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Synthetic biology enables the production of small molecules by recombinant microbes for pharma, food, and materials applications. The secretion of products reduces the cost of separation and purification, but it is challenging to engineer due to the limited understanding of the transporter proteins' functions. Here we describe a method for genome-wide transporter disruption that, in combination with a metabolite biosensor, enables the identification of transporters impacting the production of a given target metabolite in yeast Saccharomyces cerevisiae. We applied the method to study the transport of xenobiotic compounds, cis,cis-muconic acid (CCM), protocatechuic acid (PCA), and betaxanthins. We found 22 transporters that influenced the production of CCM or PCA. The transporter of the 12-spanner drug:H(+) antiporter (DHA1) family Tpo2p was further confirmed to import CCM and PCA in Xenopus expression assays. We also identified three transporter proteins (Qdr1p, Qdr2p, and Apl1p) involved in betaxanthins transport. In summary, the described method enables high-throughput transporter identification for small molecules in cell factories., Highlights • Transporter engineering is important in strain development. • 361 non-essential native transporters can be disrupted via CRISPR-Cas9 in yeast S. cerevisiae. • Biosensors enable high-throughput screening of transporter mutants. • Transport of cis,cis-muconic (CCM), protocatechuic (PCA) acids, and betaxanthins was engineered. • Tpo2p was validated as an importer of CCM and PCA in Xenopus expression assays.

Background Cell line-specific, genome-scale metabolic models enable rigorous and systematic in silico investigation of cellular metabolism. Such models have recently become available for Chinese hamster ovary (CHO) cells. However, a key ingredient, namely an experimentally validated biomass function that summarizes the cellular composition, was so far missing. Here, we close this gap by providing extensive experimental data on the biomass composition of 13 parental and producer CHO cell lines under various conditions. Results We report total protein, lipid, DNA, RNA and carbohydrate content, cell dry mass, and detailed protein and lipid composition. Furthermore, we present meticulous data on exchange rates between cells and environment and provide detailed experimental protocols on how to determine all of the above. The biomass composition is converted into cell line- and condition-specific biomass functions for use in cell line-specific, genome-scale metabolic models of CHO. Finally, flux balance analysis (FBA) is used to demonstrate consistency between in silico predictions and experimental analysis. Conclusions Our study reveals a strong variability of the total protein content and cell dry mass across cell lines. However, the relative amino acid composition is independent of the cell line and condition and thus needs not be explicitly measured for each new cell line. In contrast, the lipid composition is strongly influenced by the growth media and thus will have to be determined in each case. These cell line-specific variations in biomass composition have a small impact on growth rate predictions with FBA, as inaccuracies in the predictions are rather dominated by inaccuracies in the exchange rate spectra. Cell-specific biomass variations only become important if the experimental errors in the exchange rate spectra drop below twenty percent.

Rosmarinic acid is a hydroxycinnamic acid ester commonly found in the Boraginaceae and Lamiaceae plant families. It exhibits various biological activities, including antioxidant, anti-inflammatory, antibacterial, antiallergic, and antiviral properties. Rosmarinic acid is used as a food and cosmetic ingredient, and several pharmaceutical applications have been suggested as well. Rosmarinic acid is currently produced by extraction from plants or chemical synthesis; however, due to limited availability of the plant sources and the complexity of the chemical synthesis method, there is an increasing interest in producing this compound by microbial fermentation. In this study, we aimed to produce rosmarinic acid by engineered baker's yeast

Rosmarinic acid is a hydroxycinnamic acid ester commonly found in the Boraginaceae and Lamiaceae plant families. It exhibits various biological activities, including antioxidant, anti-inflammatory, antibacterial, antiallergic, and antiviral properties. Rosmarinic acid is used as a food and cosmetic ingredient, and several pharmaceutical applications have been suggested as well. Rosmarinic acid is currently produced by extraction from plants or chemical synthesis; however, due to limited availability of the plant sources and the complexity of the chemical synthesis method, there is an increasing interest in producing this compound by microbial fermentation. In this study, we aimed to produce rosmarinic acid by engineered baker's yeast Saccharomyces cerevisiae. Multiple biosynthetic pathway variants, carrying only plant genes or a combination of plant and Escherichia coli genes, were implemented using a full factorial design of experiment. Through analysis of variances, the effect of each enzyme variant (factors), together with possible interactions between these factors, was assessed. The best pathway variant produced 2.95 ± 0.08 mg/L rosmarinic acid in mineral medium with glucose as the sole carbon source. Increasing the copy number of rosmarinic acid biosynthetic genes increased the titer to 5.93 ± 0.06 mg/L. The study shows the feasibility of producing rosmarinic acid by yeast fermentation.

