Production of lycopene by metabolically-engineered Escherichia coli

Escherichia coli strain CAR001 that produces β-carotene was genetically engineered to produce lycopene by deleting genes encoding zeaxanthin glucosyltransferase (crtX) and lycopene β-cyclase (crtY) from the crtEXYIB operon. The resulting strain, LYC001, produced 10.5 mg lycopene/l (6.5 mg/g dry cell weight, DCW). Modulating expression of genes encoding α-ketoglutarate dehydrogenase, succinate dehydrogenase and transaldolase B within central metabolic modules increased NADPH and ATP supplies, leading to a 76 % increase of lycopene yield. Ribosome binding site libraries were further used to modulate expression of genes encoding 1-deoxy-d-xylulose-5-phosphate synthase (dxs) and isopentenyl diphosphate isomerase (idi) and the crt gene operon, which improved the lycopene yield by 32 %. The optimal strain LYC010 produced 3.52 g lycopene/l (50.6 mg/g DCW) in fed-batch fermentation.     

Production of Lycopene in the Non-Carotenoid-Producing Yeast Yarrowia lipolytica

The codon-optimized genes crtB and crtI of Pantoea ananatis were expressed in Yarrowia lipolytica under the control of the TEF1 promoter of Y. lipolytica. Additionally, the rate-limiting genes for isoprenoid biosynthesis in Y. lipolytica, GGS1 and HMG1, were overexpressed to increase the production of lycopene. All of the genes were also expressed in a Y. lipolytica strain with POX1 to POX6 and GUT2 deleted, which led to an increase in the size of lipid bodies and a further increase in lycopene production. Lycopene is located mainly within lipid bodies, and increased lipid body formation leads to an increase in the lycopene storage capacity of Y. lipolytica. Growth-limiting conditions increase the specific lycopene content. Finally, a yield of 16 mg g⁻¹ (dry cell weight) was reached in fed-batch cultures, which is the highest value reported so far for a eukaryotic host.     

Yield and kinetic constants estimation in the production of hydroxy fatty acids from oleic acid in a bioreactor by Pseudomonas aeruginosa 42A2

We modelled the production of hydroxy fatty acids from oleic acid by Pseudomonas aeruginosa 42A2 in a bioreactor with a non-dispersive aeration system. First, we designed an adapted wetted-wall gas-absorption column, offering a k _La value of 39.9 h^?1, to enhance oxygen absorption in the culture media and prevent foam formation. Then, we analysed different kinetic models to simulate the yield coefficients and the kinetic constants in this bacterial transformation. Monod model fitting (μ _max1?=?0.51 h^?1, K _S1?=?1.60 C-mol l^?1, μ _max2?=?0.12 h^?1, K _S2?=?0.035 C-mol l^?1, and k ₂?=?0.033 h^?1) showed a good accuracy with the experimental data sets and was chosen for its simplicity. Lastly, mass balances were carried out to establish the stoichiometry of this biotransformation with the following yield coefficients, Υ _X/OA, Υ _{X/(10S)-HPOME} and Υ _{(10S)-HPOME/(7S10S)-HPOME} of 0.172, 0.347 and 2.388 C-mol C-mol^?1, respectively.     

Studies on the production of shikimic acid using the <Emphasis Type="Italic">aroK</Emphasis> knockout strain of <Emphasis Type="Italic">Bacillus megaterium</Emphasis>

Shikimic acid has various pharmaceutical and industrial applications. It is the sole chemical building block for the antiviral drug oseltamivir (Tamiflu^®) and one of the potent pharmaceutical intermediates with three chiral centres. Here we report a modified strain of Bacillus megaterium with aroK (shikimate kinase) knock out to block the aromatic biosynthetic pathway downstream of shikimic acid. Homologous recombination based gene disruption approach was used for generating aroK knock out mutant of B. megaterium. Shake flask cultivation showed shikimic acid yield of 2.98 g/L which is ~6 times more than the wild type (0.53 g/L). Furthermore, the shikimate kinase activity was assayed and it was 32 % of the wild type. Effect of various carbon sources on the production of shikimic acid was studied and fructose (4 %, w/v) was found to yield maximum shikimic acid (4.94 g/L). The kinetics of growth and shikimic acid production by aroK knockout mutant was studied in 10 L bioreactor and the yield of shikimic acid had increased to 6 g/L which is ~12 fold higher over the wild type. It is evident from the results that aroK gene disruption had an immense effect in enhancing the shikimic acid production.     

