Predictive and Accelerated Metabolic Engineering Network

Resultado final

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

Publicaciones

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

Autores: Christoph S Börlin, Jens Nielsen, Verena Siewers
Publicado en: FEMS Microbiology Letters, Edición 367/13, 2020, ISSN 1574-6968
Editor: Microbiology Letters
DOI: 10.1093/femsle/fnaa107

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

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

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

Autores: 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
Publicado en: Metabolic Engineering, 2020, ISSN 1096-7176
Editor: Academic Press
DOI: 10.1016/j.ymben.2020.07.006

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

Autores: Jasmin Hafner, Homa MohammadiPeyhani, Anastasia Sveshnikova, Alan Scheidegger, Vassily Hatzimanikatis
Publicado en: ACS Synthetic Biology, Edición 9/6, 2020, Página(s) 1479-1482, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.0c00052

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

Autores: Anna K. Wronska, Meinske P. Haak, Ellen Geraats, Eva Bruins Slot, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran
Publicado en: Applied and Environmental Microbiology, Edición 86/12, 2020, ISSN 0099-2240
Editor: 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

Autores: Mathew M. Jessop‐Fabre, Jonathan Dahlin, Mathias B. Biron, Vratislav Stovicek, Birgitta E. Ebert, Lars M. Blank, Itay Budin, Jay D. Keasling, Irina Borodina
Publicado en: Biotechnology Journal, Edición 14/9, 2019, Página(s) 1900013, ISSN 1860-6768
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-17910-1

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Autores: Gang Li; Yating Hu; Hao Wang; Aleksej Zelezniak; Boyang Ji; Jan Zrimec; Jens Nielsen
Publicado en: Crossref, Edición 2, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/2020.04.01.019620

Engineering microbial fatty acid metabolism for biofuels and biochemicals

Autores: Eko Roy Marella, Carina Holkenbrink, Verena Siewers, Irina Borodina
Publicado en: Current Opinion in Biotechnology, Edición 50, 2018, Página(s) 39-46, ISSN 0958-1669
Editor: 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

Autores: Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis
Publicado en: Bioinformatics, 2018, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty499

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

Autores: Farshad Darvishi, Mehdi Ariana, Eko Roy Marella, Irina Borodina
Publicado en: Applied Microbiology and Biotechnology, Edición 102/14, 2018, Página(s) 5925-5938, ISSN 0175-7598
Editor: Springer Verlag
DOI: 10.1007/s00253-018-9099-x

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

Autores: Søren D Petersen, Jie Zhang, Jae S Lee, Tadas Jakočiūnas, Lise M Grav, Helene F Kildegaard, Jay D Keasling, Michael K Jensen
Publicado en: Nucleic Acids Research, 2018, ISSN 0305-1048
Editor: 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

Autores: 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
Publicado en: FEMS Yeast Research, Edición 18/3, 2018, ISSN 1567-1364
Editor: Oxford Academic
DOI: 10.1093/femsyr/foy012

Lighting up yeast cell factories by transcription factor-based biosensors

Autores: Vasil D'Ambrosio, Michael K. Jensen
Publicado en: FEMS Yeast Research, Edición 17/7, 2017, ISSN 1567-1364
Editor: Oxford University Press
DOI: 10.1093/femsyr/fox076

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

Autores: Eko Roy Marella, Jonathan Dahlin, Marie Inger Dam, Jolanda ter Horst, Hanne Bjerre Christensen, Suresh Sudarsan, Guokun Wang, Carina Holkenbrink, Irina Borodina
Publicado en: Metabolic Engineering, 2019, ISSN 1096-7176
Editor: 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

Autores: 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
Publicado en: Frontiers in Genetics, Edición 10, 2019, ISSN 1664-8021
Editor: Frontiers Media
DOI: 10.3389/fgene.2019.00747

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

Autores: Christoph S Börlin, Nevena Cvetesic, Petter Holland, David Bergenholm, Verena Siewers, Boris Lenhard, Jens Nielsen
Publicado en: FEMS Yeast Research, Edición 19/2, 2018, ISSN 1567-1364
Editor: Fems Yeast Research
DOI: 10.1093/femsyr/foy128

A bioinformatic pipeline to analyze ChIP-exo datasets

Autores: Christoph S Börlin, David Bergenholm, Petter Holland, Jens Nielsen
Publicado en: Biology Methods and Protocols, Edición 4/1, 2019, ISSN 2396-8923
Editor: Biology Methods & Protocols
DOI: 10.1093/biomethods/bpz011

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

Autores: 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
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: 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

Autores: Petter Holland, David Bergenholm, Christoph S Börlin, Guodong Liu, Jens Nielsen
Publicado en: Nucleic Acids Research, Edición 47/10, 2019, Página(s) 4986-5000, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkz253

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

Autores: Noushin Hadadi, Homa MohammadiPeyhani, Ljubisa Miskovic, Marianne Seijo, Vassily Hatzimanikatis
Publicado en: Proceedings of the National Academy of Sciences, Edición 116/15, 2019, Página(s) 7298-7307, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.1818877116

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

Autores: Pierre Salvy, Vassily Hatzimanikatis
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: 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

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

Vitamin requirements and biosynthesis in Saccharomyces cerevisiae

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

Directed evolution of VanR biosensor specificity in yeast

Autores: Vasil D'Ambrosio, Subrata Pramanik, Kati Goroncy, Tadas Jakočiūnas, David Schönauer, Mehdi D. Davari, Ulrich Schwaneberg, Jay D. Keasling, Michael K. Jensen
Publicado en: Biotechnology Notes, Edición 1, 2020, Página(s) 9-15, ISSN 2665-9069
Editor: 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

Autores: Salvy, Pierre; Hatzimanikatis, Vassily
Publicado en: Edición 1, 2020
Editor: TBA
DOI: 10.1101/590992

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