Editorial:4th Applied Synthetic Biology in Europe

International audienc

The CENTAURS race. Performance evaluation of an election algorithm on a ring

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Gene Expression Noise Produces Cell-to-Cell Heterogeneity in Eukaryotic Homologous Recombination Rate

Variation in gene expression among genetically identical individual cells (called gene expression noise) directly contributes to phenotypic diversity. Whether such variation can impact genome stability and lead to variation in genotype remains poorly explored. We addressed this question by investigating whether noise in the expression of genes affecting homologous recombination (HR) activity either directly (RAD52) or indirectly (RAD27) confers cell-to-cell heterogeneity in HR rate in Saccharomyces cerevisiae. Using cell sorting to isolate subpopulations with various expression levels, we show that spontaneous HR rate is highly heterogeneous from cell-to-cell in clonal populations depending on the cellular amount of proteins affecting HR activity. Phleomycin-induced HR is even more heterogeneous, showing that RAD27 expression variation strongly affects the rate of recombination from cell-to-cell. Strong variations in HR rate between subpopulations are not correlated to strong changes in cell cycle stage. Moreover, this heterogeneity occurs even when simultaneously sorting cells at equal expression level of another gene involved in DNA damage response (BMH1) that is upregulated by DNA damage, showing that the initiating DNA damage is not responsible for the observed heterogeneity in HR rate. Thus gene expression noise seems mainly responsible for this phenomenon. Finally, HR rate non-linearly scales with Rad27 levels showing that total amount of HR cannot be explained solely by the time- or population-averaged Rad27 expression. Altogether, our data reveal interplay between heterogeneity at the gene expression and genetic levels in the production of phenotypic diversity with evolutionary consequences from microbial to cancer cell populations

Biochemical and biophysics studies of cell wall of industrial yeasts

Cilj ovog rada je bio odrediti udio komponenti stanične stijenke kvasca Saccharomyces cerevisiae: manoproteina, β-1,3-glukana, β-1,6 glukana i hitina, koristeći novo razvijenu metodu koja se temelji na enzimskim i kemijskim metodama. Ova metoda je testirana na različitim sojevima kvasca i došlo se do zaključka da uvjeti rasta imaju utjecaj na udio staničnih komponenti. Metoda je korištena za procjenu sastava stanične stijenke industrijskih sojeva (autolizirani i osušeni sojevi) koji su bili pod utjecajem različitih fermentacijskih i drugih procesa. Korišteni su i fenotipski testovi da se uoči i potvrdi da rast različitih sojeva ovisi o sastavu hranjive podloge. U drugom dijelu rada je promatran utjecaj etanol stresa na rast te na udio komponenti stanične stijenke različitih laboratorijskih sojeva kvasca.The aim of this study was to quantify the amount of specific components in the cell wall of yeast Saccharomyces cerevisiae, namely mannoproteins, β-1,3-glucans and β-1,6-glucans and chitin using newly developed enzymatic and chemical method. These new methods were validated on various cell wall mutants and it was observed that growth conditions have strong effects on the amount of cell wall components. This method was used to evaluate cell wall composition of industrial yeasts (autolysed and dried yeast) that were subjected to different fermentation and treatment processes. The phenotypic assay was used to confirm and to notice how the growth of various strains depends on composition of medium. The second part of the project was to examine the effect of ethanol stress on cell wall composition and to analyze cell wall composition in industrial yeast cells, to determine whether culture/process conditions have an impact on cell wall composition