Protoplast isolation for species in the Chamelaucium group and the effect of antioxidant enzymes (superoxide dismutase and catalase) on protoplast viability

An effective protocol for protoplast isolation from young leaves and somatic embryogenic cells of species in the Chamelaucium group and the use of superoxide dismutase (SOD) and catalase (CAT) to enhance protoplast viability are described. Mesophyll protoplasts were isolated from young leaves of a white Geraldton waxflower (Chamelaucium uncinatum) line 583, using a mixture of 1% (w/v) cellulase R10, 0.5% (w/v) macerozyme R10, and 0.1% (w/v) pectolyase. Viability of isolated mesophyll protoplasts increased dramatically when SOD and CAT were added. The highest increase of 7.61-fold in viability and 4.34-fold of viable protoplast yield were achieved when a combination of SOD at 500 units mL^?1 and CAT at 2,000 units mL^?1 was added to the enzyme mixture. Somatic embryogenic cell-derived protoplasts were isolated from embryogenic suspension cells of C. uncinatum line 583 when 1% (w/v) hemicellulase was added to a combination of 2% (w/v) cellulase R10, and 1% (w/v) macerozyme R10. Addition of SOD at 500 units mL^?1 and CAT at 2,000 units mL^?1 to the enzyme mixture improved viability only slightly, to above 90%, but improved yield significantly (6.6-fold). This combination of enzymes was also used to isolate protoplasts from embryogenic suspension cells of Chamelaucium repens and from young leaves of C. uncinatum, Actinodium calocephalum, Verticordia etheliana, Verticordia grandis, Verticordia hughanii, and Verticordia mitchelliana successfully with viability >80% and viable yield >7?×?10⁵ cells g^?1 fresh weight (or per milliliter packed cell volume in the case of suspension cells).     

Combining Genotype Improvement and Statistical Media Optimization for Isoprenoid Production in E. coli

Isoprenoids are a large and diverse class of compounds that includes many high value natural products and are thus in great demand. To meet the increasing demand for isoprenoid compounds, metabolic engineering of microbes has been used to produce isoprenoids in an economical and sustainable manner. To achieve high isoprenoid yields using this technology, the availability of metabolic precursors feeding the deoxyxylulose phosphate (DXP) pathway, responsible for isoprenoid biosynthesis, has to be optimized. In this study, phosphoenolpyruvate, a vital DXP pathway precursor, was enriched by deleting the genes encoding the carbohydrate phosphotransferase system (PTS) in E. coli. Production of lycopene (a C40 isoprenoid) was maximized by optimizing growth medium and culture conditions. In optimized conditions, the lycopene yield from PTS mutant was seven fold higher than that obtained from the wild type strain. This resulted in the highest reported specific yield of lycopene produced from the DXP pathway in E. coli to date (20,000 µg/g dry cell weight). Both the copy number of the plasmid encoding the lycopene biosynthetic genes and the expression were found to be increased in the optimized media. Deletion of PTS together with a similar optimization strategy was also successful in enhancing the production of amorpha-1,4-diene, a distinct C15 isoprenoid, suggesting that the approaches developed herein can be generally applied to optimize production of other isoprenoids.     

