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Applied Microbiology and Biotechnology (v.68, #4)
Optimization and scale up of industrial fermentation processes by F. R. Schmidt (pp. 425-435).
To increase product yields and to ensure consistent product quality, key issues of industrial fermentations, process optimization and scale up are aimed at maintaining optimum and homogenous reaction conditions minimizing microbial stress exposure and enhancing metabolic accuracy. For each individual product, process and facility, suitable strategies have to be elaborated by a comprehensive and detailed process characterization, identification of the most relevant process parameters influencing product yield and quality and their establishment as scale-up parameters to be kept constant as far as possible. Physical variables, which can only be restrictedly kept constant as single parameters, may be combined with other pertinent parameters to appropriate mathematical groups or dimensionless terms. Process characterization is preferably based on real-time or near real-time data collected by in situ and on-line measurements and may be facilitated by supportive approaches and tools like neural network based chemometric data analysis and modelling, clarification of the mixing and stream conditions through computational fluid dynamics and scale-down simulations. However, as fermentation facilities usually are not strictly designed according to scale-up criteria and the process conditions in the culture vessels thus may differ significantly and since any strategy and model can only insufficiently consider and reflect the highly complex interdependence and mutual interaction of fermentation parameters, successful scale up in most cases is not the result of a conclusive and straight-lined experimental strategy, but rather will be the outcome of a separate process development and optimization on each scale. This article gives an overview on the problems typically coming along with fermentation process optimization and scale up, and presents currently applied scale-up strategies while considering future technologies, with emphasis on Escherichia coli as one of the most commonly fermented organisms.
Optimization and scale up of industrial fermentation processes by F. R. Schmidt (pp. 425-435).
To increase product yields and to ensure consistent product quality, key issues of industrial fermentations, process optimization and scale up are aimed at maintaining optimum and homogenous reaction conditions minimizing microbial stress exposure and enhancing metabolic accuracy. For each individual product, process and facility, suitable strategies have to be elaborated by a comprehensive and detailed process characterization, identification of the most relevant process parameters influencing product yield and quality and their establishment as scale-up parameters to be kept constant as far as possible. Physical variables, which can only be restrictedly kept constant as single parameters, may be combined with other pertinent parameters to appropriate mathematical groups or dimensionless terms. Process characterization is preferably based on real-time or near real-time data collected by in situ and on-line measurements and may be facilitated by supportive approaches and tools like neural network based chemometric data analysis and modelling, clarification of the mixing and stream conditions through computational fluid dynamics and scale-down simulations. However, as fermentation facilities usually are not strictly designed according to scale-up criteria and the process conditions in the culture vessels thus may differ significantly and since any strategy and model can only insufficiently consider and reflect the highly complex interdependence and mutual interaction of fermentation parameters, successful scale up in most cases is not the result of a conclusive and straight-lined experimental strategy, but rather will be the outcome of a separate process development and optimization on each scale. This article gives an overview on the problems typically coming along with fermentation process optimization and scale up, and presents currently applied scale-up strategies while considering future technologies, with emphasis on Escherichia coli as one of the most commonly fermented organisms.
Biotechnological production and application of vitamin E: current state and prospects by Henry E. Valentin; Qungang Qi (pp. 436-444).
Tocochromanols (tocopherols and tocotrienols) are important lipophilic antioxidants for animals and humans. Their biological activity is expressed as vitamin E activity. This article describes the current need for vitamin E production, and compares different strategies to engineer the vitamin E content in photosynthetic bacteria and plants, with a focus on oilseed as target tissues. The current status of biotechnological advances in tocochromanol pathway engineering is summarized, and current limitations in our understanding of the tocochromanol biosynthetic pathway are discussed.
Biotechnological production and application of vitamin E: current state and prospects by Henry E. Valentin; Qungang Qi (pp. 436-444).
Tocochromanols (tocopherols and tocotrienols) are important lipophilic antioxidants for animals and humans. Their biological activity is expressed as vitamin E activity. This article describes the current need for vitamin E production, and compares different strategies to engineer the vitamin E content in photosynthetic bacteria and plants, with a focus on oilseed as target tissues. The current status of biotechnological advances in tocochromanol pathway engineering is summarized, and current limitations in our understanding of the tocochromanol biosynthetic pathway are discussed.
Microbial xanthophylls by Prakash Bhosale; Paul S. Bernstein (pp. 445-455).
Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.
Microbial xanthophylls by Prakash Bhosale; Paul S. Bernstein (pp. 445-455).
Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.
Microbiological control in stem cell banks: approaches to standardisation by Fernando Cobo; Glyn N. Stacey; Charles Hunt; Carmen Cabrera; Ana Nieto; Rosa Montes; José Luis Cortés; Purificación Catalina; Angela Barnie; Ángel Concha (pp. 456-466).
The transplant of cells of human origin is an increasingly complex sector of medicine which entails great opportunities for the treatment of a range of diseases. Stem cell banks should assure the quality, traceability and safety of cultures for transplantation and must implement an effective programme to prevent contamination of the final product. In donors, the presence of infectious micro-organisms, like human immunodeficiency virus, hepatitis B virus, hepatitis C virus and human T cell lymphotrophic virus, should be evaluated in addition to the possibility of other new infectious agents (e.g. transmissible spongiform encephalopathies and severe acute respiratory syndrome). The introduction of the nucleic acid amplification can avoid the window period of these viral infections. Contamination from the laboratory environment can be achieved by routine screening for bacteria, fungi, yeast and mycoplasma by European pharmacopoeia tests. Fastidious micro-organisms, and an adventitious or endogenous virus, is a well-known fact that will also have to be considered for processes involving in vitro culture of stem cells. It is also a standard part of current good practice in stem cell banks to carry out routine environmental microbiological monitoring of the cleanrooms where the cell cultures and their products are prepared. The risk of viral contamination from products of animal origin, like bovine serum and mouse fibroblasts as a “feeder layer” for the development of embryonic cell lines, should also be considered. Stem cell lines should be tested for prion particles and a virus of animal origin that assure an acceptable quality.
