"uuid","repository link","title","author","contributor","publication year","abstract","subject topic","language","publication type","publisher","isbn","issn","patent","patent status","bibliographic note","access restriction","embargo date","faculty","department","research group","programme","project","coordinates"
"uuid:69c3e926-0517-4dbc-8635-df290f0e5889","http://resolver.tudelft.nl/uuid:69c3e926-0517-4dbc-8635-df290f0e5889","De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology","Nijkamp, J.F.; Van den Broek, M.A.; Datema, E.; De Kok, S.; Bosman, L.; Luttik, M.A.H.; Daran-Lapujade, P.A.S.; Vongsangnak, W.; Nielsen, J.; Heijne, W.H.M.; Klaassen, P.; Paddon, C.J.; Platt, D.; Kötter, P.; Van Ham, R.C.; Reinders, M.J.T.; Pronk, J.T.; De Ridder, D.; Daran, J.M.","","2012","Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN.PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN.PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN.PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN.PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.","OA-Fund TU Delft","en","journal article","BioMed Central","","","","","","","","Electrical Engineering, Mathematics and Computer Science","Intelligent Systems","","","",""
"uuid:7fe3f786-1291-45e1-b1a2-812d9ec8d4bf","http://resolver.tudelft.nl/uuid:7fe3f786-1291-45e1-b1a2-812d9ec8d4bf","Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production","Harris, D.M.; Van der Krogt, Z.A.; Klaassen, P.; Raamsdonk, L.M.; Hage, S.; Van den Berg, M.A.; Bovenberg, R.A.L.; Pronk, J.T.; Daran, J.M.","","2009","OA Fund TU Delft Background Since the discovery of the antibacterial activity of penicillin by Fleming 80 years ago, improvements of penicillin titer were essentially achieved by classical strain improvement through mutagenesis and screening. The recent sequencing of Penicillium chrysogenum strain Wisconsin1255-54 and the availability of genomics tools such as DNA-microarray offer new perspective. Results In studies on ?-lactam production by P. chrysogenum, addition and omission of a side-chain precursor is commonly used to generate producing and non-producing scenarios. To dissect effects of penicillinG production and of its side-chain precursor phenylacetic acid (PAA), a derivative of a penicillinG high-producing strain without a functional penicillin-biosynthesis gene cluster was constructed. In glucose-limited chemostat cultures of the high-producing and cluster-free strains, PAA addition caused a small reduction of the biomass yield, consistent with PAA acting as a weak-organic-acid uncoupler. Microarray-based analysis on chemostat cultures of the high-producing and cluster-free strains, grown in the presence and absence of PAA, showed that: (i) Absence of a penicillin gene cluster resulted in transcriptional upregulation of a gene cluster putatively involved in production of the secondary metabolite aristolochene and its derivatives, (ii) The homogentisate pathway for PAA catabolism is strongly transcriptionally upregulated in PAA-supplemented cultures (iii) Several genes involved in nitrogen and sulfur metabolism were transcriptionally upregulated under penicillinG producing conditions only, suggesting a drain of amino-acid precursor pools. Furthermore, the number of candidate genes for penicillin transporters was strongly reduced, thus enabling a focusing of functional analysis studies. Conclusion This study demonstrates the usefulness of combinatorial transcriptome analysis in chemostat cultures to dissect effects of biological and process parameters on gene expression regulation. This study provides for the first time clear-cut target genes for metabolic engineering, beyond the three genes of the ?-lactam pathway.","","en","journal article","BioMed Central","","","","","","","","Applied Sciences","Biotechnology","","","",""
