Model-Based Construction And Optimisation Of Versatile Chassis Yeast Strains For Production Of Valuable Lipid And Aromatic Compounds

Livrables

Technological fact sheets on CHASSY strains

NOVA will produce a technological fact sheet of the chassis yeasts developed in this project. This will be used to inform specific SMEs identified by CHASSY as potential lead users of CHASSY technology and platform strains.

Library of branded publishable information (leaflets, posters, booklets, slide-set, etc.)

The development of an effective communication infrastructure to communicate to the relevant stakeholders outside CHASSY will be led by NOVA. Publishable information material (leaflets, brochures) that will be updated as the project progresses will feature in the communication strategy.

The CHASSY public access website up and running

NOVA is responsible for developing an effective communication infrastructure to communicate to the relevant stakeholders outside CHASSY. A website as well as an external platform for displaying information about the project objectives, activities and results to interested parties and stakeholders and the public is an activity that will feature in the communication strategy.

External stakeholder workshop

An external stakeholder workshop will be organised in the final year of the project

Publications

Production of octanoic acid in Saccharomyces cerevisiae : Investigation of new precursor supply engineering strategies and intrinsic limitations

Auteurs: Florian Wernig, Leonie Baumann, Eckhard Boles, Mislav Oreb
Publié dans: Biotechnology and Bioengineering, 2021, ISSN 0006-3592
Éditeur: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.27814

Metabolic Engineering for Unusual Lipid Production in Yarrowia lipolytica

Auteurs: Young-Kyoung Park, Jean-Marc Nicaud
Publié dans: Microorganisms, Numéro 8/12, 2020, Page(s) 1937, ISSN 2076-2607
Éditeur: MDPI
DOI: 10.3390/microorganisms8121937

High-Throughput Screening of an Octanoic Acid Producer Strain Library Enables Detection of New Targets for Increasing Titers in Saccharomyces cerevisiae

Auteurs: Leonie Baumann, Stefan Bruder, Johannes Kabisch, Eckhard Boles, Mislav Oreb
Publié dans: ACS Synthetic Biology, 2021, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.0c00600

Multidimensional engineering of Saccharomyces cerevisiae for efficient synthesis of medium-chain fatty acids

Auteurs: Zhiwei Zhu, Yating Hu, Paulo Gonçalves Teixeira, Rui Pereira, Yun Chen, Verena Siewers, Jens Nielsen
Publié dans: Nature Catalysis, Numéro 3/1, 2020, Page(s) 64-74, ISSN 2520-1158
Éditeur: Nature
DOI: 10.1038/s41929-019-0409-1

A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

Auteurs: Linnea Österberg, Iván Domenzain, Julia Münch, Jens Nielsen, Stefan Hohmann, Marija Cvijovic
Publié dans: PLOS Computational Biology, Numéro 17/4, 2021, Page(s) e1008891, ISSN 1553-7358
Éditeur: PLOS Computational Biology
DOI: 10.1371/journal.pcbi.1008891

Fusing α and β subunits of the fungal fatty acid synthase leads to improved production of fatty acids

Auteurs: Florian Wernig, Sandra Born, Eckhard Boles, Martin Grininger, Mislav Oreb
Publié dans: Scientific Reports, Numéro 10/1, 2020, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-020-66629-y

A Yarrowia lipolytica Strain Engineered for Pyomelanin Production

Auteurs: Macarena Larroude, Djamila Onésime, Olivier Rué, Jean-Marc Nicaud, Tristan Rossignol
Publié dans: Microorganisms, Numéro 9/4, 2021, Page(s) 838, ISSN 2076-2607
Éditeur: MDPI
DOI: 10.3390/microorganisms9040838

Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production

Auteurs: Leonie Baumann, Tyler Doughty, Verena Siewers, Jens Nielsen, Eckhard Boles, Mislav Oreb
Publié dans: FEMS Yeast Research, Numéro 21/2, 2021, ISSN 1567-1356
Éditeur: Blackwell
DOI: 10.1093/femsyr/foab011

Increasing jojoba-like wax ester production in Saccharomyces cerevisiae by enhancing very long-chain, monounsaturated fatty acid synthesis

Auteurs: Leonie Wenning, Christer S. Ejsing, Florian David, Richard R. Sprenger, Jens Nielsen, Verena Siewers
Publié dans: Microbial Cell Factories, Numéro 18/1, 2019, ISSN 1475-2859
Éditeur: BioMed Central
DOI: 10.1186/s12934-019-1098-9

Extracting novel hypotheses and findings from RNA-seq data

Auteurs: Tyler Doughty, Eduard Kerkhoven
Publié dans: FEMS Yeast Research, Numéro 20/2, 2020, ISSN 1567-1356
Éditeur: Blackwell
DOI: 10.1093/femsyr/foaa007

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Auteurs: Benjamín J Sánchez, Cheng Zhang, Avlant Nilsson, Petri‐Jaan Lahtvee, Eduard J Kerkhoven, Jens Nielsen
Publié dans: Molecular Systems Biology, Numéro 13/8, 2017, Page(s) 935, ISSN 1744-4292
Éditeur: Nature Publishing Group
DOI: 10.15252/msb.20167411

Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production

Auteurs: Robert Mans, Jean-Marc G Daran, Jack T Pronk
Publié dans: Current Opinion in Biotechnology, Numéro 50, 2018, Page(s) 47-56, ISSN 0958-1669
Éditeur: Elsevier BV
DOI: 10.1016/j.copbio.2017.10.011

Heterologous transporter expression for improved fatty alcohol secretion in yeast

Auteurs: Yating Hu, Zhiwei Zhu, Jens Nielsen, Verena Siewers
Publié dans: Metabolic Engineering, Numéro 45, 2018, Page(s) 51-58, ISSN 1096-7176
Éditeur: Academic Press
DOI: 10.1016/j.ymben.2017.11.008

Genome editing in Kluyveromyces and Ogataea yeasts using a broad-host-range Cas9/gRNA co-expression plasmid

Auteurs: Hannes Juergens, Javier A Varela, Arthur R Gorter de Vries, Thomas Perli, Veronica J M Gast, Nikola Y Gyurchev, Arun S Rajkumar, Robert Mans, Jack T Pronk, John P Morrissey, Jean-Marc G Daran
Publié dans: FEMS Yeast Research, Numéro 18/3, 2018, ISSN 1567-1364
Éditeur: Oxford Academic
DOI: 10.1093/femsyr/foy012

FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae

Auteurs: Michal A. Świat, Sofia Dashko, Maxime den Ridder, Melanie Wijsman, John van der Oost, Jean-Marc Daran, Pascale Daran-Lapujade
Publié dans: Nucleic Acids Research, Numéro 45/21, 2017, Page(s) 12585-12598, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkx1007

Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals

Auteurs: Tao Yu, Yongjin J. Zhou, Leonie Wenning, Quanli Liu, Anastasia Krivoruchko, Verena Siewers, Jens Nielsen, Florian David
Publié dans: Nature Communications, Numéro 8, 2017, Page(s) 15587, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/ncomms15587

Barriers and opportunities in bio-based production of hydrocarbons

Auteurs: Yongjin J. Zhou, Eduard J. Kerkhoven, Jens Nielsen
Publié dans: Nature Energy, 2018, ISSN 2058-7546
Éditeur: Nature
DOI: 10.1038/s41560-018-0197-x

Synthetic biology tools for engineering Yarrowia lipolytica

Auteurs: M. Larroude, T. Rossignol, J.-M. Nicaud, R. Ledesma-Amaro
Publié dans: Biotechnology Advances, 2018, ISSN 0734-9750
Éditeur: Elsevier BV
DOI: 10.1016/j.biotechadv.2018.10.004

A Yeast-Based Biosensor for Screening of Short- and Medium-Chain Fatty Acid Production

Auteurs: Leonie Baumann, Arun S. Rajkumar, John P. Morrissey, Eckhard Boles, Mislav Oreb
Publié dans: ACS Synthetic Biology, 2018, ISSN 2161-5063
Éditeur: American Chemical Society
DOI: 10.1021/acssynbio.8b00309

Expansion and Diversification of MFS Transporters in Kluyveromyces marxianus

Auteurs: Javier A. Varela, Martina Puricelli, Noemi Montini, John P. Morrissey
Publié dans: Frontiers in Microbiology, Numéro 9, 2019, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2018.03330

Biological Parts for Kluyveromyces marxianus Synthetic Biology

Auteurs: Arun S. Rajkumar, Javier A. Varela, Hannes Juergens, Jean-Marc G. Daran, John P. Morrissey
Publié dans: Frontiers in Bioengineering and Biotechnology, Numéro 7, 2019, ISSN 2296-4185
Éditeur: Frontiers Media SA
DOI: 10.3389/fbioe.2019.00097

A modular Golden Gate toolkit for Yarrowia lipolytica synthetic biology

Auteurs: Macarena Larroude, Young‐Kyoung Park, Paul Soudier, Monika Kubiak, Jean‐Marc Nicaud, Tristan Rossignol
Publié dans: Microbial Biotechnology, 2019, ISSN 1751-7915
Éditeur: John Wiley & Sons Ltd and Society for Applied Microbiology
DOI: 10.1111/1751-7915.13427

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Auteurs: Hongzhong Lu, Feiran Li, Benjamín J. Sánchez, Zhengming Zhu, Gang Li, Iván Domenzain, Simonas Marcišauskas, Petre Mihail Anton, Dimitra Lappa, Christian Lieven, Moritz Emanuel Beber, Nikolaus Sonnenschein, Eduard J. Kerkhoven, Jens Nielsen
Publié dans: Nature Communications, Numéro 10/1, 2019, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-11581-3

Connecting central carbon and aromatic amino acid metabolisms to improve de novo 2-phenylethanol production in Saccharomyces cerevisiae

Auteurs: Else-Jasmijn Hassing, Philip A. de Groot, Vita R. Marquenie, Jack T. Pronk, Jean-Marc G. Daran
Publié dans: Metabolic Engineering, Numéro 56, 2019, Page(s) 165-180, ISSN 1096-7176
Éditeur: Academic Press
DOI: 10.1016/j.ymben.2019.09.011