Microbiological control in stem cell banks: approaches to standardisation by Fernando Cobo; Glyn N. Stacey; Charles Hunt; Carmen Cabrera; Ana Nieto; Rosa Montes; José Luis Cortés; Purificación Catalina; Angela Barnie; Ángel Concha (pp. 456-466).
The transplant of cells of human origin is an increasingly complex sector of medicine which entails great opportunities for the treatment of a range of diseases. Stem cell banks should assure the quality, traceability and safety of cultures for transplantation and must implement an effective programme to prevent contamination of the final product. In donors, the presence of infectious micro-organisms, like human immunodeficiency virus, hepatitis B virus, hepatitis C virus and human T cell lymphotrophic virus, should be evaluated in addition to the possibility of other new infectious agents (e.g. transmissible spongiform encephalopathies and severe acute respiratory syndrome). The introduction of the nucleic acid amplification can avoid the window period of these viral infections. Contamination from the laboratory environment can be achieved by routine screening for bacteria, fungi, yeast and mycoplasma by European pharmacopoeia tests. Fastidious micro-organisms, and an adventitious or endogenous virus, is a well-known fact that will also have to be considered for processes involving in vitro culture of stem cells. It is also a standard part of current good practice in stem cell banks to carry out routine environmental microbiological monitoring of the cleanrooms where the cell cultures and their products are prepared. The risk of viral contamination from products of animal origin, like bovine serum and mouse fibroblasts as a “feeder layer” for the development of embryonic cell lines, should also be considered. Stem cell lines should be tested for prion particles and a virus of animal origin that assure an acceptable quality.
Production of 3-hydroxypropionaldehyde using a two-step process with Lactobacillus reuteri by Y. Doleyres; P. Beck; S. Vollenweider; C. Lacroix (pp. 467-474).
3-Hydroxypropionaldehyde (3-HPA) produced by Lactobacillus reuteri is a broad-spectrum antimicrobial substance of glycerol conversion. The aim of the present work was to optimize 3-HPA production by Lb. reuteri ATCC 53608 using a two-step process. The first step was the production of Lb. reuteri cells in optimal conditions. Cells were then harvested by centrifugation and suspended in glycerol solution, which the resting cells bioconverted to 3-HPA. The effect of biomass concentration, temperature, glycerol concentration, anaerobic/micro-aerophilic conditions, and incubation time was studied for high 3-HPA production. 3-HPA accumulation was limited by the death of cells in contact with high concentrations of 3-HPA. However, a very high 3-HPA concentration of 235±3 mM was obtained after 45 min of incubation at 30°C in 400 mM glycerol for an initial free-cell concentration of 1.6±0.3×1010 viable cells/ml. A high viability was maintained at low temperatures in the range 5–15°C, but with a slightly lower yield of 3-HPA at 5°C compared with higher temperatures, up to 37°C. Successive 1-h incubations of Lb. reuteri cells in 200 mM glycerol at 15°C to tentatively reuse the cells resulted in decreasing 3-HPA concentrations at the end of each cycle, with two successful production cycles yielding high 3-HPA concentrations of 147±1 mM and 128±2 mM.
Production of 3-hydroxypropionaldehyde using a two-step process with Lactobacillus reuteri by Y. Doleyres; P. Beck; S. Vollenweider; C. Lacroix (pp. 467-474).
3-Hydroxypropionaldehyde (3-HPA) produced by Lactobacillus reuteri is a broad-spectrum antimicrobial substance of glycerol conversion. The aim of the present work was to optimize 3-HPA production by Lb. reuteri ATCC 53608 using a two-step process. The first step was the production of Lb. reuteri cells in optimal conditions. Cells were then harvested by centrifugation and suspended in glycerol solution, which the resting cells bioconverted to 3-HPA. The effect of biomass concentration, temperature, glycerol concentration, anaerobic/micro-aerophilic conditions, and incubation time was studied for high 3-HPA production. 3-HPA accumulation was limited by the death of cells in contact with high concentrations of 3-HPA. However, a very high 3-HPA concentration of 235±3 mM was obtained after 45 min of incubation at 30°C in 400 mM glycerol for an initial free-cell concentration of 1.6±0.3×1010 viable cells/ml. A high viability was maintained at low temperatures in the range 5–15°C, but with a slightly lower yield of 3-HPA at 5°C compared with higher temperatures, up to 37°C. Successive 1-h incubations of Lb. reuteri cells in 200 mM glycerol at 15°C to tentatively reuse the cells resulted in decreasing 3-HPA concentrations at the end of each cycle, with two successful production cycles yielding high 3-HPA concentrations of 147±1 mM and 128±2 mM.
Production of organic acids by Corynebacterium glutamicum under oxygen deprivation by Shohei Okino; Masayuki Inui; Hideaki Yukawa (pp. 475-480).
Under oxygen deprivation, aerobic Corynebacterium glutamicum produce organic acids from glucose at high yields in mineral medium even though their proliferation is arrested. To develop a new, high-productivity bioprocess based on these unique features, characteristics of organic acid production by C. glutamicum under oxygen deprivation were investigated. The main organic acids produced from glucose under these conditions were lactic acid and succinic acid. Addition of bicarbonate, which is a co-substrate for anaplerotic enzymes, increased the glucose consumption rate, leading to increased organic acid production rates. With increasing concentration of bicarbonate, the yield of succinic acid increased, whereas that of lactic acid decreased. There was a direct correlation between cell concentration and organic acid production rates even at elevated cell densities, and productivities of lactic acid and succinic acid were 42.9 g l−1 h−1 and 11.7 g l−1 h−1, respectively, at a cell concentration of 60 g dry cell l−1. This cell-recycling continuous reaction demonstrated that rates of organic acid production by C. glutamicum could be maintained for at least 360 h.
