Showing papers in "Biotechnology and Bioengineering in 2010"
TL;DR: It is demonstrated that biomass and lipid production by the selected mutants can be improved by physiological manipulation and the feasibility of increasing lipid production through redirecting photosynthetically assimilated carbon away from starch synthesis to neutral lipid synthesis is confirmed.
Abstract: Starch and neutral lipids are two major carbon storage compounds in many microalgae and plants. Lipids are more energy rich and have often been used as food and fuel feedstocks. Genetic engineering of the lipid biosynthesis pathway to overproduce lipid has achieved only limited success. We hypothesize that through blocking the competing pathway to produce starch, overproduction of neutral lipid may be achieved. This hypothesis was tested using the green microalga Chlamydomonas reinhardtii and its low starch and starchless mutants. We discovered that a dramatic increase in neutral lipid content and the neutral lipid/total lipid ratio occurred among the mutants under high light and nitrogen starvation. BAFJ5, one of the mutants defective in the small subunit of ADP-glucose pyrophosphorylase, accumulated neutral and total lipid of up to 32.6% and 46.4% of dry weight (DW) or 8- and 3.5-fold higher, respectively, than the wild-type. These results confirmed the feasibility of increasing lipid production through redirecting photosynthetically assimilated carbon away from starch synthesis to neutral lipid synthesis. However, some growth impairment was observed in the low starch and starchless mutants, possibly due to altered energy partitioning in PSII, with more excitation energy dissipated as heat and less to photochemical conversion. This study demonstrated that biomass and lipid production by the selected mutants can be improved by physiological manipulation. Biotechnol. Bioeng. 2010;107: 258-268. (c) 2010 Wiley Periodicals, Inc.
391 citations
TL;DR: The present study provides a practical benchmark, which allows comparison of microalgal production systems with different footprints, as well as terrestrial systems, to find the organism that had the best dry biomass and/or lipid production profile in large‐scale cultures.
Abstract: Biomass and lipid productivity, lipid content, and quantitative and qualitative lipid composition are critical parameters in selecting microalgal species for commercial scale-up production. This study compares lipid content and composition, and lipid and biomass productivity during logarithmic, late logarithmic, and stationary phase of Nannochloropsis sp., Isochrysis sp., Tetraselmis sp., and Rhodomonas sp. grown in L1-, f/2-, and K-medium. Of the tested species, Tetraselmis sp. exhibited a lipid productivity of 3.9–4.8 g m−2 day−1 in any media type, with comparable lipid productivity by Nannochloropsis sp. and Isochrysis sp. when grown in L1-medium. The dry biomass productivity of Tetraselmis sp. (33.1–45.0 g m−2 day−1) exceeded that of the other species by a factor 2–10. Of the organisms studied, Tetraselmis sp. had the best dry biomass and/or lipid production profile in large-scale cultures. The present study provides a practical benchmark, which allows comparison of microalgal production systems with different footprints, as well as terrestrial systems.
376 citations
TL;DR: In this paper, the influence of substrate mechanical stiffness on the heart cell phenotype and functional properties was investigated using 3, 22, 50, and 144-kPa polyacrylamide (PA) gel stiffness.
Abstract: Adult cardiomyocytes (CM) retain little capacity to regenerate, which motivates efforts to engineer heart tissues that can emulate the functional and mechanical properties of native myocardium. Although the effects of matrix stiffness on individual CM have been explored, less attention was devoted to studies at the monolayer and the tissue level. The purpose of this study was to characterize the influence of substrate mechanical stiffness on the heart cell phenotype and functional properties. Neonatal rat heart cells were seeded onto collagen-coated polyacrylamide (PA) substrates with Young's moduli of 3, 22, 50, and 144 kPa. Collagen-coated glass coverslips without PA represented surfaces with effectively “infinite” stiffness. The local elastic modulus of native neonatal rat heart tissue was measured to range from 4.0 to 11.4 kPa (mean value of 6.8 kPa) and for native adult rat heart tissue from 11.9 to 46.2 kPa (mean value of 25.6 kPa), motivating our choice of the above PA gel stiffness. Overall, by 120 h of cultivation, the lowest stiffness PA substrates (3 kPa) exhibited the lowest excitation threshold (ET; 3.5 ± 0.3 V/cm), increased troponin I staining (52% positively stained area) but reduced cell density, force of contraction (0.18 ± 0.1 mN/mm2), and cell elongation (aspect ratio = 1.3–1.4). Higher stiffness (144 kPa) PA substrates exhibited reduced troponin I staining (30% positively stained area), increased fibroblast density (70% positively stained area), and poor electrical excitability. Intermediate stiffness PA substrates of stiffness comparable to the native adult rat myocardium (22–50 kPa) were found to be optimal for heart cell morphology and function, with superior elongation (aspect ratio > 4.3), reasonable ET (ranging from 3.95 ± 0.8 to 4.4 ± 0.7 V/cm), high contractile force development (ranging from 0.52 ± 0.2 to 1.60 ± 0.6 mN/mm2), and well-developed striations, all consistent with a differentiated phenotype. Biotechnol. Bioeng. 2010;105: 1148–1160. © 2009 Wiley Periodicals, Inc.
349 citations
TL;DR: A massively parallel microfluidic device that passively separates pathogenic bacteria cells from diluted blood with macroscale performance is presented for the first time and it is expected that this parallelizable, robust, and label‐free approach would be useful for filtration of blood as well as for other cell separation and concentration applications from large volume samples.
Abstract: Cell separation is broadly useful for applications in clinical diagnostics, biological research, and potentially regenerative medicine. Recent attention has been paid to label-free size-based techniques that may avoid the costs or clogging issues associated with centrifugation and mechanical filtration. We present for the first time a massively parallel microfluidic device that passively separates pathogenic bacteria cells from diluted blood with macroscale performance. The device was designed to process large sample volumes in a high-throughput, continuous manner using 40 single microchannels placed in a radial array with one inlet and two rings of outlets. Each single channel consists of a short focusing, gradual expansion and collection region and uses unique differential transit times due to size-dependent inertial lift forces as a method of cell separation. The gradual channel expansion region is shown to manipulate cell equilibrium positions close to the microchannel walls, critical for higher efficiency collection. We demonstrate >80% removal of pathogenic bacteria from blood after two passes of the single channel system. The massively parallel device can process 240 mL/h with a throughput of 400 million cells/min. We expect that this parallelizable, robust, and label-free approach would be useful for filtration of blood as well as for other cell separation and concentration applications from large volume samples.