Fast metabolite quantification methods are required for high throughput screening of microbial strains obtained by combinatorial or evolutionary engineering approaches. In this study, a rapid RIP-LC-MS/MS (RapidRIP) method for high-throughput quantitative metabolomics was developed and validated that was capable of quantifying 102 metabolites from central, amino acid, energy, nucleotide, and cofactor metabolism in less than 5 minutes. The method was shown to have comparable sensitivity and resolving capability as compared to a full length RIP-LC-MS/MS method (FullRIP). The RapidRIP method was used to quantify the metabolome of seven industrial strains of E. coli revealing significant differences in glycolytic, pentose phosphate, TCA cycle, amino acid, and energy and cofactor metabolites were found. These differences translated to statistically and biologically significant differences in thermodynamics of biochemical reactions between strains that could have implications when choosing a host for bioprocessing.

L-serine is a promising building block biochemical with a high theoretical production yield from glucose. Toxicity of L-serine is however prohibitive for high-titer production in E. coli. Here, E. coli lacking L-serine degradation pathways was evolved for improved tolerance by gradually increasing L-serine concentration from 3 to 100g/L using adaptive laboratory evolution (ALE). Genome sequencing of isolated clones revealed multiplication of genetic regions, as well as mutations in thrA, thereby showing a potential mechanism of serine inhibition. Additional mutations were evaluated by MAGE combined with amplicon sequencing, revealing role of rho, lrp, pykF, eno, and rpoB on tolerance and fitness in minimal medium. Production using the tolerant strains resulted in 37g/L of L-serine with a 24% mass yield. The resulting titer is similar to the highest production reported for any organism thereby highlighting the potential of ALE for industrial biotechnology.

We present a selection design that couples S-adenosylmethionine–dependent methylation to growth. We demonstrate its use in improving the enzyme activities of not only N-type and O-type methyltransferases by 2-fold but also an acetyltransferase of another enzyme category when linked to a methylation pathway in Escherichia coli using adaptive laboratory evolution. We also demonstrate its application for drug discovery using a catechol O-methyltransferase and its inhibitors entacapone and tolcapone. Implementation of this design in Saccharomyces cerevisiae is also demonstrated., Author summary Many important biological processes require methylation, e.g., DNA methylation and synthesis of flavoring compounds, neurotransmitters, and antibiotics. Most methylation reactions in cells are catalyzed by S-adenosylmethionine (SAM)–dependent methyltransferases (Mtases) using SAM as a methyl donor. Thus, SAM-dependent Mtases have become an important enzyme category of biotechnological interests and as healthcare targets. However, functional implementation and engineering of SAM-dependent Mtases remains difficult and is neither cost effective nor high throughput. Here, we are able to address these challenges by establishing a synthetic biology approach, which links Mtase activity to cell growth such that higher Mtase activity ultimately leads to faster cell growth. We show that better-performing variants of the examined Mtases can be readily obtained by growth selection after repetitive cell passages. We also demonstrate the usefulness of our approach for discovery of Mtase-specific drug candidates. We further show our approach is not only applicable in bacteria, exemplified by Escherichia coli, but also in eurkaryotic organisms such as budding yeast Saccharomyces cerevisiae.