Production of organic acids by Corynebacterium glutamicum under oxygen deprivation by Shohei Okino; Masayuki Inui; Hideaki Yukawa (pp. 475-480).
Under oxygen deprivation, aerobic Corynebacterium glutamicum produce organic acids from glucose at high yields in mineral medium even though their proliferation is arrested. To develop a new, high-productivity bioprocess based on these unique features, characteristics of organic acid production by C. glutamicum under oxygen deprivation were investigated. The main organic acids produced from glucose under these conditions were lactic acid and succinic acid. Addition of bicarbonate, which is a co-substrate for anaplerotic enzymes, increased the glucose consumption rate, leading to increased organic acid production rates. With increasing concentration of bicarbonate, the yield of succinic acid increased, whereas that of lactic acid decreased. There was a direct correlation between cell concentration and organic acid production rates even at elevated cell densities, and productivities of lactic acid and succinic acid were 42.9 g l−1 h−1 and 11.7 g l−1 h−1, respectively, at a cell concentration of 60 g dry cell l−1. This cell-recycling continuous reaction demonstrated that rates of organic acid production by C. glutamicum could be maintained for at least 360 h.
Optimization of erythritol and glycerol accumulation in conidia of Beauveria bassiana by solid-state fermentation, using response surface methodology by Federico Tarocco; Roberto E. Lecuona; Alicia S. Couto; Jorge A. Arcas (pp. 481-488).
Entomopathogenic fungi are widely produced for use as mycoinsecticides. Therefore, improvement of the shelf life of fungal propagules under good and adverse conditions should be a pre-requisite of their production. In order to improve conidial physiology as well as mycoinsecticide efficiency, culture conditions may be varied. The Doehlert design was used to generate response surfaces with an estimation of the parameters of the quadratic model allowing the study of three different factors at a different number of levels. This experimental design was applied to optimize water activity (a w), pH, and fermentation time for Beauveria bassiana conidial production and accumulation of polyols in solid-state fermentation. Thus, it was possible to identify the region in the experimental range in which the optimum values of these parameters were simultaneously achieved. Maximal conidia production was achieved at pH 5–6 and a w=0.999. Under these conditions, polyol accumulation was 3 mg erythritol/g conidia and 29.6 mg glycerol/g conidia. However, maximal polyol accumulation was achieved at pH 4.5 and a w 0.950; erythritol production increased 33-fold and glycerol production 4.5-fold. Under these conditions conidia production was 1,000 times lower. The possibilities of increasing the quality of the biocontrol agent without neglecting yield are discussed.
Optimization of erythritol and glycerol accumulation in conidia of Beauveria bassiana by solid-state fermentation, using response surface methodology by Federico Tarocco; Roberto E. Lecuona; Alicia S. Couto; Jorge A. Arcas (pp. 481-488).
Entomopathogenic fungi are widely produced for use as mycoinsecticides. Therefore, improvement of the shelf life of fungal propagules under good and adverse conditions should be a pre-requisite of their production. In order to improve conidial physiology as well as mycoinsecticide efficiency, culture conditions may be varied. The Doehlert design was used to generate response surfaces with an estimation of the parameters of the quadratic model allowing the study of three different factors at a different number of levels. This experimental design was applied to optimize water activity (a w), pH, and fermentation time for Beauveria bassiana conidial production and accumulation of polyols in solid-state fermentation. Thus, it was possible to identify the region in the experimental range in which the optimum values of these parameters were simultaneously achieved. Maximal conidia production was achieved at pH 5–6 and a w=0.999. Under these conditions, polyol accumulation was 3 mg erythritol/g conidia and 29.6 mg glycerol/g conidia. However, maximal polyol accumulation was achieved at pH 4.5 and a w 0.950; erythritol production increased 33-fold and glycerol production 4.5-fold. Under these conditions conidia production was 1,000 times lower. The possibilities of increasing the quality of the biocontrol agent without neglecting yield are discussed.
Recombinant production of serine hydroxymethyl transferase from Streptococcus thermophilus and its preliminary evaluation as a biocatalyst by L. Vidal; J. Calveras; P. Clapés; P. Ferrer; G. Caminal (pp. 489-497).
The glyA gene encoding a serine hydroxymethyl transferase (SHMT) with threonine aldolase activity was isolated from Streptococcus thermophilus YKA-184 chromosomal DNA. This aldolase is a pyridoxal 5′-phosphate-dependent enzyme that stereospecifically catalyzes the interconversion of l-threonine to glycine and acetaldehyde. The enzyme was overexpressed in Escherichia coli M15 as a recombinant protein of 45 kDa with a His6-tag at its N-terminus. The recombinant enzyme was purified to homogeneity by a single chromatographic step using Ni-nitrilotriacetic acid affinity, obtaining a high activity-recovery yield (83%). Lyophilized and precipitated enzymes were stable at least for 10 weeks when stored at −20°C and 4°C. It was observed that the K m for l-allo-threonine was 38-fold higher than that for l-threonine, suggesting this enzyme can be classified as a specific l-allo-threonine aldolase. The optimum pH range of threonine aldolase activity for the recombinant SHMT was pH 6–7. When tested for aldol addition reactions with non-natural aldehydes, such as benzyloxyacetaldehyde and (R)-N-Cbz-alaninal, two possible β-hydroxy-α-amino acid diastereoisomers were produced, but with moderate stereospecificity. The enzyme showed potential as a biocatalyst for the stereoselective synthesis of β-hydroxy-α-amino acids.