Target-oriented discovery of a new esterase-producing strain Enterobacter sp. ECU1107 for whole cell-catalyzed production of (2S,3R)-3-phenylglycidate as a chiral synthon of Taxol

A new strain, Enterobacter sp. ECU1107, was identified among over 200 soil isolates using a two-step screening strategy for the enantioselective synthesis of (2S,3R)-3-phenylglycidate methyl ester (PGM), a key intermediate for production of a potent anticancer drug Taxol^®. An organic–aqueous biphasic system was employed to reduce spontaneous hydrolysis of the substrate PGM and isooctane was found to be the most suitable organic solvent. The temperature and pH optima of the whole cell-mediated bioreaction were 40 °C and 6.0, respectively. Under these reaction conditions, the enantiomeric excess (ee _s) of (2S,3R)-PGM recovered was greater than 99 % at approximately 50 % conversion. The total substrate loading in batch reaction could reach 600 mM. By using whole cells of Enterobacter sp. ECU1107, (2S,3R)-PGM was successfully prepared in decagram scale in a 1.0-l mechanically stirred reactor, affording the chiral epoxy ester in >99 % ee _s and 43.5 % molar yield based on the initial load of racemic substrate.     

Pannonibacter indica sp. nov., a highly arsenate-tolerant bacterium isolated from a hot spring in India

A novel aerobic bacterium, strain HT23^T, able to grow on 500 mM sodium arsenate was isolated from a hot-spring sediment sample collected from Athamallik, Orissa, India. Cells of this isolate were Gram negative. Heterotrophic growth was observed at pH 6.0–11.0 and 20–45 °C. Optimum growth was observed at 37 °C and pH 7.0–10.0. The major polar lipids are diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl choline and phosphatidyl monomethyl ethanolamine. The major isoprenoid quinone was Q-10. 16S rRNA gene sequence analysis indicated that the bacterium clustered with the genus Pannonibacter and showed 98.9 % similarity with Pannonibacter phragmitetus C6-19^T (DSM 14782^T) and 98 % with the P. phragmitetus group B and P. phragmitetus group E strains. Levels of DNA–DNA relatedness between the strain HT23^T and P. phragmitetus C6-19^T (DSM 14782^T) and other strains of P. phragmitetus group B and group E strains were below 55 %. On the basis of phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence analysis and DNA–DNA hybridization data, strain HT23^T is considered to represent a novel species of the genus Pannonibacter, for which the name Pannonibacter indica sp. nov. is proposed. The type strain is HT23^T (=JCM 16851^T = DSM 23407^T = LMG 25769^T).     

Increased production of γ-lactones from hydroxy fatty acids by whole Waltomyces lipofer cells induced with oleic acid

Among several fatty acids tested, oleic acid was selected as the most efficient inducer for the production of 4-hydroxydodecanoic acid, a metabolite of β-oxidation, by Waltomyces lipofer. Cells were induced by incubation for 12 h in a medium containing 10 g l^?1 yeast extract, 10 g l^?1 peptone, 5 g l^?1 oleic acid, 1 g l^?1 glucose, and 0.05 % (w/v) Tween 80. The optimal reaction conditions for the production of γ-lactones by induced cells were pH 6.5, 35 °C, 200 rpm, 0.71 M Tris, 60 g l^?1 hydroxy fatty acid, and 20 g l^?1 cells. Non-induced cells produced 38 g l^?1 γ-dodecalactone from 60 g l^?1 10-hydroxystearic acid after 30 h, with a conversion yield of 63 % (w/w) and a productivity of 1.3 g l^?1 h^?1 under the optimized conditions, whereas induced cells produced 51 g l^?1 γ-dodecalactone from 60 g l^?1 10-hydroxystearic acid after 30 h, with a conversion yield of 85 % (w/w) and a productivity of 1.7 g l^?1 h^?1. The conversion yield and productivity of induced cells were 22 % and 1.3-fold higher, respectively, than those of non-induced cells. Induced cells also produced 28 g l^?1 γ-decalactone and 12 g l^?1 γ-butyrolactone from 60 g l^?1 12-hydroxystearic acid and 60 g l^?1 10-hydroxydecanoic acid, respectively, after 30 h. The concentration, conversion yield, and productivity of γ-dodecalactone and γ-decalactone are the highest reported thus far. This is the first study on the biotechnological production of γ-butyrolactone.     

