Project description:A biosensor, consisting of the prokaryotic cis,cis-muconic acid-binding transcriptional activator BenM and an engineered reporter was successfully transplanted into bakers yeast Saccharomyces cerevisiae. RNAseq data used to assess the transcription orthogonality of BenM in yeast cells is presented here.
Project description:Agricultural wastes and other non-food sources can be used to produce biofuels. Despite multiple attempts using engineered yeast strains expressing exogenous genes, the native Saccharomyces cerevisiae produces low amount of second generations of biofuels. Here, we focused on Znf1, a non-fermentable carbon transcription factor and the suppressor protein Bud21 to overcome this challenge. Several mutants of engineered S. cerevisiae strains were engineered to enhance production of biofuels and xylose-derived compounds such as xylitol. This study demonstrates Znf1's novel transcriptional regulatory control of xylose and offer an initial step toward a more sustainable production of advanced biofuels from xylose.
Project description:Model-guided chassis strain design has the potential to accelerate cellfactory development. In this experiment genetic targets were identified in silico and implemented in vivo to design a yeast chassis strain for enhanced production of succinic, malic and fumaric acid. The phenotype of engineered chassis strains was further optimised through adaptive laboratory evolution. RNA-seq analysis of engineered yeast chassis strains, evolved strains and wild-type (CEN.PK background)was performed to determine the effect of engineered gene deletions and evolution on the transcriptome.
Project description:F. Boonekamp et al., (2019) describe an innocuous watermarking strategy for coding regions that enables the discrimination of DNA and mRNA by sequencing through a k-mer approach and facilitates selective editing of watermarked and non-watermarked sequences. Shot-gun proteomics (LFQ) was performed on the parent and the engineered yeast strain. *Corresponding author: Pascale Daran-Lapujade (p.a.s.daran-lapujade@tudelft.nl). Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
Project description:Dataset aims to uncover beneficial mutations on yeast strains (CEN.PK 113-11D based) engineered for polyamine over-production. We observed substantial heterogeneity between colony sizes and polyamine titers obtained between parent and final strains. Further physiological characterization of re-streaked colonies confirmed this phenotype, meaning that the sudden heterogeneity is heritable. Sequencing data presented here is used for identification differences between these mutated and parental strains.
Project description:We have engineered the chromatin-modifying apparatus and formulated a novel technology, termed Clickable Chromatin Enrichment with parallel DNA sequencing (CliEn-seq), to probe genome-wide chromatin modification within living cells. Examine (E)-hex-2-en-5-ynylation mediated by engineered G9a Y1154A and GLP1 Y1211A in HEK293T cells.
Project description:Excess/residual urea is a pervasion problem in wine and Sake fermentation. We sought to reduce residual urea levels (to reduce ethyl carbamate leves) by engineering the Sake yeast strain K7 to constitutively express either the urea amidolyase (Dur1,2) or urea importer (Dur3). We sought to then compare the gene expression profiles of the metabolically engineered yeast strains to the parental strain during fermentation. Engineered strains would hopefully have gene expression profiles that were minimally different from the parental strain.