Recombinant production of serine hydroxymethyl transferase from Streptococcus thermophilus and its preliminary evaluation as a biocatalyst by L. Vidal; J. Calveras; P. Clapés; P. Ferrer; G. Caminal (pp. 489-497).
The glyA gene encoding a serine hydroxymethyl transferase (SHMT) with threonine aldolase activity was isolated from Streptococcus thermophilus YKA-184 chromosomal DNA. This aldolase is a pyridoxal 5′-phosphate-dependent enzyme that stereospecifically catalyzes the interconversion of l-threonine to glycine and acetaldehyde. The enzyme was overexpressed in Escherichia coli M15 as a recombinant protein of 45 kDa with a His6-tag at its N-terminus. The recombinant enzyme was purified to homogeneity by a single chromatographic step using Ni-nitrilotriacetic acid affinity, obtaining a high activity-recovery yield (83%). Lyophilized and precipitated enzymes were stable at least for 10 weeks when stored at −20°C and 4°C. It was observed that the K m for l-allo-threonine was 38-fold higher than that for l-threonine, suggesting this enzyme can be classified as a specific l-allo-threonine aldolase. The optimum pH range of threonine aldolase activity for the recombinant SHMT was pH 6–7. When tested for aldol addition reactions with non-natural aldehydes, such as benzyloxyacetaldehyde and (R)-N-Cbz-alaninal, two possible β-hydroxy-α-amino acid diastereoisomers were produced, but with moderate stereospecificity. The enzyme showed potential as a biocatalyst for the stereoselective synthesis of β-hydroxy-α-amino acids.
Efficient production of (2S)-flavanones by Escherichia coli containing an artificial biosynthetic gene cluster by Ikuo Miyahisa; Masafumi Kaneko; Nobutaka Funa; Hisashi Kawasaki; Hiroyuki Kojima; Yasuo Ohnishi; Sueharu Horinouchi (pp. 498-504).
For the fermentative production of plant-specific flavanones (naringenin, pinocembrin) by Escherichia coli, a plasmid was constructed which carried an artificial biosynthetic gene cluster, including PAL encoding a phenylalanine ammonia-lyase from a yeast, ScCCL encoding a cinnamate/coumarate:CoA ligase from the actinomycete Streptomyces coelicolor A3(2), CHS encoding a chalcone synthase from a licorice plant and CHI encoding a chalcone isomerase from the Pueraria plant. The recombinant E. coli cells produced (2S)-naringenin from tyrosine and (2S)-pinocembrin from phenylalanine. When the two subunit genes of acetyl-CoA carboxylase from Corynebacterium glutamicum were expressed under the control of the T7 promoter and the ribosome-binding sequence in the recombinant E. coli cells, the flavanone yields were greatly increased, probably because enhanced expression of acetyl-CoA carboxylase increased a pool of malonyl-CoA that was available for flavanone synthesis. Under cultural conditions where E. coli at a cell density of 50 g/l was incubated in the presence of 3 mM tyrosine or phenylalanine, the yields of naringenin and pinocembrin reached about 60 mg/l. The fermentative production of flavanones in E. coli is the first step in the construction of a library of flavonoid compounds and un-natural flavonoids in bacteria.
Efficient production of (2S)-flavanones by Escherichia coli containing an artificial biosynthetic gene cluster by Ikuo Miyahisa; Masafumi Kaneko; Nobutaka Funa; Hisashi Kawasaki; Hiroyuki Kojima; Yasuo Ohnishi; Sueharu Horinouchi (pp. 498-504).
For the fermentative production of plant-specific flavanones (naringenin, pinocembrin) by Escherichia coli, a plasmid was constructed which carried an artificial biosynthetic gene cluster, including PAL encoding a phenylalanine ammonia-lyase from a yeast, ScCCL encoding a cinnamate/coumarate:CoA ligase from the actinomycete Streptomyces coelicolor A3(2), CHS encoding a chalcone synthase from a licorice plant and CHI encoding a chalcone isomerase from the Pueraria plant. The recombinant E. coli cells produced (2S)-naringenin from tyrosine and (2S)-pinocembrin from phenylalanine. When the two subunit genes of acetyl-CoA carboxylase from Corynebacterium glutamicum were expressed under the control of the T7 promoter and the ribosome-binding sequence in the recombinant E. coli cells, the flavanone yields were greatly increased, probably because enhanced expression of acetyl-CoA carboxylase increased a pool of malonyl-CoA that was available for flavanone synthesis. Under cultural conditions where E. coli at a cell density of 50 g/l was incubated in the presence of 3 mM tyrosine or phenylalanine, the yields of naringenin and pinocembrin reached about 60 mg/l. The fermentative production of flavanones in E. coli is the first step in the construction of a library of flavonoid compounds and un-natural flavonoids in bacteria.
Aluminum- and mild steel-binding peptides from phage display by Rongjun Zuo; Dogan Örnek; Thomas K. Wood (pp. 505-509).
Using a phage library displaying random peptides of 12 amino acids on its surface, several peptides were found that bind to aluminum and mild steel. Like other metal-binding peptides, no obvious consensus motif has been found for these peptides. However, most of them are rich in hydroxyl-containing amino acids, serine or threonine, or contain histidine. For the aluminum-binding peptides, peptides with a higher number of hydroxyl-containing amino acids bind to the aluminum surface more tightly. For example, Val-Pro-Ser-Ser-Gly-Pro-Gln-Asp-Thr-Arg-Thr-Thr, which contains five hydroxyl-containing amino acid residues, was selected four-fold more frequently than a peptide containing only one serine, suggesting an important role for the hydroxyl-containing amino acids in the metal–peptide interaction.