L-serine is a widely used amino acid that has been proposed as a potential building block biochemical. The high theoretical yield from glucose makes a fermentation based production attractive. In order to achieve this goal, serine degradation to pyruvate and glycine in E. coli MG1655 was prevented by deletion of three L-serine deaminases sdaA, sdaB, and tdcG, as well as serine hydroxyl methyl transferase (SHMT) encoded by glyA. Upon overexpression of the serine production pathway, consisting of a feedback resistant version of serA along with serB and serC, this quadruple deletion strain showed a very high serine production yield (0.45 g/g glucose) during small-scale batch fermentation in minimal medium. Serine, however, was found to be highly toxic even at low concentrations to this strain, which lead to slow growth and production during fed batch fermentation, resulting in a serine production of 8.3 g/L. The production strain was therefore evolved by random mutagenesis to achieve increased tolerance towards serine. Additionally, overexpression of eamA, a cysteine/homoserine transporter was demonstrated to increase serine tolerance from 1.6 g/L to 25 g/L. During fed batch fermentation, the resulting strain lead to the serine production titer of 11.7 g/L with yield of 0.43 g/g glucose, which is the highest yield reported so far for any organism.

Background In the future, oil- and gas-derived polymers may be replaced with bio-based polymers, produced from renewable feedstocks using engineered cell factories. Acrylic acid and acrylic esters with an estimated world annual production of approximately 6 million tons by 2017 can be derived from 3-hydroxypropionic acid (3HP), which can be produced by microbial fermentation. For an economically viable process 3HP must be produced at high titer, rate and yield and preferably at low pH to minimize downstream processing costs. Results Here we describe the metabolic engineering of baker’s yeast Saccharomyces cerevisiae for biosynthesis of 3HP via a malonyl-CoA reductase (MCR)-dependent pathway. Integration of multiple copies of MCR from Chloroflexus aurantiacus and of phosphorylation-deficient acetyl-CoA carboxylase ACC1 genes into the genome of yeast increased 3HP titer fivefold in comparison with single integration. Furthermore we optimized the supply of acetyl-CoA by overexpressing native pyruvate decarboxylase PDC1, aldehyde dehydrogenase ALD6, and acetyl-CoA synthase from Salmonella entericaSEacsL641P. Finally we engineered the cofactor specificity of the glyceraldehyde-3-phosphate dehydrogenase to increase the intracellular production of NADPH at the expense of NADH and thus improve 3HP production and reduce formation of glycerol as by-product. The final strain produced 9.8 ± 0.4 g L−1 3HP with a yield of 13 % C-mol C-mol−1 glucose after 100 h in carbon-limited fed-batch cultivation at pH 5. The 3HP-producing strain was characterized by 13C metabolic flux analysis and by transcriptome analysis, which revealed some unexpected consequences of the undertaken metabolic engineering strategy, and based on this data, future metabolic engineering directions are proposed. Conclusions In this study, S. cerevisiae was engineered for high-level production of 3HP by increasing the copy numbers of biosynthetic genes and improving flux towards precursors and redox cofactors. This strain represents a good platform for further optimization of 3HP production and hence an important step towards potential commercial bio-based production of 3HP. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0451-5) contains supplementary material, which is available to authorized users.

In this study, field trials on fine and coarse spray quality application of pesticides on apples were performed. The main objectives were to study the variation of pesticide residue levels in individual fruits versus composite samples, and the effect of standard fine spray quality application versus coarse spray quality application on residue levels. The applications included boscalid, bupirimate, captan, fenoxycarb, indoxacarb, pirimicarb, pyraclostrobin and thiophanate-methyl. Apples were collected from four zones in the tree and pesticide residues were detected in the individual apples. None of the results for the pesticides residues measured in individual apples exceeded the EU Maximum Residue Levels (MRLs). However, there was a large variation in the residues levels in the apples, with levels from 0.01 to 1.4 mg kg −1 for captan, the pesticide with the highest variation, and from 0.01 to 0.2 mg kg −1 for pyraclostrobin, the pesticide with the lowest variation. Residues of fenoxycarb and indoxacarb were only found in a few apples, probably due to the early application time of these two compounds. The evaluation of the effect of spray quality did not show any major difference between fine and coarse spray quality, except for carbendazim, the degradation product of thiophanate-methyl, where fine spray quality resulted in higher carbendazim residue levels than coarse spray quality. To examine the relationship between individual results and average results from ten apples, 20 composite samples were statistically constructed from sets of ten of the individual results. The variability factors for the individual samples ( n = 80) at the 97.5 percentile were calculated for both standard and air induction nozzle application and were in the range of 0.9–9.4. The variability factor of seven used when EU member states calculate possible exceeding of Acute Reference Dose (ARfD) was adequate to encompass almost all the average results from the analyses of ten individual apples. However, for captan up to 9% of the results were not covered depending on which of the mathematically constructed composite concentrations was chosen. The variability factor of three, recommend by Codex, seems to be too low, because up to 30% of the apple samples for captan were not covered if the worst case scenario was chosen. The factor of three seems was also too low for thiophanate-methyl.

