Pretreated sugarcane bagasse matches performance of synthetic media for lipid production with Yarrowia lipolytica.

Engineered strains of Yarrowia lipolytica with modified lipid profiles and other desirable properties for microbial oil production are widely reported but are almost exclusively characterized in synthetic laboratory-grade media. Ensuring translatable performance between synthetic media and industrially scalable lignocellulosic feedstocks is a critical challenge. Yarrowia lipolytica growth and lipid production were characterized in media derived from two-step acid-catalyzed glycerol pretreatment of sugarcane bagasse. Fermentation performance was benchmarked against laboratory-grade synthetic growth media, including detailed characterization of media composition, nitrogen utilization, biomass and lipid production, and fatty acid product profile. A Yarrowia lipolytica strain modified to enable xylose consumption consumed all sugars, glycerol, and acetic acid, accumulating lipids to 34-44 % of cell dry weight. Growth and lipid content when grown in sugarcane bagasse-derived media were equivalent to or better than that observed with synthetic media. These sugarcane bagasse-derived media are suitable for transferable development of Yarrowia lipolytica fermentations from synthetic media.

Chromogenic fusion proteins as alternative textiles dyes.

The widespread adoption of fast fashion has led to a significant waste problem associated with discarded textiles. Using proteins to color textiles can serve as a sustainable alternative to chemical dyes as well as reduce the demand for new raw materials. Here, we explore the use of chromogenic fusion proteins, consisting of a chromoprotein and a carbohydrate-binding module (CBM), as coloring agents for cellulose-based textiles such as cotton. We examined the color properties of chromoproteins AeBlue, SpisPink and Ultramarine alone and fused to CBM under various conditions. AeBlue, SpisPink and Ultramarine exhibited visible color between pH 4-9 and temperatures ranging from 4 to 45℃. Fusing CBM Clos from Clostridium thermocellum and CBM Ch2 from Trichoderma reesei to the chromoproteins had no effect on the chromoprotein color properties. Furthermore, binding assays showed that chromoprotein fusions did not affect binding of CBMs to cellulosic materials. Cotton samples bound with Ultramarine-Clos exhibited visible purple color that faded progressively over time as the samples dried. Applying 10% 8000 polyethylene glycol to cotton samples markedly preserved the color over extended periods. Overall, this work highlights the potential of chromoprotein-CBM fusions for textile dying which could be applied as a color maintenance technology or for reversible coloring of textiles for events or work wear, contributing to sustainable practices and introducing new creative opportunities for the industry.

Improving phytase production in Pichia pastoris fermentations through de-repression and methanol induction optimization.

Pichia pastoris (Komagataella phaffii) is a fast-growing methylotrophic yeast with the ability to assimilate several carbon sources such as methanol, glucose, or glycerol. It has been shown to have outstanding secretion capability with a variety of heterologous proteins. In previous studies, we engineered P. pastoris to co-express Escherichia coli AppA phytase and the HAC1 transcriptional activator using a bidirectional promoter. Phytase production was characterized in shake flasks and did not reflect industrial conditions. In the present study, phytase expression was explored and optimized using instrumented fermenters in continuous and fed-batch modes. First, the production of phytase was investigated under glucose de-repression in continuous culture at three dilution factors, 0.5 d-1 , 1 d-1 , and 1.5 d-1 . The fermenter parameters of these cultures were used to inform a kinetic model in batch and fed-batch modes for growth and phytase production. The kinetic model developed aided to design the glucose-feeding profile of a fed-batch culture. Kinetic model simulations under glucose de-repression and fed-batch conditions identified optimal phytase productivity at the specific growth rate of 0.041 h-1 . Validation of the model simulation with experimental data confirmed the feasibility of the model to predict phytase production in our newly engineered strain. Methanol was used only to induce the expression of phytase at high cell densities. Our results showed that high phytase production required two stages, the first stage used glucose under de-repression conditions to generate biomass while expressing phytase, and stage two used methanol to induce phytase expression. The production of phytase was improved 3.5-fold by methanol induction compared to the expression with glucose alone under de-repression conditions to a final phytase activity of 12.65 MU/L. This final volumetric phytase production represented an approximate 36-fold change compared to the flask fermentations. Finally, the phytase protein produced was assayed to confirm its molecular weight, and pH and temperature profiles. This study highlights the importance of optimizing protein production in P. pastoris when using novel promoters and presents a general approach to performing bioprocess optimization in this important production host.