Aluminum- and mild steel-binding peptides from phage display by Rongjun Zuo; Dogan Örnek; Thomas K. Wood (pp. 505-509).
Using a phage library displaying random peptides of 12 amino acids on its surface, several peptides were found that bind to aluminum and mild steel. Like other metal-binding peptides, no obvious consensus motif has been found for these peptides. However, most of them are rich in hydroxyl-containing amino acids, serine or threonine, or contain histidine. For the aluminum-binding peptides, peptides with a higher number of hydroxyl-containing amino acids bind to the aluminum surface more tightly. For example, Val-Pro-Ser-Ser-Gly-Pro-Gln-Asp-Thr-Arg-Thr-Thr, which contains five hydroxyl-containing amino acid residues, was selected four-fold more frequently than a peptide containing only one serine, suggesting an important role for the hydroxyl-containing amino acids in the metal–peptide interaction.
Protein engineering of toluene-o-xylene monooxygenase from Pseudomonas stutzeri OX1 for enhanced chlorinated ethene degradation and o-xylene oxidation by Gönül Vardar; Thomas K. Wood (pp. 510-517).
Toluene-o-xylene monooxygenase (ToMO) from Pseudomonas stutzeri OX1 has been shown to degrade all chlorinated ethenes individually and as mixtures. Here, DNA shuffling of the alpha hydroxylase fragment of ToMO (TouA) and saturation mutagenesis of the TouA active site residues I100, Q141, T201, F205, and E214 were used to enhance the degradation of chlorinated aliphatics. The ToMO mutants were identified using a chloride ion screen and then were further examined by gas chromatography. Escherichia coli TG1/pBS(Kan)ToMO expressing TouA saturation mutagenesis variant I100Q was identified that has 2.8-fold better trichloroethylene (TCE) degradation activity (apparent V max of 1.77 nmol min−1 mg−1 protein−1 vs 0.63 nmol min−1 mg−1 protein−1). Another variant, E214G/D312N/M399V, has 2.5-fold better cis-1,2-dichloroethylene (cis-DCE) degradation activity (apparent V max of 8.4 nmol min−1 mg−1 protein−1 vs 3.3 nmol min−1 mg−1 protein−1). Additionally, the hydroxylation regiospecificity of o-xylene and naphthalene were altered significantly for ToMO variants A107T/E214A, T201G, and T201S. Variant T201S produced 2.0-fold more 2,3-dimethylphenol (2,3-DMP) from o-xylene than the wild-type ToMO, whereas variant A107T/E214A had 6.0-fold altered regiospecificity for 2,3-DMP formation. Variant A107T/E214A also produced 3.0-fold more 2-naphthol from naphthalene than the wild-type ToMO, whereas the regiospecificity of variant T201S was altered to synthesize 3.0-fold less 2-naphthol, so that it made almost exclusively 1-naphthol (96%). Variant T201G was more regiospecific than variants A107T/E214A and T201S and produced 100% 3,4-DMP from o-xylene and >99% 1-naphthol from naphthalene. Hence, ToMO activity was enhanced for the degradation of TCE and cis-DCE and for the regiospecific hydroxylation of o-xylene and naphthalene through DNA shuffling and saturation mutagenesis.
Protein engineering of toluene-o-xylene monooxygenase from Pseudomonas stutzeri OX1 for enhanced chlorinated ethene degradation and o-xylene oxidation by Gönül Vardar; Thomas K. Wood (pp. 510-517).
Toluene-o-xylene monooxygenase (ToMO) from Pseudomonas stutzeri OX1 has been shown to degrade all chlorinated ethenes individually and as mixtures. Here, DNA shuffling of the alpha hydroxylase fragment of ToMO (TouA) and saturation mutagenesis of the TouA active site residues I100, Q141, T201, F205, and E214 were used to enhance the degradation of chlorinated aliphatics. The ToMO mutants were identified using a chloride ion screen and then were further examined by gas chromatography. Escherichia coli TG1/pBS(Kan)ToMO expressing TouA saturation mutagenesis variant I100Q was identified that has 2.8-fold better trichloroethylene (TCE) degradation activity (apparent V max of 1.77 nmol min−1 mg−1 protein−1 vs 0.63 nmol min−1 mg−1 protein−1). Another variant, E214G/D312N/M399V, has 2.5-fold better cis-1,2-dichloroethylene (cis-DCE) degradation activity (apparent V max of 8.4 nmol min−1 mg−1 protein−1 vs 3.3 nmol min−1 mg−1 protein−1). Additionally, the hydroxylation regiospecificity of o-xylene and naphthalene were altered significantly for ToMO variants A107T/E214A, T201G, and T201S. Variant T201S produced 2.0-fold more 2,3-dimethylphenol (2,3-DMP) from o-xylene than the wild-type ToMO, whereas variant A107T/E214A had 6.0-fold altered regiospecificity for 2,3-DMP formation. Variant A107T/E214A also produced 3.0-fold more 2-naphthol from naphthalene than the wild-type ToMO, whereas the regiospecificity of variant T201S was altered to synthesize 3.0-fold less 2-naphthol, so that it made almost exclusively 1-naphthol (96%). Variant T201G was more regiospecific than variants A107T/E214A and T201S and produced 100% 3,4-DMP from o-xylene and >99% 1-naphthol from naphthalene. Hence, ToMO activity was enhanced for the degradation of TCE and cis-DCE and for the regiospecific hydroxylation of o-xylene and naphthalene through DNA shuffling and saturation mutagenesis.
Gene expression analysis of Escherichia coli grown in miniaturized bioreactor platforms for high-throughput analysis of growth and genomic data by Paolo Boccazzi; Andrea Zanzotto; Nicolas Szita; Sanchita Bhattacharya; Klavs F. Jensen; Anthony J. Sinskey (pp. 518-532).