"uuid:ccedae52-2933-4189-a121-10b1b4d8ab03","http://resolver.tudelft.nl/uuid:ccedae52-2933-4189-a121-10b1b4d8ab03","Saccharomyces cerevisiae strains tor second-generation ethanol production: from academie exploration to industrial implementation","Jansen, Mickel L.A. (DSM); Bracher, J.M. (TU Delft BT/Industriele Microbiologie); Papapetridis, I. (TU Delft BT/Industriele Microbiologie); Verhoeven, M.D. (TU Delft BT/Industriele Microbiologie); de Bruijn, J.A. (DSM); de Waal, P. (DSM); van Maris, A.J.A. (TU Delft BT/Industriele Microbiologie; AlbaNova University Center); Klaassen, P (DSM); Pronk, J.T. (TU Delft BT/Industriele Microbiologie)","","2017","The recent start-up of several full-scale ‘second generation’ ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains, this minireview describes key metabolic engineering strategies that have been developed to address these challenges. Additionally, it outlines how proof-of-concept studies, often developed in academic settings, can be used for the development of robust strain platforms that meet the requirements for industrial application. Fermentation performance of current engineered industrial S. cerevisiae strains is no longer a bottleneck in efforts to achieve the projected outputs of the first large-scale second-generation ethanol plants. Academic and industrial yeast research will continue to strengthen the economic value position of second-generation ethanol production by further improving fermentation kinetics, product yield and cellular robustness under process conditions.","biofuels; metabolic engineering; ndustrial fermentation; yeast biotechnology; pentose fermentation; biomass hydrolysates","en","journal article","","","","","","","","","","","BT/Industriele Microbiologie","","",""
"uuid:113d8e73-d8f4-4825-92f0-6950a582af0b","http://resolver.tudelft.nl/uuid:113d8e73-d8f4-4825-92f0-6950a582af0b","The Penicillium chrysogenum transporter PcAraT enables high-affinity, glucose-insensitive l-arabinose transport in Saccharomyces cerevisiae","Bracher, J.M. (TU Delft BT/Industriele Microbiologie); Verhoeven, M.D. (TU Delft BT/Industriele Microbiologie); Wisselink, H. Wouter (Isobionics); Crimi, B. (TU Delft BT/Industriele Microbiologie; UMR9002-CNRS-UM); Nijland, Jeroen G. (Rijksuniversiteit Groningen); Driessen, Arnold J.M. (Rijksuniversiteit Groningen); Klaassen, Paul (DSM); van Maris, A.J.A. (TU Delft BT/Industriele Microbiologie; AlbaNova University Center); Daran, J.G. (TU Delft BT/Industriele Microbiologie); Pronk, J.T. (TU Delft BT/Industriele Microbiologie)","","2018","Background: l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these feedstocks by engineered pentose-metabolizing S. cerevisiae strains. Results: Chemostat-based transcriptome analysis yielded 16 putative sugar transporter genes in the filamentous fungus Penicillium chrysogenum whose transcript levels were at least threefold higher in l-arabinose-limited cultures than in d-glucose-limited and ethanol-limited cultures. Of five genes, that encoded putative transport proteins and showed an over 30-fold higher transcript level in l-arabinose-grown cultures compared to d-glucose-grown cultures, only one (Pc20g01790) restored growth on l-arabinose upon expression in an engineered l-arabinose-fermenting S. cerevisiae strain in which the endogenous l-arabinose transporter, GAL2, had been deleted. Sugar transport assays indicated that this fungal transporter, designated as PcAraT, is a high-affinity (K m = 0.13 mM), high-specificity l-arabinose-proton symporter that does not transport d-xylose or d-glucose. An l-arabinose-metabolizing S. cerevisiae strain in which GAL2 was replaced by PcaraT showed 450-fold lower residual substrate concentrations in l-arabinose-limited chemostat cultures than a congenic strain in which l-arabinose import depended on Gal2 (4.2 × 10-3 and 1.8 g L-1, respectively). Inhibition of l-arabinose transport by the most abundant sugars in hydrolysates, d-glucose and d-xylose was far less pronounced than observed with Gal2. Expression of PcAraT in a hexose-phosphorylation-deficient, l-arabinose-metabolizing S. cerevisiae strain enabled growth in media supplemented with both 20 g L-1 l-arabinose and 20 g L-1 d-glucose, which completely inhibited growth of a congenic strain in the same condition that depended on l-arabinose transport via Gal2. Conclusion: Its high affinity and specificity for l-arabinose, combined with limited sensitivity to inhibition by d-glucose and d-xylose, make PcAraT a valuable transporter for application in metabolic engineering strategies aimed at engineering S. cerevisiae strains for efficient conversion of lignocellulosic hydrolysates.","l-Arabinose transporter; Metabolic engineering; Penicillium; Proton symport; Second-generation bioethanol; Sugar transport; Transcriptome; Yeast","en","journal article","","","","","","","","","","","BT/Industriele Microbiologie","","",""