Non-covalent binding tags for batch and flow biocatalysis.

Enzyme immobilization offers considerable advantage for biocatalysis in batch and continuous flow reactions. However, many currently available immobilization methods require that the surface of the carrier is chemically modified to allow site specific interactions with their cognate enzymes, which requires specific processing steps and incurs associated costs. Two carriers (cellulose and silica) were investigated here, initially using fluorescent proteins as models to study binding, followed by assessment of industrially relevant enzyme performance (transaminases and an imine reductase/glucose oxidoreductase fusion). Two previously described binding tags, the 17 amino acid long silica-binding peptide from the Bacillus cereus CotB protein and the cellulose binding domain from the Clostridium thermocellum, were fused to a range of proteins without impairing their heterologous expression. When fused to a fluorescent protein both tags conferred high avidity specific binding with their respective carriers (low nanomolar Kd values). The CotB peptide (CotB1p) induced protein aggregation in the transaminase and imine reductase/glucose oxidoreductase fusions when incubated with the silica carrier. The Clostridium thermocellum cellulose binding domain (CBDclos) allowed immobilization of all the proteins tested, but immobilization led to loss of enzymatic activity in the transaminases (< 2-fold) and imine reductase/glucose oxidoreductase fusion (> 80%). A transaminase-CBDclos fusion was then successfully used to demonstrate the application of the binding tag in repetitive batch and a continuous-flow reactor.

An enhanced electron transport chain improved astaxanthin production in Phaffia rhodozyma.

Astaxanthin (AX) is a carotenoid pigment with antioxidant properties widely used as a feed supplement. Wild-type strains of Phaffia rhodozyma naturally produce low AX yields, but we increased AX yields 50-fold in previous research using random mutagenesis of P. rhodozyma CBS6938 and fermentation optimization. On that study, genome changes were linked with phenotype, but relevant metabolic changes were not resolved. In this study, the wild-type and the superior P. rhodozyma mutant strains were grown in chemically defined media and instrumented fermenters. Differential kinetic, metabolomics, and transcriptomics data were collected. Our results suggest that carotenoid production was mainly associated with cell growth and had a positive regulation of central carbon metabolism metabolites, amino acids, and fatty acids. In the stationary phase, amino acids associated with the TCA cycle increased, but most of the fatty acids and central carbon metabolism metabolites decreased. TCA cycle metabolites were in abundance and media supplementation of citrate, malate, α-ketoglutarate, succinate, or fumarate increased AX production in the mutant strain. Transcriptomic data correlated with the metabolic and genomic data and found a positive regulation of genes associated with the electron transport chain suggesting this to be the main driver for improved AX production in the mutant strain.

Oxidative stress induced by plasma-activated water stimulates astaxanthin production in Phaffia rhodozyma.

Astaxanthin is used extensively in the nutraceutical, aquaculture, and cosmetic industries. The current market necessitates higher astaxanthin production from Phaffia rhodozyma (P. rhodozyma) due to its higher cost compared to chemical synthesis. In this study, a bubble discharge reactor was developed to generate plasma-activated water (PAW) to produce PAW-made yeast malt (YM) medium. Due to oxidative stress induced by PAW, strains cultured in 15 and 30 min-treated PAW-made medium produced 7.9 ± 1.2 % and 12.6 ± 1.4 % more carotenoids with 15.5 ± 3.3 % and 22.1 ± 1.3 % more astaxanthin, respectively. Reactive oxygen species (ROS) assay results showed that ROS generated by plasma-water interactions elevated intracellular ROS levels. Proteomic analysis revealed increased expression of proteins involved in the cellular response to oxidative stress as well as carotenoid biosynthesis, both of which contribute to higher yields of astaxanthin. Overall, this study supports the potential of PAW to increase astaxanthin yields for industrial-scale production.