Enantioselective hydrolysis of racemic styrene oxide and its substituted derivatives using newly-isolated Sphingopyxis sp. exhibiting a novel epoxide hydrolase activity

(S)-Styrene oxide, (S)-2-chlorostyrene oxide (CSO), (S)-3-CSO and (S)-4-CSO with 99.9 %ee were obtained with a yield of 20.6, 39.3, 28.7 and 26.8 % from 4 mM corresponding racemic substrates using 10 mg cells of a newly-isolated Sphingopyxis sp. at pH 8.0 and 25 °C in 1 ml 100 mM Tris/HCl buffer after 420, 100, 120 and 55 min, respectively. For racemic 2CSO, well-known for one of the racemates that is difficult to obtained in enantiomerically pure form, (S)-2-CSO with 99.9 %ee, 39.3 % yield (theoretical yield 50 %) and enantiomeric ratio of 42.1 was obtained. The newly-isolated strain can thus be used as whole-cell biocatalyst in the production of various (S)-CSO with a chlorine group at different positions.     

Two-helper-strain co-culture system: a novel method for enhancement of 2-keto-l-gulonic acid production

A novel two-helper-strain co-culture system (TSCS) was developed to enhance 2-keto-l-gulonic acid (2-KLG) productivity for vitamin C production. Bacillus megaterium and B. cereus (with a seeding culture ratio of 1:3, v/v), used as helper strains, increased the 2-KLG yield using Ketogulonigenium vulgare compared to the conventional one-helper-strain (either B. cereus or B. megaterium) co-culture system (OSCS). After 45 h cultivation, 2-KLG concentration in the TSCS (69 g l^?1) increased by 8.9 and 7 % over that of the OSCS (B. cereus: 63.4 g l^?1; B. megaterium: 64.5 g l^?1). The fermentation period of TSCS was 4 h shorter than that of OSCS (B. cereus). The increased cell numbers of K. vulgare stimulated by the two helper strains possibly explain the enhanced 2-KLG yield. The results imply that TSCS is a viable method for enhancing industrial production of 2-KLG.     

Increased Carotenoid Production by the Food Yeast Candida utilis through Metabolic Engineering of the Isoprenoid Pathway

The yeast Candida utilis does not possess an endogenous biochemical pathway for the synthesis of carotenoids. The central isoprenoid pathway concerned with the synthesis of prenyl lipids is present in C. utilis and active in the biosynthesis of ergosterol. In our previous study, we showed that the introduction of exogenous carotenoid genes, crtE, crtB, and crtI, responsible for the formation of lycopene from the precursor farnesyl pyrophosphate, results in the C. utilis strain that yields lycopene at 1.1 mg per g (dry weight) of cells (Y. Miura, K. Kondo, T. Saito, H. Shimada, P. D. Fraser, and N. Misawa, Appl. Environ. Microbiol. 64:1226–1229, 1998). Through metabolic engineering of the isoprenoid pathway, a sevenfold increase in the yield of lycopene has been achieved. The influential steps in the pathway that were manipulated were 3-hydroxy methylglutaryl coenzyme A (HMG-CoA) reductase, encoded by the HMG gene, and squalene synthase, encoded by the ERG9 gene. Strains overexpressing the C. utilis HMG-CoA reductase yielded lycopene at 2.1 mg/g (dry weight) of cells. Expression of the HMG-CoA catalytic domain alone gave 4.3 mg/g (dry weight) of cells; disruption of the ERG9 gene had no significant effect, but a combination of ERG9 gene disruption and the overexpression of the HMG catalytic domain yielded lycopene at 7.8 mg/g (dry weight) of cells. The findings of this study illustrate how modifications in related biochemical pathways can be utilized to enhance the production of commercially desirable compounds such as carotenoids.     