The aim of this study was to investigate the amount of pesticide residues in fruits and vegetables from South America. A total of 724 samples of 46 different fruits and vegetables from eight South American countries were collected in 2007. In 19% of the samples no residues were found, 72% of samples contained pesticide residues at or below MRL, and 8.4% of samples contained pesticide residues above MRL. Thiabendazole, imazalil and chlorpyrifos were the pesticide most frequently found. Thirty-seven pesticides were found with frequencies higher that 1% in the samples. The results emphasize the need for continuous monitoring of pesticide residues, especially in imported fruits and vegetables.

The differences in residue pattern between Italy and South Africa, the main exporters of table grapes to the Danish market, were investigated. The results showed no major differences with respect to the number of samples with residues, with residues being found in 54-78% of the samples. Exceedances of the European Union maximum residue limit (MRL) were found in five samples from Italy. A number of samples were rinsed to study the possible reduction of residues. For copper, iprodione, procymidone and dithiocarbamates a significant effect of rinsing was found (20-49% reduction of residues). However, no significant effect was found for organophosphorus pesticides and pyrethroids, whereas the number of samples with residues of benzilates, phenylamids and triazoles was insufficient to demonstrate any significant effects. An intake calculation showed that the average intake from Italian grapes was 3.9 microg day(-1) for pesticides and 21 microg day(-1) for copper. Correspondingly, the intakes from South African grapes were 2.6 and 5.7 microg day(-1), respectively. When the total exposure of pesticides from grapes were related to acceptable daily intake, expressed as the sum of Hazard Quotients, the exposure were approximately 0.5% for Italian samples and 1% for South African samples.

L-serine is a widely used amino acid that has been proposed as a potential building block biochemical. The high theoretical yield from glucose makes a fermentation based production attractive. In order to achieve this goal, serine degradation to pyruvate and glycine in E. coli MG1655 was prevented by deletion of three L-serine deaminases sdaA, sdaB, and tdcG, as well as serine hydroxyl methyl transferase (SHMT) encoded by glyA. Upon overexpression of the serine production pathway, consisting of a feedback resistant version of serA along with serB and serC, this quadruple deletion strain showed a very high serine production yield (0.45 g/g glucose) during small-scale batch fermentation in minimal medium. Serine, however, was found to be highly toxic even at low concentrations to this strain, which lead to slow growth and production during fed batch fermentation, resulting in a serine production of 8.3 g/L. The production strain was therefore evolved by random mutagenesis to achieve increased tolerance towards serine. Additionally, overexpression of eamA, a cysteine/homoserine transporter was demonstrated to increase serine tolerance from 1.6 g/L to 25 g/L. During fed batch fermentation, the resulting strain lead to the serine production titer of 11.7 g/L with yield of 0.43 g/g glucose, which is the highest yield reported so far for any organism.

A method for analysing carbamates and other relatively polar pesticides by LC–MS–MS with electrospray ionisation has been developed. The method is based on extraction by ultrasonication using a methanolic ammonium acetate–acetic acid buffer. After centrifugation the samples are filtered in Miniprep filter HPLC vials and detected by LC–MS–MS. To compensate for variations in the MS response [ 13 C 6 ]-carbaryl was used as internal standard and matrix-matched pesticide solutions were used as external standards for the quantification. The method has been validated for the matrices apple, avocado, carrot, lettuce, orange, potato and wheat at the spiking levels—0.02; 0.04 and 0.20 mg kg−1. Recoveries were generally in the range 70–120%. Results from participation in three intercomparisons proved the accuracy of the method. As the analytical procedure does not include any concentration or cleanup steps, it is easy and fast to perform, making it applicable for routine analysis in large pesticide monitoring programmes.

