Effect of heating rate on pDNA production by E. coli

The effects of heating rate (HR) on the performance of two-phase (batch followed by fed-batch) high cell-density cultivations (HCDC) of E. coli DH5α for the production of plasmid DNA (pDNA) were investigated. Optimal temperatures for the HCDC, as selected from shake flask experiments at constant temperatures between 30 and 45 °C, were 35 °C for biomass accumulation in the batch phase and 42 °C for inducing pDNA replication during the fed-batch. In HCDC the temperature was increased at HR of 0.025, 0.05, 0.10 and 0.25 °C/min and the performance of the cultivations were compared to a HCDC run at constant temperature (35 °C). Compared to constant 35 °C, heat-induced HCDC accumulated up to 50% less biomass within the same cultivation time and acetate and glucose accumulated to high concentrations. The overall specific productivity (Q_P) and average pDNA yield (Y_p/x) in HCDC at 35 °C were 0.22 ± 0.02 mg/g h and 5.3 ± 0.00 mg/g, respectively. Such parameters were maximum at a HR of 0.05 °C/min, reaching 0.56 ± 0.06 mg/g h and 9.3 ± 0.6 mg/g, respectively. At HR above 0.5 °C/min, Y_p/x remained relatively constant, whereas Q_P tended to decrease. The supercoiled pDNA fraction remained around 80% at all HR. Bioreactors were equipped with a capacitance/conductivity probe. In all cases biomass concentration correlated closely with the capacitance signal and acetate and glucose accumulation was accompanied by an increase in the conductivity signal. Thus, it was possible to calculate acetate and biomass concentrations, as well as μ, from online capacitance and conductivity signals using estimators. Altogether, in this study it was shown that it is possible to maximize pDNA productivity by choosing an appropriate HR and that relevant parameters can be estimated by capacitance/conductivity signals, which are useful for better process control and development.     

Uncovering the gene knockout landscape for improved lycopene production in E. coli

Systematic and combinatorial genetic approaches for the identification of gene knockout and overexpression targets have been effectively employed in the improvement of cellular phenotypes. Previously, we demonstrated how two of these tools, metabolic modeling and transposon mutagenesis, can be combined to identify strains of interest spanning the metabolic landscape of recombinant lycopene production in Escherichia coli. However, it is unknown how to best select multiple-gene knockout targets. Hence, this study seeks to understand how the overall order of gene selection, or search trajectory, biases the exploration and topology of the metabolic landscape. In particular, transposon mutagenesis and selection were employed in the background of eight different knockout genotypes. Collectively, 800,000 mutants were analyzed in hopes of exhaustively identifying all advantageous gene knockout targets. Several interesting observations, including clusters of gene functions, recurrence, and divergent genotypes, demonstrate the complexity of mapping only one genotype to one phenotype. One particularly interesting mutant, the ΔhnrΔyliE genotype, exhibited a drastically improved lycopene production capacity in basic minimal medium in comparison to the best strains identified in previous studies.     

Manipulating redox and ATP balancing for improved production of succinate in E. coli

Redox and energy balance plays a key role in determining microbial fitness. Efforts to redirect bacterial metabolism often involve overexpression and deletion of genes surrounding key central metabolites, such as pyruvate and acetyl-coA. In the case of metabolic engineering of Escherichia coli for succinate production, efforts have mainly focused on the manipulation of key pyruvate metabolizing enzymes. E. coli AFP111 strain lacking ldhA, pflB and ptsG encoded activities accumulates acetate and ethanol as well as shows poor anaerobic growth on rich and minimal media. To address these issues, we first deleted genes (adhE, ackA-pta) involved in byproduct formation downstream of acetyl-CoA followed by the deletion of iclR and pdhR to activate the glyoxylate pathway. Based on data from these studies, we hypothesized that the succinate productivity was limited by the insufficient ATP generation. Genome-scale thermodynamics-based flux balance analysis indicated that overexpression of ATP-forming PEPCK from Actinobacillus succinogenes in an ldhA, pflB and ptsG triple mutant strain could result in an increase in biomass and succinate flux. Testing of this prediction confirmed that PEPCK overexpression resulted in a 60% increase in biomass and succinate formation in the ldhA, pflB, ptsG mutant strain.     