Influence of mixing and shear stress on Chlorella vulgaris, Scenedesmus obliquus, and Chlamydomonas reinhardtii

Photosynthetic activity (PA) and growth of different microalgae species (Chlorella vulgaris, Scenedesmus obliquus, and Chlamydomonas reinhardtii) depends in addition to other factors on mixing (tip speed) and shear stress (friction velocity) and was studied in a stirring tank (microcosm). In order to detect cause–effect relationships for an increase in photosynthetic activity, experiments were conducted under different pH values (6.0–8.5) and CO₂ concentrations (0.038 and 4 % (v/v)). The PA was determined as the effective quantum yield by pulse amplitude modulation during a stepwise increase of the tip speed from 0 to 589 cm s^?1 (friction velocity: 0–6.05 cm s^?1) in short-term experiments. The increase caused a distinctive pattern of PA of each species. Compared to 0 cm s^?1, C. vulgaris and S. obliquus showed a 4.0 and 4.8 % higher PA at the optimum tip speed of 126 cm s^?1 (friction velocity of 2.09 cm s^?1) and a 48 and 71 % higher growth, respectively. At 203 cm s^?1, the PA dropped to the value of the unstirred control, while at 589 cm s^?1, the PA decreased of up to 7 and 8 %. In contrast, C. reinhardtii showed 7 % stronger growth at 126 cm s^?1, while the PA decreased about 15 % at an increase of tip speed to 589 cm s^?1. For all investigated microalgae, the pattern of PA and higher growth was not only explained by the main contributing factors like light supply, nutrient supply, and overcoming diffusion gradients. The results indicate that hydrodynamic forces have a stimulating effect on the physiological processes within the cells.     

Production of 2-butanol from crude glycerol by a genetically-engineered Klebsiella pneumoniae strain

Klebsiella pneumoniae was engineered to produce 2-butanol from crude glycerol as a sole carbon source by expressing acetolactate synthase (ilvIH), keto-acid reducto-isomerase (ilvC) and dihydroxy-acid dehydratase (ilvD) from K. pneumoniae, and α-ketoisovalerate decarboxylase (kivd) and alcohol dehydrogenase (adhA) from Lactococcus lactis. Engineered K. pneumonia, ?ldhA/pBR-iBO (ilvIH–ilvC–ilvD–kivd–adhA), produced 2-butanol (160 mg l^?1) from crude glycerol. To increase the yield of 2-butanol, we eliminated the 2,3-butanediol pathway from the recombinant strain by inactivating α-acetolactate decarboxylase (adc). This further engineering step improved the yield of 2-butanol from 160 to 320 mg l^?1. This represents the first successful attempt to produce 2-butanol from crude glycerol.     

Erratum to: Production of isobutanol from crude glycerol by a genetically-engineered Klebsiella pneumoniae strain

Klebsiella pneumoniae was engineered to produce isobutanol from crude glycerol as a sole carbon source by expressing acetolactate synthase (ilvIH), keto-acid reducto-isomerase (ilvC) and dihydroxy-acid dehydratase (ilvD) from K. pneumoniae, and α-ketoisovalerate decarboxylase (kivd) and alcohol dehydrogenase (adhA) from Lactococcus lactis. Engineered K. pneumonia, ?ldhA/pBR-iBO (ilvIH–ilvC–ilvD–kivd–adhA), produced isobutanol (160 mg l^?1) from crude glycerol. To increase the yield of isobutanol, we eliminated the 2,3-butanediol pathway from the recombinant strain by inactivating α-acetolactate decarboxylase (adc). This further engineering step improved the yield of isobutanol from 160 to 320 mg l^?1. This represents the first successful attempt to produce isobutanol from crude glycerol.     

Effect of Potassium and Nitrogen Fertilizer on Switchgrass Productivity and Nutrient Removal Rates under Two Harvest Systems on a Low Potassium Soil

Biomass demand for energy will lead to utilization of marginal, low fertility soil. Application of fertilizer to such soil may increase switchgrass (Panicum virgatum L.) biomass production. In this three-way factorial field experiment, biomass yield response to potassium (K) fertilizer (0 and 68 kg?K?ha^?1) on nitrogen (N)-sufficient and N-deficient switchgrass (0 and 135 kg?N?ha^?1) was evaluated under two harvest systems. Harvest system included harvesting once per year after frost (December) and twice per year in summer (July) at boot stage and subsequent regrowth after frost. Under the one-cut system, there was no response to N or K only (13.4 Mg?ha^?1) compared to no fertilizer (12.4 Mg?ha^?1). Switchgrass receiving both N and K (14.6 Mg?ha^?1) produced 18 % greater dry matter (DM) yield compared to no fertilizer check. Under the two-cut harvest system, N only (16.0 Mg?ha^?1) or K only (14.1 Mg?ha^?1) fertilizer produced similar DM to no fertilizer (15.1 Mg?ha^?1). Switchgrass receiving both N and K in the two-cut system (19.2 Mg?ha^?1) produced the greatest (P?<?0.05) DM yield, which was 32 % greater than switchgrass receiving both N and K in the one-cut system. Nutrient removal (biomass?×?nutrient concentration) was greatest in plots receiving both N and K, and the two-cut system had greater nutrient removal than the one-cut system. Based on these results, harvesting only once during winter months reduces nutrient removal in harvested biomass and requires less inorganic fertilizer for sustained yields from year to year compared to two-cut system.     