Combining high-throughput growth physiology and global gene expression data analysis is of significant value for integrating metabolism and genomics. We compared global gene expression using 500 ng of total RNA from Escherichia coli cultures grown in rich or defined minimal media in a miniaturized 50-μl bioreactor. The microbioreactor was fabricated out of poly(dimethylsiloxane) (PDMS) and glass and equipped to provide on-line, optical measurements. cDNA labeling for microarray hybridizations was performed with the GeniconRLS system. From these experiments, we found that the expression of 232 genes increased significantly in cells grown in minimum medium, including genes involved in amino acid biosynthesis and central metabolism. The expression of 275 genes was significantly elevated in cells grown in rich medium, including genes involved in the translational and motility apparatuses. In general, these changes in gene expression levels were similar to those observed in 1,000-fold larger cultures. The increasing rate at which complete genomic sequences of microorganisms are becoming available offers an unprecedented opportunity for investigating these organisms. Our results from microscale cultures using just 500 ng of total RNA indicate that high-throughput integration of growth physiology and genomics will be possible with novel biochemical platforms and improved detection technologies.
Gene expression analysis of Escherichia coli grown in miniaturized bioreactor platforms for high-throughput analysis of growth and genomic data by Paolo Boccazzi; Andrea Zanzotto; Nicolas Szita; Sanchita Bhattacharya; Klavs F. Jensen; Anthony J. Sinskey (pp. 518-532).
Combining high-throughput growth physiology and global gene expression data analysis is of significant value for integrating metabolism and genomics. We compared global gene expression using 500 ng of total RNA from Escherichia coli cultures grown in rich or defined minimal media in a miniaturized 50-μl bioreactor. The microbioreactor was fabricated out of poly(dimethylsiloxane) (PDMS) and glass and equipped to provide on-line, optical measurements. cDNA labeling for microarray hybridizations was performed with the GeniconRLS system. From these experiments, we found that the expression of 232 genes increased significantly in cells grown in minimum medium, including genes involved in amino acid biosynthesis and central metabolism. The expression of 275 genes was significantly elevated in cells grown in rich medium, including genes involved in the translational and motility apparatuses. In general, these changes in gene expression levels were similar to those observed in 1,000-fold larger cultures. The increasing rate at which complete genomic sequences of microorganisms are becoming available offers an unprecedented opportunity for investigating these organisms. Our results from microscale cultures using just 500 ng of total RNA indicate that high-throughput integration of growth physiology and genomics will be possible with novel biochemical platforms and improved detection technologies.
Hydrogen production by Rhodobacter sphaeroides strain O.U.001 using spent media of Enterobacter cloacae strain DM11 by Kaushik Nath; Anish Kumar; Debabrata Das (pp. 533-541).
Combined dark and photo-fermentation was carried out to study the feasibility of biological hydrogen production. In dark fermentation, hydrogen was produced by Enterobacter cloacae strain DM11 using glucose as substrate. This was followed by a photo-fermentation process. Here, the spent medium from the dark process (containing unconverted metabolites, mainly acetic acid etc.) underwent photo-fermentation by Rhodobacter sphaeroides strain O.U.001 in a column photo-bioreactor. This combination could achieve higher yields of hydrogen by complete utilization of the chemical energy stored in the substrate. Dark fermentation was studied in terms of several process parameters, such as initial substrate concentration, initial pH of the medium and temperature, to establish favorable conditions for maximum hydrogen production. Also, the effects of the threshold concentration of acetic acid, light intensity and the presence of additional nitrogen sources in the spent effluent on the amount of hydrogen produced during photo-fermentation were investigated. The light conversion efficiency of hydrogen was found to be inversely proportional to the incident light intensity. In a batch system, the yield of hydrogen in the dark fermentation was about 1.86 mol H2 mol−1 glucose; and the yield in the photo-fermentation was about 1.5–1.72 mol H2 mol−1 acetic acid. The overall yield of hydrogen in the combined process, considering glucose as the preliminary substrate, was found to be higher than that in a single process.
Hydrogen production by Rhodobacter sphaeroides strain O.U.001 using spent media of Enterobacter cloacae strain DM11 by Kaushik Nath; Anish Kumar; Debabrata Das (pp. 533-541).
Combined dark and photo-fermentation was carried out to study the feasibility of biological hydrogen production. In dark fermentation, hydrogen was produced by Enterobacter cloacae strain DM11 using glucose as substrate. This was followed by a photo-fermentation process. Here, the spent medium from the dark process (containing unconverted metabolites, mainly acetic acid etc.) underwent photo-fermentation by Rhodobacter sphaeroides strain O.U.001 in a column photo-bioreactor. This combination could achieve higher yields of hydrogen by complete utilization of the chemical energy stored in the substrate. Dark fermentation was studied in terms of several process parameters, such as initial substrate concentration, initial pH of the medium and temperature, to establish favorable conditions for maximum hydrogen production. Also, the effects of the threshold concentration of acetic acid, light intensity and the presence of additional nitrogen sources in the spent effluent on the amount of hydrogen produced during photo-fermentation were investigated. The light conversion efficiency of hydrogen was found to be inversely proportional to the incident light intensity. In a batch system, the yield of hydrogen in the dark fermentation was about 1.86 mol H2 mol−1 glucose; and the yield in the photo-fermentation was about 1.5–1.72 mol H2 mol−1 acetic acid. The overall yield of hydrogen in the combined process, considering glucose as the preliminary substrate, was found to be higher than that in a single process.
Isolation of dipicolinic acid as an insecticidal toxin from Paecilomyces fumosoroseus by Ali Asaff; Carlos Cerda-García-Rojas; Mayra de la Torre (pp. 542-547).