Author Correction: Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals

Auteurs: Yu, Tao; Zhou, Yongjin J.; Wenning, Leonie; Liu, Quanli; Krivoruchko, Anastasia; Siewers, Verena; Nielsen, Jens; David, Florian
Publié dans: Nature Communications, Numéro 1, 2018, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/ncomms16220

Origin of Lactose Fermentation in Kluyveromyces lactis by Interspecies Transfer of a Neo-functionalized Gene Cluster during Domestication

Auteurs: Javier A. Varela, Martina Puricelli, Raúl A. Ortiz-Merino, Romina Giacomobono, Stephanie Braun-Galleani, Kenneth H. Wolfe, John P. Morrissey
Publié dans: Current Biology, 2019, ISSN 0960-9822
Éditeur: Cell Press
DOI: 10.1016/j.cub.2019.10.044

De novo biosynthesis of 8-hydroxyoctanoic acid via a medium-chain length specific fatty acid synthase and cytochrome P450 in Saccharomyces cerevisiae

Auteurs: Florian Wernig, Eckhard Boles, Mislav Oreb
Publié dans: Metabolic Engineering Communications, Numéro 10, 2020, Page(s) e00111, ISSN 2214-0301
Éditeur: Elsevier BV
DOI: 10.1016/j.mec.2019.e00111

A set of Yarrowia lipolytica CRISPR/Cas9 vectors for exploiting wild-type strain diversity

Auteurs: Macarena Larroude, Heykel Trabelsi, Jean-Marc Nicaud, Tristan Rossignol
Publié dans: Biotechnology Letters, 2020, ISSN 0141-5492
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s10529-020-02805-4

Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts

Auteurs: Tyler W. Doughty, Iván Domenzain, Aaron Millan-Oropeza, Noemi Montini, Philip A. de Groot, Rui Pereira, Jens Nielsen, Céline Henry, Jean-Marc G. Daran, Verena Siewers, John P. Morrissey
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-16073-3

Rational engineering of Kluyveromyces marxianus to create a chassis for the production of aromatic products

Auteurs: Arun S. Rajkumar, John P. Morrissey
Publié dans: Microbial Cell Factories, Numéro 19/1, 2020, ISSN 1475-2859
Éditeur: BioMed Central
DOI: 10.1186/s12934-020-01461-7

Yarrowia lipolytica chassis strains engineered to produce aromatic amino acids via the shikimate pathway

Auteurs: Macarena Larroude, Jean‐Marc Nicaud, Tristan Rossignol
Publié dans: Microbial Biotechnology, 2020, ISSN 1751-7915
Éditeur: Wiley
DOI: 10.1111/1751-7915.13745

Microbiological strategies to produce beer and wine with reduced ethanol concentration

Auteurs: Javier Varela, Cristian Varela
Publié dans: Current Opinion in Biotechnology, Numéro 56, 2019, Page(s) 88-96, ISSN 0958-1669
Éditeur: Elsevier BV
DOI: 10.1016/j.copbio.2018.10.003

Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species

Auteurs: Iván Domenzain, Feiran Li, Eduard J Kerkhoven, Verena Siewers
Publié dans: FEMS Yeast Research, Numéro 21/1, 2021, ISSN 1567-1364
Éditeur: FEMS Yeast Research
DOI: 10.1093/femsyr/foab002

An atlas of human metabolism

Auteurs: Jonathan L. Robinson, Pınar Kocabaş, Hao Wang, Pierre-Etienne Cholley, Daniel Cook, Avlant Nilsson, Mihail Anton, Raphael Ferreira, Iván Domenzain, Virinchi Billa, Angelo Limeta, Alex Hedin, Johan Gustafsson, Eduard J. Kerkhoven, L. Thomas Svensson, Bernhard O. Palsson, Adil Mardinoglu, Lena Hansson, Mathias Uhlén, Jens Nielsen
Publié dans: Science Signaling, Numéro 13/624, 2020, Page(s) eaaz1482, ISSN 1937-9145
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/scisignal.aaz1482

FALCONET: an R package to accelerate automatic visualisation of genome scale metabolic models

Auteurs: Lu, Hongzhong; Zhu, Zhengming; Kerkhoven, Eduard J; Nielsen, Jens
Publié dans: Numéro 5, 2019
Éditeur: BioRxiv
DOI: 10.1101/662056

Multidimensional engineering for the production of fatty acid derivatives in Saccharomyces cerevisiae

Auteurs: Hu, Yating
Publié dans: Numéro 1, 2019, ISBN 978-91-7905-174-7
Éditeur: not applicable

Approaching absolute quantification using label-free shotgun proteomics coupled with external protein standards spiked in yeast extracts

Auteurs: Millan Oropeza, Aaron; Blein-Nicolas, Melisande; Zivy, Michel; Monnet, Véronique; Henry, Celine
Publié dans: http://sfeap2018.ipbs.fr/, Numéro 3, 2018
Éditeur: HAL archive

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