless, the accumulation of intracellular proline against butanol stress required a metabolic conversion of glutamate through the specific biosynthetic ProB-ProA-ProI route. Thus, exogenous addition of glutamate, but not proline, enhanced butanol tolerance. These findings serve as a practical knowledge to enhance B. subtilis 168 butanol tolerance, and demonstrate means to engineer the bacterial host to promote higher butanol/alcohol tolerance of B. subtilis 168 for the production of butanol and other alcohol biocommodities.

Coordination of metabolic pathways: Enhanced carbon conservation in 1,3-propanediol production by coupling with optically pure lactate biosynthesis

Metabolic engineering has emerged as a powerful tool for bioproduction of both fine and bulk chemicals. The natural coordination among different metabolic pathways contributes to the complexity of metabolic modification, which hampers the development of biorefineries. Herein, the coordination between the oxidative and reductive branches of glycerol metabolism was rearranged in Klebsiella oxytoca to improve the 1,3-propanediol production. After deliberating on the product value, carbon conservation, redox balance, biological compatibility and downstream processing, the lactate-producing pathway was chosen for coupling with the 1,3-propanediol-producing pathway. Then, the other pathways of 2,3-butanediol, ethanol, acetate, and succinate were blocked in sequence, leading to improved d-lactate biosynthesis, which as return drove the 1,3-propanediol production. Meanwhile, efficient co-production of 1,3-propanediol and l-lactate was also achieved by replacing ldhD with ldhL from Bacillus coagulans. The engineered strains PDL-5 and PLL co-produced over 70g/L 1,3-propanediol and over 100g/L optically pure d-lactate and l-lactate, respectively, with high conversion yields of over 0.95mol/mol from glycerol.

Simultaneous saccharification and fermentation of hemicellulose to butanol by a non-sporulating Clostridium species

Production of lignocellulosic butanol has drawn increasing attention. However, currently few microorganisms can produce biofuels, particularly butanol, from lignocellulosic biomass via simultaneous saccharification and fermentation. Here we report discovery of a wild-type, mesophilic Clostridium sp. strain MF28 that ferments xylan to produce butanol (up to 3.2g/L) without the addition of saccharolytic enzymes and without any chemical pretreatments. Application of selective pressure from 2-deoxy-d-glucose facilitated isolation of strain MF28, which exhibits inactivation of genes (gid and ccp genes) responsible for carbon catabolite repression, thus allowing strain MF28 to simultaneously ferment a combination of glucose (30g/L), xylose (15g/L), and arabinose (15g/L) to produce 11.9g/L of butanol. Strain MF28 possesses several unique features: (i) non-sporulating, (ii) no acetone/ethanol, (iii) complete hemicellulose-binding enzymatic domain, and (iv) absence of carbon catabolite repression. These unique characteristics demonstrate the industrial potential of strain MF28 for cost-effective biofuel generation from lignocellulosic biomass.

The comprehensive profile of fermentation products during in situ CO2 recycling by Rubisco-based engineered Escherichia coli

BACKGROUND

In our previous study, the feasibility of Rubisco-based engineered E. coli (that contains heterologous phosphoribulokinase (PrkA) and Rubisco) for in situ CO2 recycling during the fermentation of pentoses or hexoses was demonstrated. Nevertheless, it is perplexing to see that only roughly 70 % of the carbon fed to the bacterial culture could be accounted for in the standard metabolic products. This low carbon recovery during fermentation occurred even though CO2 emission was effectively reduced by Rubisco-based engineered pathway.

RESULTS

In this study, the heterologous expression of form I Rubisco was found to enhance the accumulation of pyruvate in Escherichia coli MZLF [E. coli BL21(DE3) Δzwf, Δldh, Δfrd]. This may be attributed to the enhanced glycolytic reaction supported by the increased biomass and the ethanol/acetate ratio. Besides, it was found that the transcription of arcA (encodes the redox-dependent transcriptional activators ArcA that positively regulates the transcription of pyruvate formate-lyase) was down-regulated in the presence of Rubisco. The enhanced accumulation of pyruvate also occurs when PrkA is co-expressed with Rubisco in E. coli MZLF. Furthermore, E. coli containing Rubisco-based engineered pathway has a distinct profile of the fermentation products, indicating CO2 was converted into fermentation products. By analyzing the ratio of total C-2 (2-carbon fermentation products) to total C-1 (1-carbon fermentation product) of MZLFB (MZLF containing Rubisco-based engineered pathway), it is estimated that 9 % of carbon is directed into Rubisco-based engineered pathway.