An HPLC-MS/MS method for the analysis of three pesticides in strawberries was developed and validated. Recoveries were measured at three spiking levels and ranged from 85 to 99% (mean recoveries). The effects of processing of strawberries ranging from rinsing to jam production were investigated for the three fungicides tolylfluanid, fenhexamid and pyrimethanil, which were applied under field conditions. Kresoxim-methyl was also applied in the field, but was not found in any of the samples investigated. The effect of parameters such as preharvest interval, dose, harvest time and observed pesticide concentration after harvest (initial concentration, mg kg(-1)), were examined with respect to possible reduction of the pesticides. The results from rinsing showed that all three pesticides were reduced on average by 37% for tolylfluanid, by 34% for fenhexamid and by 19% for pyrimethanil. For tolylfluanid and fenhexamid, the initial concentration significantly affected the reduction. For fenhexamid, dose could also have a minor influence on reduction. For pyrimethanil, none of the parameters significantly influenced the reduction. For jam production, cooking significantly reduced tolylfluanid by an average of 91%. For fenhexamid and pyrimethanil, a smaller reduction was seen, 25% and 33%, respectively. The reduction of tolylfluanid and pyrimethanil was affected by the preharvest interval, while fenhexamid was affected by the initial concentration. The unit-to-unit variability of fungicide contents was also investigated and the variability factors for the three fungicides were from 1.9 to 2.8.

An analytical method for separation and quantitative determination of nine dithiocarbamates (DTCs) in fruits and vegetables by using LC-MS/MS was developed, validated and applied to samples purchased in local supermarkets. The nine DTCs were ziram, ferbam, thiram, maneb, zineb, nabam, metiram, mancozeb and propineb. Validation parameters of mean recovery for two matrices at two concentration levels, relative repeatability (RSDr), relative within-laboratory reproducibility (RSDR) and LOD were obtained for the nine DTCs. The results from the analysis of fruits and vegetables served as the basis for an exposure assessment within the given commodities and a risk assessment by comparing the calculated exposure to the acceptable daily intake and acute reference dose for various exposure groups. The analysis indicated positive findings of DTCs in apples, pears, plums, table grapes, papaya and broccoli at concentrations ranging from 0.03 mg/kg to 2.69 mg/kg expressed as the equivalent amount of CS2. None of the values exceeded the Maximum residue level (MRL) set by the European Union, and furthermore, it was not possible to state whether illegal use had taken place or not, because a clear differentiation between the various DTCs in the LC-MS/MS analysis was lacking. The exposure and risk assessment showed that only for maneb in the case of apples and apple juice, the acute reference dose was exceeded for infants in the United Kingdom and for children in Germany, respectively.

A method for the simultaneous determination of 33 pesticides or degradation products together with patulin in apples by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed. The method involved homogenization of the apples, extraction with ammonium acetate-acetic acid solution in methanol-water by ultrasonication, filtration, and determination by LC-MS/MS. The repeatability and within-laboratory reproducibility for the three spiking levels 0.02, 0.04 and 0.2 mg kg(-1) were between 4% and 35%. In general, the repeatability and reproducibility were about 10-20%. The limits of quantification (LOQs) were between 0.01 and 0.14 mg kg(-1). The method was used on incurred samples from parts of the ISAFRUIT project financed by the European Commission under the 6th Framework Programme. Samples were analysed at four different stages: after harvest, after storage (controlled), after a water bath, and after 28 days at room temperature. Pesticide residues were found at all stages, but no significant differences in the concentration were seen between the stages analysed. The concentration decreased significantly only for tolylfluanid after storage at room temperature for 28 days when only 0-6% of the original amount of tolylfluanid remained in the apples. No patulin was found in the apples stored for 28 days at room temperature and no growth of Penicillium expansum was observed on these apples. However, when the apples were inoculated with a spore suspension of P. expansum, high concentrations of patulin were found.

Udgivelsesdato: November Chlormequat is a plant growth regulator widely used on cereals, and there is general concern that it may impair human fertility. A LC-MS/MS method for the analysis of chlormequat in milk and serum was developed and validated in connection with an investigation on the effect of chlormequat on pig reproduction. Validation of the method was based on recovery tests at three spiking levels, determined as double determinations and repeated at least four times. Samples were extracted with methanol-water-acetic acid, centrifuged, filtrated and determined by LC-MS/MS. The mean recoveries were in the range 80-110%, and the LOD was 0.2 ng/g for serum and 0.3 ng/g for milk. The values for repeatability and reproducibility were within 2/3 of the limits given by the Horwitz equation. Samples of pig serum (59) and sow milk (27) were analyzed using the method. Chlormequat was determined in four milk samples in the range of 0.4 ng/g to 1.2 ng/g and in all serum samples in the range of 0.2 ng/g-4.0 ng/g.