Bioengineered textiles with peptide binders that capture SARS-CoV-2 viral particles.

The use of personal protective equipment (PPE), face masks and ventilation are key strategies to control the transmission of respiratory viruses. However, most PPE provides physical protection that only partially prevents the transmission of viral particles. Here, we develop textiles with integrated peptide binders that capture viral particles. We fuse peptides capable of binding the receptor domain of the spike protein on the SARS-CoV-2 capsid to the cellulose-binding domain from the Trichoderma reesei cellobiohydrolase II protein. The hybrid peptides can be attached to the cellulose fibres in cotton and capture SARS-CoV-2 viral particles with high affinity. The resulting bioengineered cotton captures 114,000 infective virus particles per cm2 and reduces onwards SARS-CoV-2 infection of cells by 500-fold. The hybrid peptides could be easily modified to capture and control the spread of other infectious pathogens or for attachment to different materials. We anticipate the use of bioengineered protective textiles in PPE, facemasks, ventilation, and furnishings will provide additional protection to the airborne or fomite transmission of viruses.

Towards commercial levels of astaxanthin production in Phaffia rhodozyma.

Astaxanthin (AX) is a potent antioxidant with increasing biotechnological and commercial potential as a feed supplement, and gives salmonids and crustaceans their attractive characteristic pink color. The red yeast Phaffia rhodozyma naturally produces AX as its main fermentation product but wild-type strains and those previously generated through classical random mutagenesis produce low yields of AX. Existing strains do not meet commercial economic requirements, fundamentally due to a lack of understanding of the underlying mechanisms and genotype-phenotype associations regarding AX production in P. rhodozyma. In the present study, screening of P. rhodozyma CBS 6938 mutant strains generated through chemical and ultra violet radiation mutagenesis delivered increased AX production yields that were then maximized using culture media optimization and fed-batch culture kinetic modeling. The whole genomes of the wild-type and eight increased production strains were sequenced to identify genomic changes. The selected strains produced 50-fold more AX than the wild-type strain with a total biomass of around 100 gDCW/L and a carotenoid production of 1 g/L. Genomic variant analyses found 368 conserved mutations across the selected strains with important mutations found in protein coding regions associated with regulators and catalysts of AX precursors in the mevalonate pathway, the electron transport chain, oxidative stress mechanisms, and carotenogenesis.

Highly efficient production of transfructosylating enzymes using low-cost sugarcane molasses by A. pullulans FRR 5284.

Fructooligosaccharides (FOS) are a type of important prebiotics and produced by transfructosylating enzymes. In this study, sugarcane molasses was used as the substrate for production of transfructosylating enzymes by Aureobasidium pullulans FRR 5284. NaNO3 was a superior nitrogen source to yeast extract for production of transfructosylating enzymes by A. pullulans FRR 5284 and decreasing the ratio of NaNO3 to yeast extract nitrogen from 1:0 to 1:1 resulted in the reduction of the total transfructosylating activity from 109.8 U/mL to 82.5 U/mL. The addition of only 4.4 g/L NaNO3 into molasses-based medium containing 100 g/L mono- and di-saccharides resulted in total transfructosylating activity of 123.8 U/mL. Scale-up of the A. pullulans FRR 5284 transfructosylating enzyme production process from shake flasks to 1 L bioreactors improved the enzyme activity and productivity to 171.7 U/mL and 3.58 U/mL/h, 39% and 108% higher than those achieved from shake flasks, respectively. Sucrose (500 g/L) was used as a substrate for extracellular, intracellular, and total A. pullulans FRR 5284 transfructosylating enzymes, with a maximum yield of 61%. Intracellular, extracellular, and total A. pullulans FRR 5284 transfructosylating enzymes from different production systems resulted in different FOS profiles, indicating that FOS profiles can be controlled by adjusting intracellular and extracellular enzyme ratios and, hence prebiotic activity.

