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

Deliverables

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

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Publications

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

Author(s): Florian Wernig, Leonie Baumann, Eckhard Boles, Mislav Oreb
Published in: Biotechnology and Bioengineering, 2021, ISSN 0006-3592
DOI: 10.1002/bit.27814

Metabolic Engineering for Unusual Lipid Production in Yarrowia lipolytica

Author(s): Young-Kyoung Park, Jean-Marc Nicaud
Published in: Microorganisms, Issue 8/12, 2020, Page(s) 1937, ISSN 2076-2607
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

Author(s): Leonie Baumann, Stefan Bruder, Johannes Kabisch, Eckhard Boles, Mislav Oreb
Published in: ACS Synthetic Biology, 2021, ISSN 2161-5063
DOI: 10.1021/acssynbio.0c00600

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

Author(s): Zhiwei Zhu, Yating Hu, Paulo Gonçalves Teixeira, Rui Pereira, Yun Chen, Verena Siewers, Jens Nielsen
Published in: Nature Catalysis, Issue 3/1, 2020, Page(s) 64-74, ISSN 2520-1158
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

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

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

Author(s): Florian Wernig, Sandra Born, Eckhard Boles, Martin Grininger, Mislav Oreb
Published in: Scientific Reports, Issue 10/1, 2020, ISSN 2045-2322
DOI: 10.1038/s41598-020-66629-y

A Yarrowia lipolytica Strain Engineered for Pyomelanin Production

Author(s): Macarena Larroude, Djamila Onésime, Olivier Rué, Jean-Marc Nicaud, Tristan Rossignol
Published in: Microorganisms, Issue 9/4, 2021, Page(s) 838, ISSN 2076-2607
DOI: 10.3390/microorganisms9040838

Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production

Author(s): Leonie Baumann, Tyler Doughty, Verena Siewers, Jens Nielsen, Eckhard Boles, Mislav Oreb
Published in: FEMS Yeast Research, Issue 21/2, 2021, ISSN 1567-1356
DOI: 10.1093/femsyr/foab011

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

Author(s): Leonie Wenning, Christer S. Ejsing, Florian David, Richard R. Sprenger, Jens Nielsen, Verena Siewers
Published in: Microbial Cell Factories, Issue 18/1, 2019, ISSN 1475-2859
DOI: 10.1186/s12934-019-1098-9

Extracting novel hypotheses and findings from RNA-seq data

Author(s): Tyler Doughty, Eduard Kerkhoven
Published in: FEMS Yeast Research, Issue 20/2, 2020, ISSN 1567-1356
DOI: 10.1093/femsyr/foaa007

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

Author(s): Benjamín J Sánchez, Cheng Zhang, Avlant Nilsson, Petri‐Jaan Lahtvee, Eduard J Kerkhoven, Jens Nielsen
Published in: Molecular Systems Biology, Issue 13/8, 2017, Page(s) 935, ISSN 1744-4292
DOI: 10.15252/msb.20167411

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

Author(s): Robert Mans, Jean-Marc G Daran, Jack T Pronk
Published in: Current Opinion in Biotechnology, Issue 50, 2018, Page(s) 47-56, ISSN 0958-1669
DOI: 10.1016/j.copbio.2017.10.011

Heterologous transporter expression for improved fatty alcohol secretion in yeast

Author(s): Yating Hu, Zhiwei Zhu, Jens Nielsen, Verena Siewers
Published in: Metabolic Engineering, Issue 45, 2018, Page(s) 51-58, ISSN 1096-7176
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

Author(s): 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
Published in: FEMS Yeast Research, Issue 18/3, 2018, ISSN 1567-1364
DOI: 10.1093/femsyr/foy012

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

Author(s): Michal A. Świat, Sofia Dashko, Maxime den Ridder, Melanie Wijsman, John van der Oost, Jean-Marc Daran, Pascale Daran-Lapujade
Published in: Nucleic Acids Research, Issue 45/21, 2017, Page(s) 12585-12598, ISSN 0305-1048
DOI: 10.1093/nar/gkx1007

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

Author(s): Tao Yu, Yongjin J. Zhou, Leonie Wenning, Quanli Liu, Anastasia Krivoruchko, Verena Siewers, Jens Nielsen, Florian David
Published in: Nature Communications, Issue 8, 2017, Page(s) 15587, ISSN 2041-1723
DOI: 10.1038/ncomms15587

Barriers and opportunities in bio-based production of hydrocarbons

Author(s): Yongjin J. Zhou, Eduard J. Kerkhoven, Jens Nielsen
Published in: Nature Energy, 2018, ISSN 2058-7546
DOI: 10.1038/s41560-018-0197-x