An improved procedure for production of human epidermal growth factor from recombinant E. coli

An improved procedure for the fermentation and purification of human epidermal growth factor (hEGF) was developed. Recombinant Escherichia coli HB-101 [lacUV5omp08hEGF] harboring plasmid lacUV5omp08hEGF encoding hEGF was used in fermentation to increase levels of hEGF. Medium composition, and the levels of inoculum, inducer (isopropyl-beta-D-thiogalactoside) and ampicillin were optimized with respect to volumetric fermentation of hEGF. As a result, the hEGF concentration reached a high value of 242 mg l(-1) and the amount of heterogeneous protein decreased by 62% compared with that before optimization in batch fermentation. High-quality hEGF was purified from the fermentation culture by centrifugation, salting-out, resuspension, recentrifugation and finally gel chromatography on a Grad-iFrac System using Sephadex G-50 superfine. The purity of hEGF and the total yield were more than 94% and higher than 36%, respectively, and SDS-PAGE of the purified hEGF demonstrated a single band corresponding to an hEGF standard. In particular, a very important phenomenon was found, i.e. that the amount of heterogenous protein in fermentation broths cultured in media with high concentrations of lactose is far less than that cultured in media with high concentrations of glucose.     

Antibiotic-free selection in E. coli: new considerations for optimal design and improved production

Background  

The increasing regulatory requirements to which biological agents are subjected will have a great impact in the field of industrial protein expression and production. There is an expectation that in a near future, there may be "zero tolerance" towards antibiotic-based selection and production systems. Besides the antibiotic itself, the antibiotic resistance gene is an important consideration. The complete absence of antibiotic-resistance gene being the only way to ensure that there is no propagation in the environment or transfer of resistance to pathogenic strains.     

Engineering improved ethanol production in Escherichia coli with a genome-wide approach

A key challenge to the commercial production of commodity chemical and fuels is the toxicity of such molecules to the microbial host. While a number of studies have attempted to engineer improved tolerance for such compounds, the majority of these studies have been performed in wild-type strains and culturing conditions that differ considerably from production conditions. Here we applied the multiscalar analysis of library enrichments (SCALEs) method and performed a growth selection in an ethanol production system to quantitatively map in parallel all genes in the genome onto ethanol tolerance and production. In order to perform the selection in an ethanol-producing system, we used a previously engineered Escherichia coli ethanol production strain (LW06; ATCC BAA-2466) (Woodruff et al., in press), as the host strain for the multiscalar genomic library analysis (>10⁶ clones for each library of 1, 2, or 4 kb overlapping genomic fragments). By testing individually selected clones, we confirmed that growth selections enriched for clones with both improved ethanol tolerance and production phenotypes. We performed combinatorial testing of the top genes identified (uspC, otsA, otsB) to investigate their ability to confer improved ethanol tolerance or ethanol production. We determined that overexpression of otsA was required for improved tolerance and productivity phenotypes, with the best performing strains showing up to 75% improvement relative to the parent production strain.     

Use of modular,synthetic scaffolds for improved production of glucaric acid in engineered E. coli

The field of metabolic engineering has the potential to produce a wide variety of chemicals in both an inexpensive and ecologically-friendly manner. Heterologous expression of novel combinations of enzymes promises to provide new or improved synthetic routes towards a substantially increased diversity of small molecules. Recently, we constructed a synthetic pathway to produce d-glucaric acid, a molecule that has been deemed a “top-value added chemical” from biomass, starting from glucose. Limiting flux through the pathway is the second recombinant step, catalyzed by myo-inositol oxygenase (MIOX), whose activity is strongly influenced by the concentration of the myo-inositol substrate. To synthetically increase the effective concentration of myo-inositol, polypeptide scaffolds were built from protein–protein interaction domains to co-localize all three pathway enzymes in a designable complex as previously described (Dueber et al., 2009). Glucaric acid titer was found to be strongly affected by the number of scaffold interaction domains targeting upstream Ino1 enzymes, whereas the effect of increased numbers of MIOX-targeted domains was much less significant. We determined that the scaffolds directly increased the specific MIOX activity and that glucaric acid titers were strongly correlated with MIOX activity. Overall, we observed an approximately 5-fold improvement in product titers over the non-scaffolded control, and a 50% improvement over the previously reported highest titers. These results further validate the utility of these synthetic scaffolds as a tool for metabolic engineering.     