Transformation of sugarcane molasses into fructooligosaccharides with enhanced prebiotic activity using whole-cell biocatalysts from Aureobasidium pullulans FRR 5284 and an invertase-deficient Saccharomyces cerevisiae 1403-7A.

Fructooligosaccharides (FOS) can be used as feed prebiotics, but are limited by high production costs. In this study, low-cost sugarcane molasses was used to produce whole-cell biocatalysts containing transfructosylating enzymes by Aureobasidium pullulans FRR 5284, followed by FOS production from molasses using the whole-cells of A. pullulans. A. pullulans in molasses-based medium produced cells and broth with a total transfructosylating activity of 123.6 U/mL compared to 61.0 and 85.8 U/mL in synthetic molasses-based and sucrose-based media, respectively. It was found that inclusion of glucose in sucrose medium reduced both transfructosylating and hydrolytic activities of the produced cells and broth. With the use of pure glucose medium, cells and broth had very low levels of transfructosylating activities and hydrolytic activities were not detected. These results indicated that A. pullulans FRR 5284 produced both constitutive and inducible enzymes in sucrose-rich media, such as molasses while it only produced constitutive enzymes in the glucose media. Furthermore, treatment of FOS solutions generated from sucrose-rich solutions using an invertase-deficient Saccharomyces yeast converted glucose to ethanol and acetic acid and improved FOS content in total sugars by 20-30%. Treated FOS derived from molasses improved the in vitro growth of nine probiotic strains by 9-63% compared to a commercial FOS in 12 h incubation. This study demonstrated the potential of using molasses to produce FOS for feed application.

High-Efficiency Biocatalytic Conversion of Thebaine to Codeine.

An enzymatic biosynthesis approach is described for codeine, the most widely used medicinal opiate, providing a more environmentally sustainable alternative to current chemical conversion, with yields and productivity compatible with industrial production. Escherichia coli strains were engineered to express key enzymes from poppy, including the recently discovered neopinone isomerase, producing codeine from thebaine. We show that compartmentalization of these enzymes in different cells is an effective strategy that allows active spatial and temporal control of reactions, increasing yield and volumetric productivity and reducing byproduct generation. Codeine is produced at a yield of 64% and a volumetric productivity of 0.19 g/(L·h), providing the basis for an industrially applicable aqueous whole-cell biotransformation process. This approach could be used to redirect thebaine-rich feedstocks arising from the U.S. reduction of opioid manufacturing quotas or applied to enable total biosynthesis and may have broader applicability to other medicinal plant compounds.

Co-utilization of acidified glycerol pretreated-sugarcane bagasse for microbial oil production by a novel Rhodosporidium strain.

Acidified glycerol pretreatment is very effective to deconstruct lignocellulosics for producing glucose. Co-utilization of pretreated biomass and residual glycerol to bioproducts could reduce the costs associated with biomass wash and solvent recovery. In this study, a novel strain Rhodosporidium toruloides RP 15, isolated from sugarcane bagasse, was selected and tested for coconversion of pretreated biomass and residual glycerol to microbial oils. In the screening trails, Rh. toruloides RP 15 demonstrated the highest oil production capacity on glucose, xylose, and glycerol among the 10 strains. At the optimal C:N molar ratio of 140:1, this strain accumulated 56.7, 38.3, and 54.7% microbial oils based on dry cell biomass with 30 g/L glucose, xylose, and glycerol, respectively. Furthermore, sugarcane bagasse medium containing 32.6 g/L glucose from glycerol-pretreated bagasse and 23.4 g/L glycerol from pretreatment hydrolysate were used to produce microbial oils by Rh. toruloides RP 15. Under the preliminary conditions without pH control, this strain produced 7.7 g/L oil with an oil content of 59.8%, which was comparable or better than those achieved with a synthetic medium. In addition, this strain also produced 3.5 mg/L carotenoid as a by-product. It is expected that microbial oil production can be significantly improved through process optimization.

Improved fermentation efficiency of S. cerevisiae by changing glycolytic metabolic pathways with plasma agitation.