Synthetic biology tools for engineering Yarrowia lipolytica

Author(s): M. Larroude, T. Rossignol, J.-M. Nicaud, R. Ledesma-Amaro
Published in: Biotechnology Advances, 2018, ISSN 0734-9750
DOI: 10.1016/j.biotechadv.2018.10.004

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

Author(s): Leonie Baumann, Arun S. Rajkumar, John P. Morrissey, Eckhard Boles, Mislav Oreb
Published in: ACS Synthetic Biology, 2018, ISSN 2161-5063
DOI: 10.1021/acssynbio.8b00309

Expansion and Diversification of MFS Transporters in Kluyveromyces marxianus

Author(s): Javier A. Varela, Martina Puricelli, Noemi Montini, John P. Morrissey
Published in: Frontiers in Microbiology, Issue 9, 2019, ISSN 1664-302X
DOI: 10.3389/fmicb.2018.03330

Biological Parts for Kluyveromyces marxianus Synthetic Biology

Author(s): Arun S. Rajkumar, Javier A. Varela, Hannes Juergens, Jean-Marc G. Daran, John P. Morrissey
Published in: Frontiers in Bioengineering and Biotechnology, Issue 7, 2019, ISSN 2296-4185
DOI: 10.3389/fbioe.2019.00097

A modular Golden Gate toolkit for Yarrowia lipolytica synthetic biology

Author(s): Macarena Larroude, Young‐Kyoung Park, Paul Soudier, Monika Kubiak, Jean‐Marc Nicaud, Tristan Rossignol
Published in: Microbial Biotechnology, 2019, ISSN 1751-7915
DOI: 10.1111/1751-7915.13427

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

Author(s): 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
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
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

Author(s): Else-Jasmijn Hassing, Philip A. de Groot, Vita R. Marquenie, Jack T. Pronk, Jean-Marc G. Daran
Published in: Metabolic Engineering, Issue 56, 2019, Page(s) 165-180, ISSN 1096-7176
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

Author(s): Yu, Tao; Zhou, Yongjin J.; Wenning, Leonie; Liu, Quanli; Krivoruchko, Anastasia; Siewers, Verena; Nielsen, Jens; David, Florian
Published in: Nature Communications, Issue 1, 2018, ISSN 2041-1723
DOI: 10.1038/ncomms16220

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

Author(s): Javier A. Varela, Martina Puricelli, Raúl A. Ortiz-Merino, Romina Giacomobono, Stephanie Braun-Galleani, Kenneth H. Wolfe, John P. Morrissey
Published in: Current Biology, 2019, ISSN 0960-9822
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

Author(s): Florian Wernig, Eckhard Boles, Mislav Oreb
Published in: Metabolic Engineering Communications, Issue 10, 2020, Page(s) e00111, ISSN 2214-0301
DOI: 10.1016/j.mec.2019.e00111

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

Author(s): Macarena Larroude, Heykel Trabelsi, Jean-Marc Nicaud, Tristan Rossignol
Published in: Biotechnology Letters, 2020, ISSN 0141-5492
DOI: 10.1007/s10529-020-02805-4

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

Author(s): 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
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-020-16073-3

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

Author(s): Arun S. Rajkumar, John P. Morrissey
Published in: Microbial Cell Factories, Issue 19/1, 2020, ISSN 1475-2859
DOI: 10.1186/s12934-020-01461-7

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

Author(s): Macarena Larroude, Jean‐Marc Nicaud, Tristan Rossignol
Published in: Microbial Biotechnology, 2020, ISSN 1751-7915
DOI: 10.1111/1751-7915.13745

Microbiological strategies to produce beer and wine with reduced ethanol concentration

Author(s): Javier Varela, Cristian Varela
Published in: Current Opinion in Biotechnology, Issue 56, 2019, Page(s) 88-96, ISSN 0958-1669
DOI: 10.1016/j.copbio.2018.10.003

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

Author(s): Iván Domenzain, Feiran Li, Eduard J Kerkhoven, Verena Siewers
Published in: FEMS Yeast Research, Issue 21/1, 2021, ISSN 1567-1364
DOI: 10.1093/femsyr/foab002

An atlas of human metabolism

Author(s): 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
Published in: Science Signaling, Issue 13/624, 2020, Page(s) eaaz1482, ISSN 1937-9145
DOI: 10.1126/scisignal.aaz1482

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

Author(s): Lu, Hongzhong; Zhu, Zhengming; Kerkhoven, Eduard J; Nielsen, Jens
Published in: Issue 5, 2019
DOI: 10.1101/662056

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

Author(s): Hu, Yating
Published in: Issue 1, 2019

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

Author(s): Millan Oropeza, Aaron; Blein-Nicolas, Melisande; Zivy, Michel; Monnet, Véronique; Henry, Celine
Published in: http://sfeap2018.ipbs.fr/, Issue 3, 2018