338 citations
TL;DR: It is concluded that thermal inkjet printing technology can be used for precise cell seeding with minor effects and damages to the printed mammalian cells.
Abstract: Thermal inkjet printing technology has been applied successfully to cell printing. However, there are concerns that printing process may cause cell damages or death. We conducted a comprehensive study of thermal inkjet printed Chinese hamster ovary (CHO) cells by evaluating cell viability and apoptosis, and possible cell membrane damages. Additionally, we studied the cell concentration of bio-ink and found optimum printing of concentrations around 8 million cells per mL. Printed cell viability was 89% and only 3.5% apoptotic cells were observed after printing. Transient pores were developed in the cell membrane of printed cells. Cells were able to repair these pores within 2 h after printing. Green fluorescent protein (GFP) DNA plasmids were delivered to CHO-S cells by co-printing. The transfection efficiency is above 30%. We conclude that thermal inkjet printing technology can be used for precise cell seeding with minor effects and damages to the printed mammalian cells. The printing process causes transient pores in cell membranes, a process which has promising applications for gene and macroparticles delivery to induce the biocompatibility or growth of engineered tissues.
309 citations
TL;DR: A metabolically engineered strain of Escherichia coli is reported that overproduces medium‐chain length fatty acids via three basic modifications: elimination of β‐oxidation, overexpression of the four subunits of acetyl‐CoA carboxylase, and expression of a plant acyl–acyl carrier protein (ACP) thioesterase from Umbellularia californica (BTE).
Abstract: The development of renewable alternatives to diesel and jet fuels is highly desirable for the heavy transportation sector, and would offer benefits over the production and use of short-chain alcohols for personal transportation. Here, we report the development of a metabolically engineered strain of Escherichia coli that overproduces medium-chain length fatty acids via three basic modifications: elimination of beta-oxidation, overexpression of the four subunits of acetyl-CoA carboxylase, and expression of a plant acyl-acyl carrier protein (ACP) thioesterase from Umbellularia californica (BTE). The expression level of BTE was optimized by comparing fatty acid production from strains harboring BTE on plasmids with four different copy numbers. Expression of BTE from low copy number plasmids resulted in the highest fatty acid production. Up to a seven-fold increase in total fatty acid production was observed in engineered strains over a negative control strain (lacking beta-oxidation), with a composition dominated by C(12) and C(14) saturated and unsaturated fatty acids. Next, a strategy for producing undecane via a combination of biotechnology and heterogeneous catalysis is demonstrated. Fatty acids were extracted from a culture of an overproducing strain into an alkane phase and fed to a Pd/C plug flow reactor, where the extracted fatty acids were decarboxylated into saturated alkanes. The result is an enriched alkane stream that can be recycled for continuous extractions. Complete conversion of C(12) fatty acids extracted from culture to alkanes has been demonstrated yielding a concentration of 0.44 g L(-1) (culture volume) undecane.
280 citations
TL;DR: The strategy of combined metabolic engineering and enzyme engineering allowed efficient bio‐based one‐step production of PLA and its copolymers, and should be generally useful for developing other engineered organisms capable of producing various unnatural polymers by direct fermentation from renewable resources.
Abstract: Polylactic acid (PLA) is a promising biomass-derived polymer, but is currently synthesized by a two-step process: fermentative production of lactic acid followed by chemical polymerization. Here we report production of PLA homopolymer and its copolymer, poly(3-hydroxybutyrate-co-lactate), P(3HB-co-LA), by direct fermentation of metabolically engineered Escherichia coli. As shown in an accompanying paper, introduction of the heterologous metabolic pathways involving engineered propionate CoA-transferase and polyhydroxyalkanoate (PHA) synthase for the efficient generation of lactyl-CoA and incorporation of lactyl-CoA into the polymer, respectively, allowed synthesis of PLA and P(3HB-co-LA) in E. coli, but at relatively low efficiency. In this study, the metabolic pathways of E. coli were further engineered by knocking out the ackA, ppc, and adhE genes and by replacing the promoters of the ldhA and acs genes with the trc promoter based on in silico genome-scale metabolic flux analysis in addition to rational approach. Using this engineered strain, PLA homopolymer could be produced up to 11 wt% from glucose. Also, P(3HB-co-LA) copolymers containing 55-86 mol% lactate could be produced up to 56 wt% from glucose and 3HB. P(3HB-co-LA) copolymers containing up to 70 mol% lactate could be produced to 46 wt% from glucose alone by introducing the Cupriavidus necator beta-ketothiolase and acetoacetyl-CoA reductase genes. Thus, the strategy of combined metabolic engineering and enzyme engineering allowed efficient bio-based one-step production of PLA and its copolymers. This strategy should be generally useful for developing other engineered organisms capable of producing various unnatural polymers by direct fermentation from renewable resources.
272 citations
TL;DR: Using poly(ethylene glycol) diacrylate hydrogels with varying polymer chain length and photolithographic patterning techniques, this work is able to provide substrates with spatially patterned, tunable mechanical properties in both gradients and distinct patterns.
Abstract: The ability of cells to migrate in response to mechanical gradients (durotaxis) and differential cell behavior in adhesion, spreading, and proliferation in response to substrate rigidity are key factors both in tissue engineering, in which materials must be selected to provide the appropriate mechanical signals, and in studies of mechanisms of diseases such as cancer and atherosclerosis, in which changes in tissue stiffness may inform cell behavior. Using poly(ethylene glycol) diacrylate hydrogels with varying polymer chain length and photolithographic patterning techniques, we are able to provide substrates with spatially patterned, tunable mechanical properties in both gradients and distinct patterns. The hydrogels can be patterned to produce anisotropic structures and exhibit patterned strain under mechanical loading. These hydrogels may be used to study cell response to substrate rigidity in both two and three dimensions and can also be used as a scaffold in tissue-engineering applications.