Metabolic engineering of E. coli for pyocyanin production

Pyocyanin is a secondary metabolite from Pseudomonas aeruginosa that belongs to the class of phenazines, which are aromatic nitrogenous compounds with numerous biological functions. Besides its antifungal and antimicrobial activities, pyocyanin is a remarkable redox-active molecule with potential applications ranging from the pharma industry to the development of microbial fuel cells. Nevertheless, pyocyanin production has been restricted to P. aeruginosa strains, limiting its practical applicability. In this study, the pyocyanin biosynthetic pathway was engineered for the first time for high level production of this compound in a heterologous host. Escherichia coli cells harboring the nine-gene pathway divided into two plasmids were able to produce and secrete pyocyanin at higher levels than some Pseudomonas aeruginosa strains. The influence of culture and induction parameters were evaluated, and the optimized conditions led to an increase of 3.5-fold on pyocyanin accumulation. Pathway balancing was achieved by testing a set of plasmids with different copy numbers to optimize the expression levels of pyocyanin biosynthetic genes, resulting in a fourfold difference in product titer among the engineered strains. Further improvements were achieved by co-expression of Vitreoscilla hemoglobin Vhb, which relieved oxygen limitations and led to a final titer of 18.8 mg/L pyocyanin. These results show promise to use E. coli for phenazines production, and the engineered strain developed here has the potential to be used in electro-fermentation systems where pyocyanin plays a role as electron-shuttle.     

Penicillin acylase production by E. coli

Enzyme production with E. coli ATCC 11105, in a complex medium using phenylacetic acid as inducer is carried out in a stirred-tank reactor of 10 dm³ and an airlift tower-loop reactor of 60 dm³ with outer loop at a temperature of 27 °C. The optimum inducer concentration was 0.8 kg/m³, which was kept constant by fed-batch operation. The optimum of the relative dissolved O₂-concentration with regard to saturation is below 10% in a stirred-tank reactor and at 35% in a tower-loop reactor. It was kept constant by parameter-adaptive control of the aeration rate. In a stirred-tank enzyme productivity is slightly higher than in a tower-loop reactor, and much higher than in a bubble column reactor.List of Symbols CPR kg/(m³ h) CO₂-production rate - OTR kg/(m³ h) O₂-transfer rate - OUR kg/(m³ h) O₂-utilization rate - PAA phenylacetic acid (inducer) - RQ = CPR/OUR respiratory quotient - X kg/m³ cell mass concentration - _m h^–1 maximum specific growth rate     

Engineering the E. coli UDP-glucose synthesis pathway for oligosaccharide synthesis

A metabolic engineering strategy was successfully applied to engineer the UDP-glucose synthesis pathway in E. coli. Two key enzymes of the pathway, phosphoglucomutase and UDP-glucose pyrophosphorylase, were overexpressed to increase the carbon flux toward UDP-glucose synthesis. When additional enzymes (a UDP-galactose epimerase and a galactosyltransferease) were introduced to the engineered strain, the increased flux to UDP-glucose synthesis led to an enhanced UDP-galactose derived disaccharide synthesis. Specifically, close to 20 mM UDP-galactose derived disaccharides were synthesized in the engineered strain, whereas in the control strain only 2.5 mM products were obtained, indicating that the metabolic engineering strategy was successful in channeling carbon flux (8-fold more) into the UDP-glucose synthesis pathway. UDP-sugar synthesis and oligosaccharide synthesis were shown to increase according to the enzyme expression levels when inducer concentration was between 0 and 0.5 mM. However, this dependence on the enzyme expression stopped when expression level was further increased (IPTG concentration was increased from 0.5 to 1 mM), indicating that other factors emerged as bottlenecks of the synthesis. Several likely bottlenecks and possible engineering strategies to further improve the synthesis are discussed.     