Several entomopathogenic fungi produce toxins that could be used as bioinsecticides in integrated pest management programs. Paecilomyces fumosoroseus is currently used for the biological control of the whiteflies Bemisia tabaci and B. argentifolii. Supernatants from submerged batch culture, where the fungus produced abundant dispersed mycelium, conidia and blastospores, were toxic to the whitefly nymphs. The most abundant metabolite was purified by HPLC and identified by mass spectrometry and NMR as dipicolinic acid. Both the dipicolinic acid produced by the fungus and the chemically synthesized compound had insecticidal activity against third-instar nymphs of the insect. Dipicolinic acid was toxic to the whitefly nymphs in bioassays involving topical applications. In submerged culture, the specific growth rate of P. fumosoroseus was 0.054 h−1, the specific glucose consumption rate was 0.1195 g g−1 h−1 and the specific dipicolinic acid production rate was 0.00012 g g−1 h−1. Dipicolinic acid was detected after 24 h when the fungus started growing; and dipicolinic acid production was directly correlated with fungal growth. Nevertheless, the yield was low and the maximal concentration was only 0.041 g l−1. The maximal concentrations of conidia and blastospores (per milliliter) were 1.4×108 and 7×107, respectively.
Isolation of dipicolinic acid as an insecticidal toxin from Paecilomyces fumosoroseus by Ali Asaff; Carlos Cerda-García-Rojas; Mayra de la Torre (pp. 542-547).
Several entomopathogenic fungi produce toxins that could be used as bioinsecticides in integrated pest management programs. Paecilomyces fumosoroseus is currently used for the biological control of the whiteflies Bemisia tabaci and B. argentifolii. Supernatants from submerged batch culture, where the fungus produced abundant dispersed mycelium, conidia and blastospores, were toxic to the whitefly nymphs. The most abundant metabolite was purified by HPLC and identified by mass spectrometry and NMR as dipicolinic acid. Both the dipicolinic acid produced by the fungus and the chemically synthesized compound had insecticidal activity against third-instar nymphs of the insect. Dipicolinic acid was toxic to the whitefly nymphs in bioassays involving topical applications. In submerged culture, the specific growth rate of P. fumosoroseus was 0.054 h−1, the specific glucose consumption rate was 0.1195 g g−1 h−1 and the specific dipicolinic acid production rate was 0.00012 g g−1 h−1. Dipicolinic acid was detected after 24 h when the fungus started growing; and dipicolinic acid production was directly correlated with fungal growth. Nevertheless, the yield was low and the maximal concentration was only 0.041 g l−1. The maximal concentrations of conidia and blastospores (per milliliter) were 1.4×108 and 7×107, respectively.
The fatty acid profile of vegetative Azotobacter vinelandii ATCC 12837: growth phase-dependence by A. Larsen; I. Sliskovic; D. Juric; C. L. Pinnock; H. Kullman; E. Segstro; G. Reinfelds; M. O. Eze (pp. 548-553).
Fatty acids of Azotobacter vinelandii ATCC 12837 were determined at various times during aerobic vegetative growth at 30°C to provide baseline data for studying the effects of chemical agents on the organism’s survival and fatty acid biosynthesis. Palmitate (16:0) was the highest at 36.7±4.3 mol% (mean±SD) after the first 5 h in fresh culture, decreasing slightly to 33.4±2.6 mol% at 49 h. The other fatty acids were therefore each normalized as a ratio of 16:0. At 5 h, as a ratio of 16:0, myristate (14:0) was 0.14±0.06, palmitoleate (16:1cΔ9–10) 0.13±0.06, oleate (18:1cΔ9–10) 0.21±0.12, cis-vaccenate (18:1cΔ11–12) 0.30±0.17 and stearate (18:0) 0.68±0.02. As the growth phase advanced to 49 h, 14:0 and 16:1cΔ9–10 increased, 18:1cΔ9–10 decreased and cis-vaccenate reciprocally increased, whereas 18:0 decreased. These suggest that the saturated fatty acid biosynthesis pathway yielded 16:0 and 18:0 in the 5-h lag period. By desaturation, 18:0 formed the unsaturated fatty acid (UFA) 18:1cΔ9–10. As the culture aged, the anaerobic UFA biosynthesis pathway formed 16:1cΔ9–10, which was elongated to 18:1cΔ11–12. These fatty acid alterations represent a homeoviscous adaptation, modulating the microbe’s membrane lipid viscosity for optimal cellular function.
The fatty acid profile of vegetative Azotobacter vinelandii ATCC 12837: growth phase-dependence by A. Larsen; I. Sliskovic; D. Juric; C. L. Pinnock; H. Kullman; E. Segstro; G. Reinfelds; M. O. Eze (pp. 548-553).
Fatty acids of Azotobacter vinelandii ATCC 12837 were determined at various times during aerobic vegetative growth at 30°C to provide baseline data for studying the effects of chemical agents on the organism’s survival and fatty acid biosynthesis. Palmitate (16:0) was the highest at 36.7±4.3 mol% (mean±SD) after the first 5 h in fresh culture, decreasing slightly to 33.4±2.6 mol% at 49 h. The other fatty acids were therefore each normalized as a ratio of 16:0. At 5 h, as a ratio of 16:0, myristate (14:0) was 0.14±0.06, palmitoleate (16:1cΔ9–10) 0.13±0.06, oleate (18:1cΔ9–10) 0.21±0.12, cis-vaccenate (18:1cΔ11–12) 0.30±0.17 and stearate (18:0) 0.68±0.02. As the growth phase advanced to 49 h, 14:0 and 16:1cΔ9–10 increased, 18:1cΔ9–10 decreased and cis-vaccenate reciprocally increased, whereas 18:0 decreased. These suggest that the saturated fatty acid biosynthesis pathway yielded 16:0 and 18:0 in the 5-h lag period. By desaturation, 18:0 formed the unsaturated fatty acid (UFA) 18:1cΔ9–10. As the culture aged, the anaerobic UFA biosynthesis pathway formed 16:1cΔ9–10, which was elongated to 18:1cΔ11–12. These fatty acid alterations represent a homeoviscous adaptation, modulating the microbe’s membrane lipid viscosity for optimal cellular function.