Production of ethanol by the yeast Saccharomyces cerevisiae is a process of global importance. In these processes, productivities and yields are pushed to their maximum possible values leading to cellular stress. Transient and lasting enhancements in tolerance and performance have been obtained by genetic engineering, forced evolution, and exposure to moderate levels of chemical and/or physical stimuli, yet the drawbacks of these methods include cost, and multi-step, complex and lengthy treatment protocols. Here, plasma agitation is shown to rapidly induce desirable phenotypic changes in S. cerevisiae after a single treatment, resulting in improved conversion of glucose to ethanol. With a complex environment rich in energetic electrons, highly-reactive chemical species, photons, and gas flow effects, plasma treatment simultaneously mimics exposure to multiple environmental stressors. A single treatment of up to 10 minutes performed using an atmospheric pressure plasma jet was sufficient to induce changes in cell membrane structure, and increased hexokinase 2 activity and secondary metabolite production. These results suggest that plasma treatment is a promising strategy that can contribute to improving metabolic activity in industrial microbial strains, and thus the practicality and economics of industrial fermentations.

A survey of the 2010 quartz crystal microbalance literature.

In 2010 there has again been an increase in the number of papers published involving piezoelectric acoustic sensors, or quartz crystal microbalances (QCM), when compared to the last period reviewed 2006-2009. The average number of QCM publications per annum was 124 in the period 2001-2005, 223 in the period 2006-9, and 273 in 2010. There are trends towards increasing use of QCM in the study of protein adsorption to surfaces (93% increase), homeostasis (67% increase), protein-protein interactions (40% increase), and carbohydrates (43% increase). New commercial systems have been released that are driving the uptake of the technology for characterisation of binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights theoretical and practical aspects of the principals that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells, and membrane interfaces.

Enantioselective epoxidation of linolenic acid catalysed by cytochrome P450(BM3) from Bacillus megaterium.

Cytochrome P450(BM3), from Bacillus megaterium, catalyses the epoxidation of linolenic acid yielding 15,16-epoxyoctadeca-9,12-dienoic acid with complete regio- and moderate enantio-selectivity (60% ee). The absolute configuration of the product is tentatively assigned as 15(R),16(S)-. The Michaelis-Menten parameters kcat and Km for the reaction were determined to be 3126 +/- 226 min(-1) and 24 +/- 6 microM respectively.

Identification of broad specificity P450CAM variants by primary screening against indole as substrate.

High-throughput screening of cytochrome P450CAM libraries, for their ability to oxidise indole to indigo and indirubin, has resulted in the identification of variants with activity towards the structurally unrelated substrate diphenylmethane.

Distamycin A affects the stability of NF-kappaB p50-DNA complexes in a sequence-dependent manner.

The effect of two different DNA minor groove binding molecules, Hoechst 33258 and distamycin A, on the binding kinetics of NF-kappaB p50 to three different specific DNA sequences was studied at various salt concentrations. Distamycin A was shown to significantly increase the dissociation rate constant of p50 from the sequences PRDII (5'-GGGAAATTCC-3') and Ig-kappa B (5'-GGGACTTTCC-3') but had a negligible effect on the dissociation from the palindromic target-kappaB binding site (5'-GGGAATTCCC-3'). By comparison, the effect of Hoechst 33258 on binding of p50 to each sequence was found to be minimal. The dissociation rates for the protein--DNA complexes increased at higher potassium chloride concentrations for the PRDII and Ig-kappaB binding motifs and this effect was magnified by distamycin A. In contrast, p50 bound to the palindromic target-kappaB site with a much higher intrinsic affinity and exhibited a significantly reduced salt dependence of binding over the ionic strength range studied, retaining a K(D) of less than 10 pM at 150 mM KCl. Our results demonstrate that the DNA binding kinetics of p50 and their salt dependence is strongly sequence-dependent and, in addition, that the binding of p50 to DNA can be influenced by the addition of minor groove-binding drugs in a sequence-dependent manner.

Biotechnology. Paper Alert.

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in biotechnology.