Strobilurins are a new class of fungicides that are active against a broad spectrum of fungi. In the present work a GC method for analysis of strobilurin fungicides was validated. The method was based on, extraction with ethyl acetate/cyclohexane, clean-up by gel permeation chromatography, (GPC) and determination of the content by gas chromatography (GC) with electron capture (EC-), nitrogen/phosphorous (NP-), and mass spectrometric (MS-) detection. Three strobilurins, azoxystrobin, kresoxim-methyl and trifloxystrobin were validated on three matrices, wheat, apple and grapes. The validation was based on recovery tests at three or four spiking levels, determined as double determinations and repeated three times (n = 6). The mean recoveries for the three detectors were in the range of 70-114%, and the LODs were between 0.004 mg/kg and 0.014 mg/kg, for all three strobilurins. The values for repeatability and reproducibility were within the limits for repeatability and reproducibility given by the Horwitz equation. Validation was not accepted for azoxystrobin in grapes on all three detectors and for azoxystrobin in apple for the MS-detector. A comparison of matrix-matched standards versus standards in solvent showed varying differences between the two calibration curves.

Lactone flavors with fruity, milky, coconut, and other aromas are widely used in the food and fragrance industries. Lactones are produced by chemical synthesis or by biotransformation of plant-sourced hydroxy fatty acids. We established a novel method to produce flavor lactones from abundant non-hydroxylated fatty acids using yeast cell factories. Oleaginous yeast Yarrowia lipolytica was engineered to perform hydroxylation of fatty acids and chain-shortening via β-oxidation to preferentially twelve or ten carbons. The strains could produce γ-dodecalactone from oleic acid and δ-decalactone from linoleic acid. Through metabolic engineering, the titer was improved 4-fold, and the final strain produced 282 mg/L γ-dodecalactone in a fed-batch bioreactor. The study paves the way for the production of lactones by fermentation of abundant fatty feedstocks.

The estimation of uncertainty of an analytical result has become important in analytical chemistry. It is especially difficult to determine uncertainties for multiresidue methods, e.g. for pesticides in fruit and vegetables, as the varieties of pesticide/commodity combinations are many. In the present study, recommendations from the International Organisation for Standardisation's (ISO) Guide to the Expression of Uncertainty and the EURACHEM/CITAC guide Quantifying Uncertainty in Analytical Measurements were followed to estimate the expanded uncertainties for 153 pesticides in fruit and vegetables. Data from in-house validation were used in the estimation of the uncertainty. No significant difference in the relative standard deviation for reproducibility (RSD(R)) were found between the different concentration levels at concentration levels exceeding 2.5 times the detection limit. Therefore, it was possible to pool the RSD(R) within a single matrix. However, a difference in RSD(R) between matrices was seen, thus the poorest RSD(R) of the investigated matrices was chosen for the uncertainty estimation. The expanded uncertainties ranged from 7 to 78% with an average of 32% and median of 32%. Furthermore, only RSD(R) contributed to the uncertainty estimation.

A proficiency test on incurred and spiked pesticide residues in wheat was organised in 2008. The test material was grown in 2007 and treated in the field with 14 pesticides formulations containing the active substances, alpha-cypermethrin, bifentrin, carbendazim, chlormequat, chlorpyrifos-methyl, difenconazole, epoxiconazole, glyphosate, iprodione, malathion, pirimicarb, prochloraz, spiroxamin and trifloxystrobin. After harvest, the test material was additionally spiked in the laboratory with three pesticides, that where the residues were too low, and axozystrobin. In total, 72 laboratories submitted results and z-scores were calculated for all laboratories and pesticides, except for glyphosate where only five laboratories submitted results and summed weighted z-scores were calculated for the laboratories with a sufficient scope. For several pesticides, the submitted results were strongly depending on the extraction procedure and consequently the assigned values were calculated based on part of the results. Acceptable z-scores were obtained by 56–97% of the participants.