Biochemical and biophysics studies of cell wall of industrial yeasts

Cilj ovog rada je bio odrediti udio komponenti stanične stijenke kvasca Saccharomyces cerevisiae: manoproteina, β-1,3-glukana, β-1,6 glukana i hitina, koristeći novo razvijenu metodu koja se temelji na enzimskim i kemijskim metodama. Ova metoda je testirana na različitim sojevima kvasca i došlo se do zaključka da uvjeti rasta imaju utjecaj na udio staničnih komponenti. Metoda je korištena za procjenu sastava stanične stijenke industrijskih sojeva (autolizirani i osušeni sojevi) koji su bili pod utjecajem različitih fermentacijskih i drugih procesa. Korišteni su i fenotipski testovi da se uoči i potvrdi da rast različitih sojeva ovisi o sastavu hranjive podloge. U drugom dijelu rada je promatran utjecaj etanol stresa na rast te na udio komponenti stanične stijenke različitih laboratorijskih sojeva kvasca.The aim of this study was to quantify the amount of specific components in the cell wall of yeast Saccharomyces cerevisiae, namely mannoproteins, β-1,3-glucans and β-1,6-glucans and chitin using newly developed enzymatic and chemical method. These new methods were validated on various cell wall mutants and it was observed that growth conditions have strong effects on the amount of cell wall components. This method was used to evaluate cell wall composition of industrial yeasts (autolysed and dried yeast) that were subjected to different fermentation and treatment processes. The phenotypic assay was used to confirm and to notice how the growth of various strains depends on composition of medium. The second part of the project was to examine the effect of ethanol stress on cell wall composition and to analyze cell wall composition in industrial yeast cells, to determine whether culture/process conditions have an impact on cell wall composition

Optimization of ethylene glycol production from (d)-xylose via a synthetic pathway implemented in Escherichia coli

BACKGROUND: Ethylene glycol (EG) is a bulk chemical that is mainly used as an anti-freezing agent and a raw material in the synthesis of plastics. Production of commercial EG currently exclusively relies on chemical synthesis using fossil resources. Biochemical production of ethylene glycol from renewable resources may be more sustainable. RESULTS: Herein, a synthetic pathway is described that produces EG in Escherichia coli through the action of (d)-xylose isomerase, (d)-xylulose-1-kinase, (d)-xylulose-1-phosphate aldolase, and glycolaldehyde reductase. These reactions were successively catalyzed by the endogenous xylose isomerase (XylA), the heterologously expressed human hexokinase (Khk-C) and aldolase (Aldo-B), and an endogenous glycolaldehyde reductase activity, respectively, which we showed to be encoded by yqhD. The production strain was optimized by deleting the genes encoding for (d)-xylulose-5 kinase (xylB) and glycolaldehyde dehydrogenase (aldA), and by overexpressing the candidate glycolaldehyde reductases YqhD, GldA, and FucO. The strain overproducing FucO was the best EG producer reaching a molar yield of 0.94 in shake flasks, and accumulating 20 g/L EG with a molar yield and productivity of 0.91 and 0.37 g/(L.h), respectively, in a controlled bioreactor under aerobic conditions. CONCLUSIONS: We have demonstrated the feasibility to produce EG from (d)-xylose via a synthetic pathway in E. coli at approximately 90 % of the theoretical yield. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12934-015-0312-7) contains supplementary material, which is available to authorized users

Advances in Metabolic Engineering of Saccharomyces cerevisiae for the Production of Industrially and Clinically Important Chemicals

Sustainable production of chemicals is of increasing importance, due to depletion of petroleum and environmental concerns. In addition to its importance in basic research as a simple, eukaryotic model organism, Saccharomyces cerevisiae has long been exploited in industry because of its physiological properties. And today, the development in genetic engineering toolbox and genome-scale metabolic models of S. cerevisiae has extended its application range to new products and bioprocesses. In addition, evolutionary engineering strategies have been useful in improving cellular properties of S. cerevisiae, such as tolerance to product toxicity and inhibitors. In this chapter, recent metabolic and evolutionary engineering studies that involve S. cerevisiae for the production of bulk chemicals and fine chemicals including flavours and pharmaceuticals are reviewed. It was shown that metabolic engineering particularly allowed the improvement of pharmaceuticals production, which will enable economic and large-scale production of many valuable pharmaceuticals. It is clear that S. cerevisiae will continue to be an important host for future metabolic engineering and metabolic pathway engineering applications to produce a variety of industrially and clinically important chemicals