Predictive and Accelerated Metabolic Engineering Network

Leistungen

A new validated method for FACS-based screening of engineered proteins
Public dissemination summary

"The Dissemination and Communication Plan will be updated by Dissemination and Communication Manager (DTU) and ESR Board on a regular basis. All the conducted activities will be registered and will eventually comprise the final ""Public dissemination summary""."

Conference I, II, and III

Three annual network conferences with the presence of all ESRs and the participation of all the beneficiaries and partner organizations. ESRs will have the opportunity to present their research objectives and results to the network, including ESR colleagues, and to receive feedback. Participants from outside of the network will be invited to each conference.

Characterized Parts Library

Characterization data on regulatory parts library incl. upload to online open-access data repository

PAcMEN website

Public website will be created in the very beginning of the project and will be maintained throughout the project duration. The website will announce the new discoveries and publications from PAcMEN ESRs, the upcoming presentations by PAcMEN ESRs at scientific and industry-relevant conferences and workshops, reports/pictures/videos from the dissemination events, press-releases in local and international media, and so on.

Comprehensive ChIP-exo and CAGE database

2 Next-generation genome-scale model of S. cerevisiae with regulatory information

TFA + Lipids Modeling of Yarrowia

Kinetic models of native metabolism and production pathway in S. cerevisiae

Temperature constraint GEM and GEM including protein synthesis

Next-generation genome-scale model of S. cerevisiae with included protein synthesis

Veröffentlichungen

The transcription factor Leu3 shows differential binding behavior in response to changing leucine availability

Autoren: Christoph S Börlin, Jens Nielsen, Verena Siewers
Veröffentlicht in: FEMS Microbiology Letters, Ausgabe 367/13, 2020, ISSN 1574-6968
Herausgeber: Microbiology Letters
DOI: 10.1093/femsle/fnaa107

Adaptive Laboratory Evolution and Reverse Engineering of Single-Vitamin Prototrophies in Saccharomyces cerevisiae

Autoren: Thomas Perli, Dewi P. I. Moonen, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran
Veröffentlicht in: Applied and Environmental Microbiology, 2020, ISSN 0099-2240
Herausgeber: American Society for Microbiology
DOI: 10.1128/aem.00388-20

Regulatory control circuits for stabilizing long-term anabolic product formation in yeast

Autoren: VasilD'Ambrosio, Eleonora Dorea, Roberto Di Blasi, Marcel van den Broek, Suresh Sudarsan, Jolanda ter Horst, Francesca Ambri, Morten O.A. Sommer, Peter Rugbjerg, Jay D.Keasling, Robert Mansb, Michael K.Jensen
Veröffentlicht in: Metabolic Engineering, 2020, ISSN 1096-7176
Herausgeber: Academic Press
DOI: 10.1016/j.ymben.2020.07.006

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power

Autoren: Jasmin Hafner, Homa MohammadiPeyhani, Anastasia Sveshnikova, Alan Scheidegger, Vassily Hatzimanikatis
Veröffentlicht in: ACS Synthetic Biology, Ausgabe 9/6, 2020, Seite(n) 1479-1482, ISSN 2161-5063
Herausgeber: American Chemical Society
DOI: 10.1021/acssynbio.0c00052

Exploiting the Diversity of Saccharomycotina Yeasts To Engineer Biotin-Independent Growth of Saccharomyces cerevisiae

Autoren: Anna K. Wronska, Meinske P. Haak, Ellen Geraats, Eva Bruins Slot, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran
Veröffentlicht in: Applied and Environmental Microbiology, Ausgabe 86/12, 2020, ISSN 0099-2240
Herausgeber: American Society for Microbiology
DOI: 10.1128/aem.00270-20

The Transcriptome and Flux Profiling of Crabtree‐Negative Hydroxy Acid‐Producing Strains of Saccharomyces cerevisiae Reveals Changes in the Central Carbon Metabolism

Autoren: Mathew M. Jessop‐Fabre, Jonathan Dahlin, Mathias B. Biron, Vratislav Stovicek, Birgitta E. Ebert, Lars M. Blank, Itay Budin, Jay D. Keasling, Irina Borodina
Veröffentlicht in: Biotechnology Journal, Ausgabe 14/9, 2019, Seite(n) 1900013, ISSN 1860-6768
Herausgeber: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/biot.201900013

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Autoren: Jie Zhang, Søren D. Petersen, Tijana Radivojevic, Andrés Ramirez, Andrés Pérez-Manríquez, Eduardo Abeliuk, Benjamín J. Sánchez, Zak Costello, Yu Chen, Michael J. Fero, Hector Garcia Martin, Jens Nielsen, Jay D. Keasling, Michael K. Jensen
Veröffentlicht in: Nature Communications, Ausgabe 11/1, 2020, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-020-17910-1

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Autoren: Gang Li; Yating Hu; Hao Wang; Aleksej Zelezniak; Boyang Ji; Jan Zrimec; Jens Nielsen
Veröffentlicht in: Crossref, Ausgabe 2, 2020, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1101/2020.04.01.019620

Engineering microbial fatty acid metabolism for biofuels and biochemicals

Autoren: Eko Roy Marella, Carina Holkenbrink, Verena Siewers, Irina Borodina
Veröffentlicht in: Current Opinion in Biotechnology, Ausgabe 50, 2018, Seite(n) 39-46, ISSN 0958-1669
Herausgeber: Elsevier BV
DOI: 10.1016/j.copbio.2017.10.002

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Autoren: Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis
Veröffentlicht in: Bioinformatics, 2018, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/bty499

Advances in synthetic biology of oleaginous yeast Yarrowia lipolytica for producing non-native chemicals