Microbial response and elimination capacity in biofilters subjected to high toluene loadings by JiHyeon Song; Kerry A. Kinney (pp. 554-559).
Elimination capacity (EC) is frequently used as a performance and design criterion for vapor-phase biofilters without further verification of the microbial quantity and activity. This study was conducted to investigate how biofilters respond to high pollutant loadings and ultimately how this affects the EC of the biofilter. Two identical laboratory-scale biofilters were maintained at an initial toluene loading rate of 46 g m−3 h−1 for a period of 24 days. After the initial biofilm development stage, the loading rates were increased to 91 g m−3 h−1 and 137 g m−3 h−1, respectively. Following a short period of pseudo-steady state, toluene removal efficiencies rapidly declined in both biofilters, with a concurrent decline in both critical and maximum ECs. The decline was mainly due to deterioration in the biodegradation activity of the biofilm and a decline in the toluene-degrading bacterial population within the biofilm phase. The findings imply that high toluene loadings accelerated the deterioration in overall performance due to a rapid accumulation of inactive biomass. As a result, care must be used when relying on EC values for biofilter design and operational purposes, since the values do not appropriately reflect the temporal changes in biodegradation activity and active biomass quantities that can occur in biofilters subjected to high inlet loadings.
Microbial response and elimination capacity in biofilters subjected to high toluene loadings by JiHyeon Song; Kerry A. Kinney (pp. 554-559).
Elimination capacity (EC) is frequently used as a performance and design criterion for vapor-phase biofilters without further verification of the microbial quantity and activity. This study was conducted to investigate how biofilters respond to high pollutant loadings and ultimately how this affects the EC of the biofilter. Two identical laboratory-scale biofilters were maintained at an initial toluene loading rate of 46 g m−3 h−1 for a period of 24 days. After the initial biofilm development stage, the loading rates were increased to 91 g m−3 h−1 and 137 g m−3 h−1, respectively. Following a short period of pseudo-steady state, toluene removal efficiencies rapidly declined in both biofilters, with a concurrent decline in both critical and maximum ECs. The decline was mainly due to deterioration in the biodegradation activity of the biofilm and a decline in the toluene-degrading bacterial population within the biofilm phase. The findings imply that high toluene loadings accelerated the deterioration in overall performance due to a rapid accumulation of inactive biomass. As a result, care must be used when relying on EC values for biofilter design and operational purposes, since the values do not appropriately reflect the temporal changes in biodegradation activity and active biomass quantities that can occur in biofilters subjected to high inlet loadings.
Biotransformation of dichloro-, trichloro-, and tetrachlorodibenzo-p-dioxin by the white-rot fungus Phlebia lindtneri by Ichiro Kamei; Ryuichiro Kondo (pp. 560-566).
The model polychlorinated dibenzo-p-dioxins (PCDDs) 2,7-dichloro-, 2,3,7-trichloro, 1,2,6,7-, 1,2,8,9-, and 1,3,6,8-tetrachlorodibenzo-p-dioxin were used as substrates for a degradation experiment with the white-rot fungus Phlebia lindtneri. 2,7-Dichlorodibenzo-p-dioxin (2,7-diCDD) was biotransformed to hydroxylated diCDD and methoxylated diCDD. With the exception of 1,3,6,8-tetrachlorodibenzo-p-dioxin, the tri- and tetrachlorodibenzo-p-dioxins were biotransformed to hydroxyl and methoxyl compounds by P. lindtneri. The degradation rate of 1,2,6,7-tetrachlorodibenzo-p-dioxin was higher than that of 2,3,7-trichlorodibenzo-p-dioxin and no degradation of 1,3,6,8-tetrachlorodibenzo-p-dioxin was observed. These results indicate that the degradation of these PCDDs depends on the chlorination patterns of the substrates. This is the first report of the hydroxylation and methoxylation of tri- to tetra-CDDs by a fungal strain.
Biotransformation of dichloro-, trichloro-, and tetrachlorodibenzo-p-dioxin by the white-rot fungus Phlebia lindtneri by Ichiro Kamei; Ryuichiro Kondo (pp. 560-566).
The model polychlorinated dibenzo-p-dioxins (PCDDs) 2,7-dichloro-, 2,3,7-trichloro, 1,2,6,7-, 1,2,8,9-, and 1,3,6,8-tetrachlorodibenzo-p-dioxin were used as substrates for a degradation experiment with the white-rot fungus Phlebia lindtneri. 2,7-Dichlorodibenzo-p-dioxin (2,7-diCDD) was biotransformed to hydroxylated diCDD and methoxylated diCDD. With the exception of 1,3,6,8-tetrachlorodibenzo-p-dioxin, the tri- and tetrachlorodibenzo-p-dioxins were biotransformed to hydroxyl and methoxyl compounds by P. lindtneri. The degradation rate of 1,2,6,7-tetrachlorodibenzo-p-dioxin was higher than that of 2,3,7-trichlorodibenzo-p-dioxin and no degradation of 1,3,6,8-tetrachlorodibenzo-p-dioxin was observed. These results indicate that the degradation of these PCDDs depends on the chlorination patterns of the substrates. This is the first report of the hydroxylation and methoxylation of tri- to tetra-CDDs by a fungal strain.