267 citations
TL;DR: The on‐demand capability to print fluidic channel structures and cells in a 3D hydrogel scaffold offers flexibility in generating perfusable 3D artificial tissue composites.
Abstract: One of the challenges in tissue engineering is to provide adequate supplies of oxygen and nutrients to cells within the engineered tissue construct. Soft-lithographic techniques have allowed the generation of hydrogel scaffolds containing a network of fluidic channels, but at the cost of complicated and often time-consuming manufacturing steps. We report a three-dimensional (3D) direct printing technique to construct hydrogel scaffolds containing fluidic channels. Cells can also be printed on to and embedded in the scaffold with this technique. Collagen hydrogel precursor was printed and subsequently crosslinked via nebulized sodium bicarbonate solution. A heated gelatin solution, which served as a sacrificial element for the fluidic channels, was printed between the collagen layers. The process was repeated layer-by-layer to form a 3D hydrogel block. The printed hydrogel block was heated to 37 degrees C, which allowed the gelatin to be selectively liquefied and drained, generating a hollow channel within the collagen scaffold. The dermal fibroblasts grown in a scaffold containing fluidic channels showed significantly elevated cell viability compared to the ones without any channels. The on-demand capability to print fluidic channel structures and cells in a 3D hydrogel scaffold offers flexibility in generating perfusable 3D artificial tissue composites.
262 citations
TL;DR: The Hydrolysis yields of the pretreated lignocellulose and those of Avicel containing the PTL showed good correlation, indicating that the nature of the residual lignin obtained after pretreatment significantly influenced hydrolysis.
Abstract: The influence of the residual lignin remaining in the cellulosic rich component of pretreated lignocellulosic substrates on subsequent enzymatic hydrolysis was assessed. Twelve lignin preparations were isolated by two isolation methods (protease treated lignin (PTL) and cellulolytic enzymatic lignin (CEL)) from three types of biomass (corn stover, poplar, and lodgepole pine) that had been pretreated by two processes (steam and organosolv pretreatments). Comparative analysis of the isolated lignin showed that the CEL contained lower amounts of carbohydrates and protein than did the PTL and that the isolated lignin from corn stover contained more carbohydrates than did the lignin derived from the poplar and lodgepole pine. The lower yields of acid insoluble lignin (AIL) obtained from the corn stover when using the PTL method indicated that the lignin from the corn stover had a higher hydrophilicity than did the lignin from the poplar and lodgepole pine. The isolated lignin preparations were added to the reaction mixture containing crystalline cellulose (Avicel) and their possible effects on enzymatic hydrolysis were assessed. It was apparent that the lignin isolated from lodgepole pine and steam pretreated poplar decreased the hydrolysis yields of Avicel, whereas the other isolated lignins did not appear to decrease the hydrolysis yields significantly. The hydrolysis yields of the pretreated lignocellulose and those of Avicel containing the PTL showed good correlation, indicating that the nature of the residual lignin obtained after pretreatment significantly influenced hydrolysis.
253 citations
TL;DR: The results indicate that cellular β‐carotene accumulation in D. salina correlates with accumulation of specific fatty acid species (C16:0 and C18:1) rather than with total fatty acid content.
Abstract: beta-Carotene is overproduced in the alga Dunaliella salina in response to high light intensities. We have studied the effects of a sudden light increase on carotenoid and fatty acid metabolism using a flat panel photobioreactor that was run in turbidostat mode to ensure a constant light regime throughout the experiments. Upon the shift to an increased light intensity, beta-carotene production commenced immediately. The first 4 h after induction were marked by constant intracellular levels of beta-carotene (2.2 g LCV(-1)), which resulted from identical increases in the production rates of cell volume and beta-carotene. Following this initial phase, beta-carotene productivity continued to increase while the cell volume productivity dropped. As a result, the intracellular beta-carotene concentration increased reaching a maximum of 17 g LCV(-1) after 2 days of light stress. Approximately 1 day before that, the maximum beta-carotene productivity of 30 pg cell(-1) day(-1) (equivalent to 37 mg LRV(-1) day(-1)) was obtained, which was about one order of magnitude larger than the average productivity reported for a commercial beta-carotene production facility, indicating a vast potential for improvement. Furthermore, by studying the light-induced changes in both beta-carotene and fatty acid metabolism, it appeared that carotenoid overproduction was associated with oil globule formation and a decrease in the degree of fatty acid unsaturation. Our results indicate that cellular beta-carotene accumulation in D. salina correlates with accumulation of specific fatty acid species (C16:0 and C18:1) rather than with total fatty acid content.
TL;DR: It is argued that the list of upregulated genes in response to the three metabolite stresses includes several genes whose overexpression would likely impart tolerance, thus making the information generated in this study, a valuable source for the development of tolerant recombinant strains.