Comparative study on the production of poly(3-hydroxybutyrate) by thermophilic Chelatococcus daeguensis TAD1: a good candidate for large-scale production

In spite of numerous advantages on operating fermentation at elevated temperatures, very few thermophilic bacteria with polyhydroxyalkanoates (PHAs)-accumulating ability have yet been found in contrast to the tremendous mesophiles with the same ability. In this study, a thermophilic poly(3-hydroxybutyrate) (PHB)-accumulating bacteria (Chelatococcus daeguensis TAD1), isolated from the biofilm of a biotrickling filter used for NOx removal, was extensively investigated and compared to other PHB-accumulating bacteria. The results demonstrate that C. daeguensis TAD1 is a growth-associated PHB-accumulating bacterium without obvious nutrient limitation, which was capable of accumulating PHB up to 83.6 % of cell dry weight (CDW, w/w) within just 24 h at 45 °C from glucose. Surprisingly, the PHB production of C. daeguensis TAD1 exhibited strong tolerance to high heat stress as well as nitrogen loads compared to that of other PHB-accumulating bacterium, while the optimal PHB amount (3.44?±?0.3 g l^?1) occurred at 50 °C and C/N?=?30 (molar) with glucose as the sole carbon source. In addition, C. daeguensis TAD1 could effectively utilize various cheap substrates (starch or glycerol) for PHB production without pre-hydrolyzed, particularly the glycerol, exhibiting the highest product yield (Y _P/S, 0.26 g PHB per gram substrate used) as well as PHB content (80.4 % of CDW, w/w) compared to other carbon sources. Consequently, C. daeguensis TAD1 is a viable candidate for large-scale production of PHB via utilizing starch or glycerol as the raw materials.     

Enhancing isoprenoid production through systematically assembling and modulating efflux pumps in Escherichia coli

Enhancement of the cellular exportation of heterologous compounds is an important aspect to improve the product yield in microbial cell factory. Efflux pumps can expel various intra- or extra-cellular substances out of microbial hosts and increase the cellular tolerance. Thus in this study, by using the hydrophobic sesquiterpene (amorphadiene) and diterpene (kaurene) as two model compounds, we attempted to improve isoprenoid production through systematically engineering the efflux pumps in Escherichia coli BL21(DE3). The pleiotropic resistant pumps, AcrAB-TolC, MdtEF-TolC from E. coli and heterologous MexAB-OprM pump from Pseudomonas aeruginosa, were overexpressed, assembled, and finely modulated. We found that overexpression of AcrB and TolC components can effectively enhance the specific yield of amorphadiene and kaurene, e.g., 31 and 37 % improvement for amorphadiene compared with control, respectively. The heterologous MexB component can enhance kaurene production with 70 % improvement which is more effective than TolC and AcrB. The results suggest that the three components of tripartite efflux pumps play varied effect to enhance isoprenoid production. Considering the highly organized structure of efflux pumps and importance of components interaction, various component combinations were constructed and the copy number of key components AcrB and TolC was finely modulated as well. The results exhibit that the combination TolC and TolC and AcrB improved the specific yield of amorphadiene with 118 %, and AcrA and TolC and AcrB improved that of kaurene with 104 %. This study indicates that assembling and finely modulating efflux pumps is an effective strategy to improve the production of heterologous compounds in E. coli.