Engineering E. coli for caffeic acid biosynthesis from renewable sugars

Caffeic acid is a valuable aromatic compound that possesses many important pharmacological activities. In structure, caffeic acid belongs to the hydroxycinnamic acid family and can be biosynthesized from the aromatic amino acid tyrosine. In the present paper, the caffeic acid biosynthesis pathway was reconstituted in engineered Escherichia coli to produce caffeic acid from simple biomass sugar glucose and xylose. Different engineering approaches were utilized to optimize the production. Specifically, two parallel biosynthesis routes leading from tyrosine to caffeic acid were studied. The copy number of the intermediate biosynthesis genes was varied to find appropriate gene doses for caffeic acid biosynthesis. Three different media, including a MOPS medium, a synthetic medium, and a rich medium, were also examined to improve the production. The highest specific caffeic acid production achieved was 38 mg/L/OD. Lastly, cultivation of engineered E. coli in a bioreactor resulted in a production of 106 mg/L caffeic acid after 4 days.     

Recombinant E. coli expressing Vitreoscilla haemoglobin prefers aerobic metabolism under microaerobic conditions: A proteome-level study

Vitreoscilla haemoglobin (VHb) expression in heterologous host was shown to enhance growth and oxygen utilization capabilities under oxygen-limited conditions. The exact mechanism by which VHb enhances the oxygen utilization under oxygen-limiting conditions is still unknown. In order to understand the role of VHb in promoting oxygen utilization, changes in the total protein profile of E. coli expressing the vgb gene under its native promoter was analysed. Two-dimensional difference gel electrophoresis (2D DIGE) was employed to quantify the differentially expressed proteins under oxygen-limiting conditions. Overexpression of proteins involved in aerobic metabolic pathways and suppression of proteins involved in non-oxidative metabolic pathways shown in this study indicates that the cells expressing VHb prefer aerobic metabolic pathways even under oxygen limitation. Under these conditions, the expression levels of proteins involved in central metabolic pathways, cellular adaptation and cell division were also found to be altered. These results imply that Vitreoscilla haemoglobin expression alters aerobic metabolism specifically, in addition to altering proteins involved in other pathways, the significance of which is not clear as of now.     

Engineering of baker's yeasts, E. coli and Bacillus hosts for the production of Bacillus subtilis Lipase A

Lipases are versatile biocatalists showing multiple applications in a wide range of biotechnological processes. The gene lipA coding for Lipase A from Bacillus subtilis was isolated by PCR amplification, cloned and expressed in Escherichia coli, Saccharomyces cerevisiae and Bacillus subtilis strains, using pBR322, YEplac112 and pUB110-derived vectors, respectively. Lipase activity analysis of the recombinant strains showed that the gene can be properly expressed in all hosts assayed, this being the first time a lipase from bacterial origin can be expressed in baker's S. cerevisiae strains. An important increase of lipase production was obtained in heterologous hosts with respect to that of parental strains, indicating that the described systems can represent a useful tool to enhance productivity of the enzyme for biotechnological applications, including the use of the lipase in bread making, or as a technological additive.     

An engineered E.coli strain for the production of glycoglycerolipids

The glycolipid synthase MG517 from Mycoplasma genitalium catalyzes the glucosyl transfer from UDPGlc to diacylglycerol producing glycoglycerolipids (GGL) (Andrés et al., 2011). The enzyme was functional in E. coli accumulating GGL in the plasma membrane. A metabolic engineering strategy for GGL production was evaluated using this microorganism. To increase the levels of GGL precursors, UDPGlc and diacylglycerol, GalU and PlsC enzymes involved in their biosynthesis were overexpressed. Seven engineered strains were obtained containing different combinations of the mg517 with galU and plsC genes. Diacylglycerol synthesis showed to be limiting and the strain overexpressing MG517 and PlsC achieved the highest GGL yield. The new lipids were mono, di- and triglucosyldiacylglycerol with different acyl combinations in each compound. It indicates that the successive glucosyl transferase activities of MG517 have different acyl chain specificity for the acceptor substrate. GGL represented up to 6mg per g of dry weight.     

Biotechnological aspects of antibody production in E. coli

The production of genetically engineered antibodies in Escherichia coli is now possible. The resulting fragments are completely functional and have antigen binding constants industinguishable from the natural antibody. This article summarizes the biochemical basis of this newly developed technology and the properties of the resulting fragments. It is likely that this technology will have an important role in antibody production for technical, medical and research uses. Screening of E. coli libraries may mount a challenge to traditional antibody production methods.