Abstract: Metabolite accumulation has pleiotropic, toxic, or beneficial effects on cell physiology, but such effects are not well understood at the molecular level. Cells respond and adapt to metabolite stress by mechanisms largely unexplored, especially in the context of multiple and simultaneous stresses. Solventogenic and related clostridia have an inherent advantage for production of biofuels and chemicals directly from cellulosic material and other complex carbohydrates, but issues of product/metabolite tolerance and related culture productivities remain. Using DNA microarray-based gene expression analysis, the transcriptional-stress responses of Clostridium acetobutylicum to fermentation acids acetate and butyrate and the solvent product butanol were analyzed and compared in the context of cell physiology. Ontological analysis demonstrated that stress by all three metabolites resulted in upregulation of genes related to post-translational modifications and chaperone activity, and downregulation of the translation-machinery genes. Motility genes were downregulated by acetate-stress only. The general metabolite stress included upregulation of numerous stress genes (dnaK, groES, groEL, hsp90, hsp18, clpC, and htrA), the solventogenic operon aad-ctfA-ctfB, and other solventogenic genes. Acetate stress downregulated expression of the butyryl-CoA- and butyrate-formation genes, while butyrate stress downregulated expression of acetate-formation genes. Pyrimidine-biosynthesis genes were downregulated by most stresses, but purine-biosynthesis genes were upregulated by acetate and butyrate, possibly for thiamine and histidine biosynthesis. Methionine-biosynthesis genes were upregulated by acetate stress, indicating a possibly conserved stress response mechanism also observed in Escherichia coli. Nitrogen-fixation gene expression was upregulated by acetate stress. Butyrate stress upregulated many iron-metabolism genes, riboflavin-biosynthesis genes, and several genes related to cellular repair from oxidative stress, such as perR and superoxide dismutases. Butanol stress upregulated the glycerol metabolism genes glpA and glpF. Surprisingly, metabolite stress had no apparent effect on the expression of the sporulation-cascade genes. It is argued that the list of upregulated genes in response to the three metabolite stresses includes several genes whose overexpression would likely impart tolerance, thus making the information generated in this study, a valuable source for the development of tolerant recombinant strains.
TL;DR: This two part series addresses PAT as it applies to processes that produce biotech therapeutic products and addresses evolution of the underlying concepts and applications in biopharmaceutical manufacturing.
Abstract: Implementing real-time product quality control meets one or both of the key goals outlined in FDA's PAT guidance: "variability is managed by the process" and "product quality attributes can be accurately and reliably predicted over the design space established for materials used, process parameters, manufacturing, environmental, and other conditions." The first part of the paper presented an overview of PAT concepts and applications in the areas of upstream and downstream processing. In this second part, we present principles and case studies to illustrate implementation of PAT for drug product manufacturing, rapid microbiology, and chemometrics. We further present our thoughts on how PAT will be applied to biotech processes going forward. The role of PAT as an enabling component of the Quality by Design framework is highlighted. Integration of PAT with the principles stated in the ICH Q8, Q9, and Q10 guidance documents is also discussed.
TL;DR: Formation and accumulation of monitored compounds in hydrolysates is demonstrated to be a function of both the feedstock and pretreatment conditions utilized, which are representative of leading pretreatment processes.
Abstract: A variety of potentially inhibitory degradation products are produced during pretreatment of lignocellulosic biomass. Qualitative and quantitative interrogation of pretreatment hydrolysates is paramount to identifying potential correlations between pretreatment chemistries and microbial inhibition in downstream bioconversion processes. In the present study, corn stover, poplar, and pine feedstocks were pretreated under eight different chemical conditions, which are representative of leading pretreatment processes. Pretreatment processes included: 0.7% H(2)SO(4), 0.07% H(2)SO(4), liquid hot water, neutral buffer solution, aqueous ammonia, lime, lime with oxygen pressurization, and wet oxidation. Forty lignocellulosic degradation products resulting from pretreatment were analyzed using high performance liquid chromatography in combination with UV spectroscopy or tandem mass spectrometry detection (HPLC-PDA-MS/MS) and ion chromatography (IC). Of these compounds, several have been reported to be inhibitory, including furfural, hydroxymethyl furfural, ferulic acid, 3,4-dihydroxybenzaldehyde, syringic acid among others. Formation and accumulation of monitored compounds in hydrolysates is demonstrated to be a function of both the feedstock and pretreatment conditions utilized.
TL;DR: The single‐vector replicon system provides high‐yield production capacity for hetero‐oligomeric proteins, yet eliminates the difficult task of identifying non‐competing virus and the need for co‐infection of multiple expression modules.
Abstract: Plant viral vectors have great potential in rapid production of important pharmaceutical proteins. However, high-yield production of hetero-oligomeric proteins that require the expression and assembly of two or more protein subunits often suffers problems due to the ''competing'' nature of viral vectors derived from the same virus. Pre- viously we reported that a bean yellow dwarf virus (BeYDV)- derived, three-component DNA replicon system allows rapid production of single recombinant proteins in plants (Huang et al., 2009. Biotechnol Bioeng 103: 706-714). In this article, we report further development of this expression system for its application in high-yield production of oli- gomeric protein complexes including monoclonal antibo- dies (mAbs) in plants. We showed that the BeYDV replicon system permits simultaneous efficient replication of two DNA replicons and thus, high-level accumulation of two recombinant proteins in the same plant cell. We also demonstrated that a single vector that contains multiple replicon cassettes was as efficient as the three-component system in driving the expression of two distinct proteins. Using either the non-competing, three-vector system or the multi-replicon single vector, we produced both the heavy and light chain subunits of a protective IgG mAb 6D8 against Ebola virus GP1 (Wilson et al., 2000. Science 287: 1664-1666) at 0.5 mg of mAb per gram leaf fresh weight within 4 days post-infiltration of Nicotiana benthamiana leaves. We further demonstrated that full-size tetrameric IgG complex containing two heavy and two light chains was efficiently assembled and readily purified, and retained its functionality in specific binding to inactivated Ebola virus. Thus, our single-vector replicon system provides high-yield production capacity for hetero-oligomeric proteins, yet eliminates the difficult task of identifying non-competing virus and the need for co-infection of multiple expression modules. The multi-replicon vector represents a significant advance in transient expression technology for antibody production in plants. Biotechnol. Bioeng. 2010;106: 9-17. 2009 Wiley Periodicals, Inc.
TL;DR: It is demonstrated that AFEX pretreatment is a viable process for conversion of bagasse and cane leaf residue into cellulosic ethanol and sugar produced by this process is found to be highly fermentable.