Autoren: Farshad Darvishi, Mehdi Ariana, Eko Roy Marella, Irina Borodina
Veröffentlicht in: Applied Microbiology and Biotechnology, Ausgabe 102/14, 2018, Seite(n) 5925-5938, ISSN 0175-7598
Herausgeber: Springer Verlag
DOI: 10.1007/s00253-018-9099-x

Modular 5′-UTR hexamers for context-independent tuning of protein expression in eukaryotes

Autoren: Søren D Petersen, Jie Zhang, Jae S Lee, Tadas Jakočiūnas, Lise M Grav, Helene F Kildegaard, Jay D Keasling, Michael K Jensen
Veröffentlicht in: Nucleic Acids Research, 2018, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gky734

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

Autoren: 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
Veröffentlicht in: FEMS Yeast Research, Ausgabe 18/3, 2018, ISSN 1567-1364
Herausgeber: Oxford Academic
DOI: 10.1093/femsyr/foy012

Lighting up yeast cell factories by transcription factor-based biosensors

Autoren: Vasil D'Ambrosio, Michael K. Jensen
Veröffentlicht in: FEMS Yeast Research, Ausgabe 17/7, 2017, ISSN 1567-1364
Herausgeber: Oxford University Press
DOI: 10.1093/femsyr/fox076

A single-host fermentation process for the production of flavor lactones from non-hydroxylated fatty acids

Autoren: Eko Roy Marella, Jonathan Dahlin, Marie Inger Dam, Jolanda ter Horst, Hanne Bjerre Christensen, Suresh Sudarsan, Guokun Wang, Carina Holkenbrink, Irina Borodina
Veröffentlicht in: Metabolic Engineering, 2019, ISSN 1096-7176
Herausgeber: Academic Press
DOI: 10.1016/j.ymben.2019.08.009

Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica

Autoren: Jonathan Dahlin, Carina Holkenbrink, Eko Roy Marella, Guokun Wang, Ulf Liebal, Christian Lieven, Dieter Weber, Douglas McCloskey, Birgitta E. Ebert, Markus J. Herrgård, Lars Mathias Blank, Irina Borodina
Veröffentlicht in: Frontiers in Genetics, Ausgabe 10, 2019, ISSN 1664-8021
Herausgeber: Frontiers Media
DOI: 10.3389/fgene.2019.00747

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

Autoren: Christoph S Börlin, Nevena Cvetesic, Petter Holland, David Bergenholm, Verena Siewers, Boris Lenhard, Jens Nielsen
Veröffentlicht in: FEMS Yeast Research, Ausgabe 19/2, 2018, ISSN 1567-1364
Herausgeber: Fems Yeast Research
DOI: 10.1093/femsyr/foy128

A bioinformatic pipeline to analyze ChIP-exo datasets

Autoren: Christoph S Börlin, David Bergenholm, Petter Holland, Jens Nielsen
Veröffentlicht in: Biology Methods and Protocols, Ausgabe 4/1, 2019, ISSN 2396-8923
Herausgeber: Biology Methods & Protocols
DOI: 10.1093/biomethods/bpz011

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

Autoren: 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
Veröffentlicht in: Nature Communications, Ausgabe 10/1, 2019, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-019-11581-3

Predictive models of eukaryotic transcriptional regulation reveals changes in transcription factor roles and promoter usage between metabolic conditions

Autoren: Petter Holland, David Bergenholm, Christoph S Börlin, Guodong Liu, Jens Nielsen
Veröffentlicht in: Nucleic Acids Research, Ausgabe 47/10, 2019, Seite(n) 4986-5000, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkz253

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

Autoren: Noushin Hadadi, Homa MohammadiPeyhani, Ljubisa Miskovic, Marianne Seijo, Vassily Hatzimanikatis
Veröffentlicht in: Proceedings of the National Academy of Sciences, Ausgabe 116/15, 2019, Seite(n) 7298-7307, ISSN 0027-8424
Herausgeber: National Academy of Sciences
DOI: 10.1073/pnas.1818877116

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Autoren: Pierre Salvy, Vassily Hatzimanikatis
Veröffentlicht in: Nature Communications, Ausgabe 11/1, 2020, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-019-13818-7

Display of functional nucleic acid polymerase on Escherichia coli surface and its application in directed polymerase evolution

Autoren: Mu‐En Chung, Kati Goroncy, Alisa Kolesnikova, David Schönauer, Ulrich Schwaneberg
Veröffentlicht in: Biotechnology and Bioengineering, 2020, ISSN 0006-3592
Herausgeber: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.27542

Vitamin requirements and biosynthesis in Saccharomyces cerevisiae

Autoren: Thomas Perli, Anna K. Wronska, Raúl A. Ortiz‐Merino, Jack T. Pronk, Jean‐Marc Daran
Veröffentlicht in: Yeast, 2020, ISSN 0749-503X
Herausgeber: John Wiley & Sons Inc.
DOI: 10.1002/yea.3461

Directed evolution of VanR biosensor specificity in yeast

Autoren: Vasil D'Ambrosio, Subrata Pramanik, Kati Goroncy, Tadas Jakočiūnas, David Schönauer, Mehdi D. Davari, Ulrich Schwaneberg, Jay D. Keasling, Michael K. Jensen
Veröffentlicht in: Biotechnology Notes, Ausgabe 1, 2020, Seite(n) 9-15, ISSN 2665-9069
Herausgeber: Biotechnology Notes
DOI: 10.1016/j.biotno.2020.01.002

ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints

Autoren: Salvy, Pierre; Hatzimanikatis, Vassily
Veröffentlicht in: Ausgabe 1, 2020
Herausgeber: TBA
DOI: 10.1101/590992

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