CONCLUSIONS

Here, we report for the first time the complete profile of fermentation products using E. coli MZLF and its derived strains. It has been shown that the expression of Rubisco alone in MZLF enhances the accumulation of pyruvate. By including the contribution of pyruvate accumulation, the perplexing problem of low carbon recovery during fermentation by E. coli containing Rubisco-based engineered pathway has been solved. 9 % of glucose consumption is directed from glycolysis to Rubisco-based engineered pathway in MZLFB. The principle characteristics of mixotroph MZLFB are the high bacterial growth and the low CO2 emission.

The Feasibility of Thermophilic Caldimonas manganoxidans as a Platform for Efficient PHB Production

Recently, poly(3-hydroxybutyrate) (PHB) has been found in a few thermophilic strains where several advantages can be gained from running fermentation at high temperatures. Caldimonas manganoxidans, a thermophilic gram-negative bacterium, was investigated for the feasibility as a PHB-producing strain. It is suggested that the best fermentation strategy for achieving the highest PHB concentration of 5.4 ± 1.1 g/L (from 20 g/L glucose) in 24 h is to use the fermentation conditions that are favored for the bacterial growth, yet temperature and pH should be chosen at conditions that are favored for the PHB content. Besides, the above fermentation conditions produce PHB that has a high molecular weight of 1274 kDa with a low polydispersity index (PDI) of 1.45, where the highest Mw of PHB of 1399 kDa (PDI of 1.32) is obtained in this study. To the best knowledge of authors, C. manganoxidans has the best PHB productivity among the thermophiles and is comparable to those common PHB-producing mesophiles.

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.

Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments

In the era of synthetic biology, techniques for rapidly constructing a designer long DNA from short DNA fragments are desired. To realize this, we attempted to establish a method for one-step DNA assembly of unprecedentedly large numbers of fragments. The basic technology is the Ordered Gene Assembly in Bacillus subtilis (OGAB) method, which uses the plasmid transformation system of B. subtilis. Since this method doesn’t require circular ligation products but needs tandem repeat ligation products, the degree of deviation in the molar concentration of the material DNAs is the only determinant that affects the efficiency of DNA assembly. The strict standardization of the size of plasmids that clone the DNA block and the measurement of the block in the state of intact plasmid improve the reliability of this step, with the coefficient of variation of the molar concentrations becoming 7%. By coupling this method with the OGAB method, one-step assembly of more than 50 DNA fragments becomes feasible.

Biosynthesis of hydrocarbons and volatile organic compounds by fungi: bioengineering potential

Recent advances in the biological production of fuels have relied on the optimization of pathways involving genes from diverse organisms. Several recent articles have highlighted the potential to expand the pool of useful genes by looking to filamentous fungi. This review highlights the enzymes and organisms used for the production of a variety of fuel types and commodity chemicals with a focus on the usefulness and promise of those from filamentous fungi.

The coupling of glycolysis and the Rubisco-based pathway through the non-oxidative pentose phosphate pathway to achieve low carbon dioxide emission fermentation

In this study, Rubisco-based engineered Escherichia coli, containing two heterologous enzymes of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and phosphoribulokinase (PrkA), has been shown to be capable of the in situ recycling of carbon dioxide (CO2) during glycolysis. Two alternative approaches have been proposed to further enhance the carbon flow from glycolysis to a Rubisco-based pathway through the non-oxidative pentose phosphate pathway (NOPPP). The first is achieved by elevating the expression of transketolase I (TktA) and the second by blocking the native oxidation-decarboxylation reaction of E. coli by deleting the zwf gene from the chromosome (designated as JB/pTA and MZB, respectively). Decreases in the CO2 yield and the CO2 evolution per unit mole of ethanol production by at least 81% and 40% are observed. It is demonstrated in this study that the production of one mole of ethanol using E. coli strain MZB, the upper limit of CO2 emission is 0.052mol.