Abstract: Sugarcane is one of the major agricultural crops cultivated in tropical climate regions of the world. Each tonne of raw cane production is associated with the generation of 130 kg dry weight of bagasse after juice extraction and 250 kg dry weight of cane leaf residue postharvest. The annual world production of sugarcane is approximately 1.6 billion tones, generating 279 MMT tones of biomass residues (bagasse and cane leaf matter) that would be available for cellulosic ethanol production. Here, we investigated the production of cellulosic ethanol from sugar cane bagasse and sugar cane leaf residue using an alkaline pretreatment: ammonia fiber expansion (AFEX). The AFEX pretreatment improved the accessibility of cellulose and hemicelluloses to enzymes during hydrolysis by breaking down the ester linkages and other lignin carbohydrate complex (LCC) bonds and the sugar produced by this process is found to be highly fermentable. The maximum glucan conversion of AFEX pretreated bagasse and cane leaf residue by cellulases was approximately 85%. Supplementation with hemicellulases during enzymatic hydrolysis improved the xylan conversion up to 95-98%. Xylanase supplementation also contributed to a marginal improvement in the glucan conversion. AFEX-treated cane leaf residue was found to have a greater enzymatic digestibility compared to AFEX-treated bagasse. Co-fermentation of glucose and xylose, produced from high solid loading (6% glucan) hydrolysis of AFEX-treated bagasse and cane leaf residue, using the recombinant Saccharomyces cerevisiae (424A LNH-ST) produced 34-36 g/L of ethanol with 92% theoretical yield. These results demonstrate that AFEX pretreatment is a viable process for conversion of bagasse and cane leaf residue into cellulosic ethanol.
TL;DR: For the synthesis of polylactic acid (PLA) and its copolymers by one‐step fermentation process, heterologous pathways involving Clostridium propionicum propionate CoA transferase (PctCp), MBEL 6‐19 polyhydroxyalkanoate (PHA) synthase 1 (PhaC1Ps6‐19) were introduced into Escherichia coli for the generation of lactyl‐CoA endogenously and incorporation of
Abstract: For the synthesis of polylactic acid (PLA) and its copolymers by one-step fermentation process, heterologous pathways involving Clostridium propionicum propionate CoA transferase (Pct(Cp)) and Pseudomonas sp. MBEL 6-19 polyhydroxyalkanoate (PHA) synthase 1 (PhaC1(Ps6-19)) were introduced into Escherichia coli for the generation of lactyl-CoA endogenously and incorporation of lactyl-CoA into the polymer, respectively. Since the wild-type PhaC1(Ps6-19) did not efficiently accept lactyl-CoA as a substrate, site directed mutagenesis as well as saturation mutagenesis were performed to improve the enzyme. The wild-type Pct(Cp) was not able to efficiently convert lactate to lactyl-CoA and was found to exert inhibitory effect on cell growth, random mutagenesis by error-prone PCR was carried out. By employing engineered PhaC1(Ps6-19) and Pct(Cp), poly(3-hydroxybutyrate-co-lactate), P(3HB-co-LA), containing 20-49 mol% lactate could be produced up to 62 wt% from glucose and 3HB. By controlling the 3HB concentration in the medium, PLA homopolymer and P(3HB-co-LA) containing lactate as a major monomer unit could be synthesized. Also, P(3HB-co-LA) copolymers containing various lactate fractions could be produced from glucose alone by introducing the Cupriavidus necator beta-ketothiolase and acetoacetyl-CoA reductase genes. Fed-batch cultures were performed to produce P(3HB-co-LA) copolymers having 9-64 mol% of lactate, and their molecular weights, thermal properties, and melt flow properties were determined.
TL;DR: Four pathways emerged from this ranking as the most promising for the biosynthesis of 3HP, and three of these pathways, including the shortest pathways discovered, were novel.
Abstract: Sustainable microbial production of high-value organic compounds such as 3-hydroxypropanoate (3HP) is becoming an increasingly attractive alternative to organic syntheses that utilize petrochemical feedstocks. We applied the Biochemical Network Integrated Computational Explorer (BNICE) framework to the automated design and evaluation of novel biosynthetic routes for the production of 3HP from pyruvate. Among the pathways generated by the BNICE framework were all of the known pathways for the production of 3HP as well as numerous novel pathways. The pathways generated by BNICE were ranked based on four criteria: pathway length, thermodynamic feasibility, maximum achievable yield to 3HP from glucose, and maximum achievable activity at which 3HP can be produced. Four pathways emerged from this ranking as the most promising for the biosynthesis of 3HP, and three of these pathways, including the shortest pathways discovered, were novel. We also discovered novel routes for the biosynthesis of 28 commercially available compounds that are currently produced exclusively through organic synthesis. Examination of the optimal pathways for the biosynthesis of these 28 compounds in E. coli revealed pyruvate and succinate to be ideal intermediates for achieving high product yields from glucose.
TL;DR: The economical analyses clearly suggest that developments in stable enzymes or their complexes as standardized parts, efficient coen enzyme recycling, and use of low-cost and more stable biomimetic coenzyme analogs, would result in much lower production costs than do microbial fermentations.
Abstract: Cell-free synthetic (enzymatic) pathway bio- transformation (SyPaB) is the assembly of a number of purified enzymes (usually more than 10) and coenzymes for the production of desired products through complicated biochemical reaction networks that a single enzyme cannot do. Cell-free SyPaB, as compared to microbial fermentation, has several distinctive advantages, such as high product yield, great engineering flexibility, high product titer, and fast reaction rate. Biocommodities (e.g., ethanol, hydrogen, and butanol) are low-value products where costs of feed- stock carbohydrates often account for � 30-70% of the prices of the products. Therefore, yield of biocommodities is the most important cost factor, and the lowest yields of profitable biofuels are estimated to be ca. 70% of the theoretical yields of sugar-to-biofuels based on sugar prices of ca. US$ 0.18 per kg. The opinion that SyPaB is too costly for producing low-value biocommodities are mainly attrib- uted to the lack of stable standardized building blocks (e.g., enzymes or their complexes), costly labile coenzymes, and replenishment of enzymes and coenzymes. In this perspec- tive, I propose design principles for SyPaB, present several SyPaB examples for generating hydrogen, alcohols, and electricity, and analyze the advantages and limitations of SyPaB. The economical analyses clearly suggest that devel- opments in stable enzymes or their complexes as standar- dized parts, efficient coenzyme recycling, and use oflow-cost and more stable biomimetic coenzyme analogs, would result in much lower production costs than do microbial fermen- tations because the stabilized enzymes have more than 3 orders of magnitude higher weight-based total turn-over numbers than microbial biocatalysts, although extra costs for enzyme purification and stabilization are spent. Biotechnol. Bioeng. 2010;105: 663-677.
TL;DR: ZFNs are created that cleave the FUT8 gene in a region encoding the catalytic core of the enzyme, allowing the functional disruption of F UT8 in any CHO cell line and will speed the production of highly active, completely nonfucosylated therapeutic antibodies.
Abstract: IgG1 antibodies produced in Chinese hamster ovary (CHO) cells are heavily alpha1,6-fucosylated, a modification that reduces antibody-dependent cellular cytotoxicity (ADCC) and can inhibit therapeutic antibody function in vivo. Addition of fucose is catalyzed by Fut8, a alpha1,6-fucosyltransferase. FUT8(-/-) CHO cell lines produce completely nonfucosylated antibodies, but the difficulty of recapitulating the knockout in protein-production cell lines has prevented the widespread adoption of FUT8(-/-) cells as hosts for antibody production. We have created zinc-finger nucleases (ZFNs) that cleave the FUT8 gene in a region encoding the catalytic core of the enzyme, allowing the functional disruption of FUT8 in any CHO cell line. These reagents produce FUT8(-/-) CHO cells in 3 weeks at a frequency of 5% in the absence of any selection. Alternately, populations of ZFN-treated cells can be directly selected to give FUT8(-/-) cell pools in as few as 3 days. To demonstrate the utility of this method in bioprocess, FUT8 was disrupted in a CHO cell line used for stable protein production. ZFN-derived FUT8(-/-) cell lines were as transfectable as wild-type, had similar or better growth profiles, and produced equivalent amounts of antibody during transient transfection. Antibodies made in these lines completely lacked core fucosylation but had an otherwise normal glycosylation pattern. Cell lines stably expressing a model antibody were made from wild-type and ZFN-generated FUT8(-/-) cells. Clones from both lines had equivalent titer, specific productivity distributions, and integrated viable cell counts. Antibody titer in the best ZFN-generated FUT8(-/-) cell lines was fourfold higher than in the best-producing clones of FUT8(-/-) cells made by standard homologous recombination in a different CHO subtype. These data demonstrate the straightforward, ZFN-mediated transfer of the Fut8- phenotype to a production CHO cell line without adverse phenotypic effects. This process will speed the production of highly active, completely nonfucosylated therapeutic antibodies.
TL;DR: Differences between power densities produced by pure and mixed cultures depend on the MFC architecture, with mixed cultures producing more power than MR‐1 MFCs even though their redox potential was less negative.
Abstract: Power densities and oxidation-reduction potentials (ORPs) of MFCs containing a pure culture of Shewanella oneidensis MR-1 were compared to mixed cultures (wastewater inoculum) in cube shaped, 1-, 2-, and 3-bottle batch-fed MFC reactor configurations. The reactor architecture influenced the relative power produced by the different inocula, with the mixed culture generating 68-480% more power than MR-1 in each MFC configuration. The mixed culture produced the maximum power density of 858 +/- 9 mW m(-2) in the cubic MFC, while MR-1 produced 148 +/- 20 mW m(-2). The higher power by the mixed culture was primarily a result of lower internal resistances than those produced by the pure culture. Power was a direct function of ohmic resistance for the mixed culture, but not for strain MR-1. ORP of the anode compartment varied with reactor configuration and inoculum, and it was always negative during maximum power production but it did not vary in proportion to power output. The ORP varied primarily at the end of the cycle when substrate was depleted, with a change from a reductive environment during maximum power production (approximately -175 mV for mixed and approximately -210 mV for MR-1 in cubic MFCs), to an oxidative environment at the end of the batch cycle ( approximately 250 mV for mixed and approximately 300 mV for MR-1). Mixed cultures produced more power than MR-1 MFCs even though their redox potential was less negative. These results demonstrate that differences between power densities produced by pure and mixed cultures depend on the MFC architecture.
TL;DR: The history of x-ome technologies such as transcriptome, proteome, metabolome, and fluxome analysis, and advanced mathematical modeling tools such as genome-scale metabolic modeling are reviewed and how they find application in industrial biotechnology is reviewed.
Abstract: The chemical industry is currently undergoing a dramatic change driven by demand for developing more sustainable processes for the production of fuels, chemicals, and materials. In biotechnological processes different microorganisms can be exploited, and the large diversity of metabolic reactions represents a rich repository for the design of chemical conversion processes that lead to efficient production of desirable products. However, often microorganisms that produce a desirable product, either naturally or because they have been engineered through insertion of heterologous pathways, have low yields and productivities, and in order to establish an economically viable process it is necessary to improve the performance of the microorganism. Here metabolic engineering is the enabling technology. Through metabolic engineering the metabolic landscape of the microorganism is engineered such that there is an efficient conversion of the raw material, typically glucose, to the product of interest. This process may involve both insertion of new enzymes activities, deletion of existing enzyme activities, but often also deregulation of existing regulatory structures operating in the cell. In order to rapidly identify the optimal metabolic engineering strategy the industry is to an increasing extent looking into the use of tools from systems biology. This involves both x-ome technologies such as transcriptome, proteome, metabolome, and fluxome analysis, and advanced mathematical modeling tools such as genome-scale metabolic modeling. Here we look into the history of these different techniques and review how they find application in industrial biotechnology, which will lead to what we here define as industrial systems biology.
TL;DR: It is demonstrated here the complete and permanent elimination of both the Bak and Bax proteins in combination in Chinese hamster ovary (CHO) cells using zinc‐finger nuclease‐mediated gene disruption.