Improved productivity of poly (3-hydroxybutyrate) (PHB) in thermophilic Chelatococcus daeguensis TAD1 using glycerol as the growth substrate in a fed-batch culture

A particularly successful polyhydroxyalkanoate (PHA) in industrial applications is poly (3-hydroxybutyrate) (PHB). However, one of the major obstacles for wider application of PHB is the cost of its production and purification. Therefore, it is desirable to discover a method for producing PHB in large quantities at a competitive price. Glycerol is a cheap and widely used carbon source that can be applied in PHB production process. There are numerous advantages to operating fermentation at elevated temperatures; only several thermophilic bacteria are able to accumulate PHB when glycerol is the growth substrate. Here, we report on the possibility of increasing PHB production at low cost using thermophilic Chelatococcus daeguensis TAD1 when glycerol is the growth substrate in a fed-batch culture. We found that (1) excess glycerol inhibited PHB accumulation and (2) organic nitrogen sources, such as tryptone and yeast extract, promoted the growth of C. daeguensis TAD1. In the batch fermentation experiments, we found that using glycerol at low concentrations as the sole carbon source, along with the addition of mixed nitrate (NH4Cl, tryptone, and yeast extract), stimulated PHB accumulation in C. daeguensis TAD1. The results showed that the PHB productivity decreased in the following order: two-stage fed-batch fermentation > fed-batch fermentation > batch fermentation. In optimized culture conditions, a PHB amount of 17.4 g l(-1) was obtained using a two-stage feeding regimen, leading to a productivity rate of 0.434 g l(-1) h(-1), which is the highest productivity rate reported for PHB to date. This high PHB biosynthetic productivity could decrease the total production cost, allowing for further development of industrial applications of PHB.

Reducing cofactors contribute to the increase of butanol production by a wild-type Clostridium sp. strain BOH3

Availability of reducing factors (e.g., NADH and NADPH) plays an important role in improving the efficacy of products conversion in cofactor-dependent production systems. In this study, nicotinic acid (NA), the precursor of NADH and NADPH, was supplemented to the growth medium of a wild-type Clostridium sp. strain BOH3. Results showed that the addition of precursor NA to the medium led to a significant increase in the levels of NADH and NADPH. Meanwhile, a maximal cell growth rate and butanol generation rate were reached by applying a two-stage pH-shift strategy, achieving 18.7g/L butanol with a yield of 24.6% and a productivity of 0.26g/Lh. The metabolic patterns were shifted towards more reduced metabolites as reflected by higher butanol-to-acetone ratio (11%) and butanol-to-acid ratio (292%). Redistributing metabolic flux to butanol via manipulations of reducing cofactor and pH shift could become an alternative tool to realize metabolic engineering goals.

Rubisco-based engineered Escherichia coli for in situ carbon dioxide recycling

In this study, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and phosphoribulokinase (PrkA) were overexpressed individually and in combination in Escherichia coli under different fermentation conditions. While wild-type E. coli produced 0.731 mol of CO2 per consumption of one mole of arabinose, engineered E. coli JB, containing both heterologous Rubisco and PrkA, produced only 0.621 mol of CO2 per consumption of one mole of arabinose. This represents a 15% reduction in CO2 emission and achieves 38% of theoretical CO2 reduction. The CO2 fixation rate of Rubisco-based engineered E. coli JB is 67 mg-CO2·mole-arabinose(-1) L(-1) h(-1), which is comparable to the performance of microalgae and cyanobacteria. It has been found that overexpressing Rubisco dramatically elevates the bacteria growth and sugar consumptions in the presence of oxygen and L-arabinose. It has been also found that overexpressing PrkA could demolish the balance of ATP regeneration, yet can be recovered simply by controlling the pH at 7.0±0.1.