Abstract: Anoxic and metabolic stresses in large-scale cell culture during biopharmaceutical production can induce apoptosis. Strategies designed to ameliorate the problem of apoptosis in cell culture have focused on mRNA knockdown of pro-apoptotic proteins and over-expression of anti-apoptotic ones. Apoptosis in cell culture involves mitochondrial permeabilization by the pro-apoptotic Bak and Bax proteins; activity of either protein is sufficient to permit apoptosis. We demonstrate here the complete and permanent elimination of both the Bak and Bax proteins in combination in Chinese hamster ovary (CHO) cells using zinc-finger nuclease-mediated gene disruption. Zinc-finger nuclease cleavage of BAX and BAK followed by inaccurate DNA repair resulted in knockout of both genes. Cells lacking Bax and Bak grow normally but fail to activate caspases in response to apoptotic stimuli. When grown using scale-down systems under conditions that mimic growth in large-scale bioreactors they are significantly more resistant to apoptosis induced by starvation, staurosporine, and sodium butyrate. When grown under starvation conditions, BAX- and BAK-deleted cells produce two- to fivefold more IgG than wild-type CHO cells. Under normal growth conditions in suspension culture in shake flasks, double-knockout cultures achieve equal or higher cell densities than unmodified wild-type cultures and reach viable cell densities relevant for large-scale industrial protein production.
TL;DR: Uridine feeding increased the levels of uridine‐ and cytidine‐activated nucleotide sugars simultaneously, which could imply that uridine is one of the limiting substrates for nucleotide sugar synthesis in the study.
Abstract: Controlling glycosylation of recombinant proteins produced by CHO cells is highly desired as it can be directed towards maintaining or increasing product quality. To further our understanding of the different factors influencing glycosylation, a glycosylation sub-array of 79 genes and a capillary electrophoresis method which simultaneously analyzes 12 nucleotides and 7 nucleotide sugars; were used to generate intracellular N-glycosylation profiles. Specifically, the effects of nucleotide sugar precursor feeding on intracellular glycosylation activities were analyzed in CHO cells producing recombinant human interferon-gamma (IFN-gamma). Galactose (+/-uridine), glucosamine (+/-uridine), and N-acetylmannosamine (ManNAc) (+/-cytidine) feeding resulted in 12%, 28%, and 32% increase in IFN-gamma sialylation as compared to the untreated control cultures. This could be directly attributed to increases in nucleotide sugar substrates, UDP-Hex ( approximately 20-fold), UDP-HexNAc (6- to 15-fold) and CMP-sialic acid (30- to 120-fold), respectively. Up-regulation of B4gal and St3gal could also have enhanced glycan addition onto the proteins, leading to more complete glycosylation (sialylation). Combined feeding of glucosamine + uridine and ManNAc + cytidine increased UDP-HexNAc and CMP-sialic acid by another two- to fourfold as compared to feeding sugar precursors alone. However, it did not lead to a synergistic increase in IFN-gamma sialylation. Other factors such as glycosyltransferase or glycan substrate levels could have become limiting. In addition, uridine feeding increased the levels of uridine- and cytidine-activated nucleotide sugars simultaneously, which could imply that uridine is one of the limiting substrates for nucleotide sugar synthesis in the study. Hence, the characterization of intracellular glycosylation activities has increased our understanding of how nucleotide sugar precursor feeding influence glycosylation of recombinant proteins produced in CHO cells. It has also led to the optimization of more effective strategies for manipulating glycan quality.
TL;DR: Image analysis of morphological development of A. niger during the cultivation process showed that the microparticles influence the morphology by collision‐induced disruption of conidia aggregates and probably also the hindrance of new spore–spore interactions in the very early stage of the process.
Abstract: Supplementation with silicate microparticles was used as novel approach to control the morphological development of Aspergillus niger, important as the major world source of citric acid and higher-value enzymes, in submerged culture. With careful variation of size and concentration of the micromaterial added, a number of distinct morphological forms including pellets of different size, free dispersed mycelium, and short hyphae fragments could be reproducibly created. Aluminum oxide particles similarly affected morphology, showing that this effect is largely independent of the chemical particle composition. Image analysis of morphological development of A. niger during the cultivation process showed that the microparticles influence the morphology by collision-induced disruption of conidia aggregates and probably also the hindrance of new spore-spore interactions in the very early stage of the process. Exemplified for different recombinant A. niger strains enzyme production could be strongly enhanced by the addition of microparticles. Linked to the formation of freely dispersed mycelium, titers for glucoamylase (GA) expressed as intracellular enzyme (88 U/mL) and fructofuranosidase secreted into the supernatant (77 U/mL), were up to fourfold higher in shake flasks. Moreover, accumulation of the undesired by-product oxalate was suppressed by up to 90%. The microparticle strategy could be successfully transferred to fructofuranosidase production in bioreactor, where a final titer of 160 U/mL could be reached. Using co-expression of GA with green fluorescent protein, enzyme production was localized in the cellular aggregates of A. niger. For pelleted growth, protein production was maximal only within a thin layer at the pellet surface and markedly decreased in the pellet interior, whereas the interaction with the microparticles created a highly active biocatalyst with the dominant fraction of cells contributing to production.
TL;DR: The community structure in the biofilm anode and suspension reflected the electron‐flow distribution and H2‐scavenging mechanism, and the presence of the homo‐acetogenic genus, Acetobacterium, was established.
Abstract: We compared the microbial community structures that developed in the biofilm anode of two microbial electrolysis cells fed with ethanol, a fermentable substrate-one where methanogenesis was allowed and another in which it was completely inhibited with 2-bromoethane sulfonate. We observed a three-way syntrophy among ethanol fermenters, acetate-oxidizing anode-respiring bacteria (ARB), and a H2 scavenger. When methanogenesis was allowed, H2-oxidizing methanogens were the H2 scavengers, but when methanogenesis was inhibited, homo-acetogens became a channel for electron flow from H2 to current through acetate. We established the presence of homo-acetogens by two independent molecular techniques: 16S rRNA gene based pyrosequencing and a clone library from a highly conserved region in the functional gene encoding formyltetrahydrofolate synthetase in homo-acetogens. Both methods documented the presence of the homo-acetogenic genus, Acetobacterium, only with methanogenic inhibition. Pyrosequencing also showed a predominance of ethanol-fermenting bacteria, primarily represented by the genus Pelobacter. The next most abundant group was a diverse community of ARB, and they were followed by H(2)-scavenging syntrophic partners that were either H2-oxidizing methanogens or homo-acetogens when methanogenesis was suppressed. Thus, the community structure in the biofilm anode and suspension reflected the electron-flow distribution and H2-scavenging mechanism.
TL;DR: The model was sensitive to cellulase‐accessible surface area; the EG2–CBHI synergy observed experimentally was only predicted at a sufficiently high cellulose surface area, and model predictions indicated that the observed decrease in hydrolysis rates following the initial rate of rapid Hydrolysis is not solely caused by product inhibition and/or thermal deactivation.
Abstract: A detailed mechanistic model of enzymatic cellulose hydrolysis has been developed. The behavior of individual cellulase enzymes and parameters describing the cellulose surface properties are included. Results obtained for individual enzymes (T. reesei endoglucanase 2 and cellobiohydrolase I) and systems with both enzymes present are compared with experimental literature data. The model was sensitive to cellulase-accessible surface area; the EG2-CBHI synergy observed experimentally was only predicted at a sufficiently high cellulose surface area. Enzyme crowding, which is more apparent at low surface areas, resulted in differences between predicted and experimental rates of hydrolysis. Model predictions also indicated that the observed decrease in hydrolysis rates following the initial rate of rapid hydrolysis is not solely caused by product inhibition and/or thermal deactivation. Surface heterogeneities, which are not accounted for in this work, may play a role in decreasing the hydrolysis rate. The importance of separating the enzyme adsorption and complexation steps is illustrated by the model's sensitivity to the rate of formation of enzyme-substrate complexes on the cellulose surface.
TL;DR: Gap‐filling methods can be used to improve metabolic network models while simultaneously leading to discovery of new metabolic gene functions, as well as predict these missing reactions or genes likely to fill these knowledge gaps.
Abstract: Genome-scale metabolic network reconstructions are built from all of the known metabolic reactions and genes in a target organism. However, since our knowledge of any organism is incomplete, these network reconstructions contain gaps. Reactions may be missing, resulting in dead-ends in pathways, while unknown gene products may catalyze known reactions. New computational methods that analyze data, such as growth phenotypes or gene essentiality, in the context of genome-scale metabolic networks, have been developed to predict these missing reactions or genes likely to fill these knowledge gaps. A growing number of experimental studies are appearing that address these computational predictions, leading to discovery of new metabolic capabilities in the target organism. Gap-filling methods can thus be used to improve metabolic network models while simultaneously leading to discovery of new metabolic gene functions.
TL;DR: Evaluating the impact of three factors, organic carbon limitation, nitrite concentrations, and dissolved oxygen concentrations on gaseous N2O and NO emissions from two sequencing batch reactors (SBRs), operated with methanol and ethanol as electron donors, suggests that for dissolved oxygen, but not for carbon limitation or nitrite exposure, N 2O emission from heterotrophic denitrification reactors can vary as a function of the electron donor used.
Abstract: The emissions of nitrous oxide (N(2)O) and nitric oxide (NO) from biological nitrogen removal (BNR) operations via nitrification and denitrification is gaining increased prominence. While many factors relevant to the operation of denitrifying reactors can influence N(2)O and NO emissions from them, the role of different organic carbon sources on these emissions has not been systematically addressed or interpreted. The overall goal of this study was to evaluate the impact of three factors, organic carbon limitation, nitrite concentrations, and dissolved oxygen concentrations on gaseous N(2)O and NO emissions from two sequencing batch reactors (SBRs), operated, respectively, with methanol and ethanol as electron donors. During undisturbed ultimate-state operation, emissions of both N(2)O and NO from either reactor were minimal and in the range of <0.2% of influent nitrate-N load. Subsequently, the two reactors were challenged with transient organic carbon limitation and nitrite pulses, both of which had little impact on N(2)O or NO emissions for either electron donor. In contrast, transient exposure to oxygen led to increased production of N(2)O (up to 7.1% of influent nitrate-N load) from ethanol grown cultures, owing to their higher kinetics and potentially lower susceptibility to oxygen inhibition. A similar increase in N(2)O production was not observed from methanol grown cultures. These results suggest that for dissolved oxygen, but not for carbon limitation or nitrite exposure, N(2)O emission from heterotrophic denitrification reactors can vary as a function of the electron donor used.
TL;DR: The use of a comparative proteomic profiling method viz. two‐dimensional difference gel electrophoresis (2D‐DIGE) to examine HCP composition in the harvest stream of CHO cell culture confirmed the suitability of using the null cell culture for immunoassay reagent generation.
Abstract: Host cell proteins (HCPs) constitute a major group of impurities for biologic drugs produced using cell culture technology. HCPs are required to be closely monitored and adequately removed in the downstream process. However, HCPs are a complex mixture of proteins with significantly diverse molecular and immunological properties. An overall understanding of the composition of HCPs and changes in their molecular properties upon changes in upstream and harvest process conditions can greatly facilitate downstream process design. This article describes the use of a comparative proteomic profiling method viz. two-dimensional difference gel electrophoresis (2D-DIGE) to examine HCP composition in the harvest stream of CHO cell culture. The effect of upstream process parameters such as cell culture media, bioreactor control strategy, feeding strategy, and cell culture duration/cell viability on HCP profile was examined using this technique. Among all the parameters studied, cell viability generated the most significant changes on the HCP profile. 2D-DIGE was also used to compare the HCP differences between monoclonal antibody producing and null cell cultures. The HCP species in production cell culture was found to be well represented in null cell culture, which confirms the suitability of using the null cell culture for immunoassay reagent generation. 2D-DIGE is complimentary to the commonly used HCP immunoassay. It provides a direct comparison of the changes in HCP composition under different conditions and can reveal properties (pI, MW) of individual species, whereas the immunoassay sensitively quantifies total HCP amount in a given sample.