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Predictive and Accelerated Metabolic Engineering Network

Deliverables

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

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

Searching for OpenAIRE data...

Publications

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

Author(s): Christoph S Börlin, Jens Nielsen, Verena Siewers
Published in: FEMS Microbiology Letters, Issue 367/13, 2020, ISSN 1574-6968
DOI: 10.1093/femsle/fnaa107

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

Author(s): Thomas Perli, Dewi P. I. Moonen, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran
Published in: Applied and Environmental Microbiology, 2020, ISSN 0099-2240
DOI: 10.1128/aem.00388-20

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

Author(s): 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
Published in: Metabolic Engineering, 2020, ISSN 1096-7176
DOI: 10.1016/j.ymben.2020.07.006

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

Author(s): Jasmin Hafner, Homa MohammadiPeyhani, Anastasia Sveshnikova, Alan Scheidegger, Vassily Hatzimanikatis
Published in: ACS Synthetic Biology, Issue 9/6, 2020, Page(s) 1479-1482, ISSN 2161-5063
DOI: 10.1021/acssynbio.0c00052

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

Author(s): Anna K. Wronska, Meinske P. Haak, Ellen Geraats, Eva Bruins Slot, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran
Published in: Applied and Environmental Microbiology, Issue 86/12, 2020, ISSN 0099-2240
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

Author(s): Mathew M. Jessop‐Fabre, Jonathan Dahlin, Mathias B. Biron, Vratislav Stovicek, Birgitta E. Ebert, Lars M. Blank, Itay Budin, Jay D. Keasling, Irina Borodina
Published in: Biotechnology Journal, Issue 14/9, 2019, Page(s) 1900013, ISSN 1860-6768
DOI: 10.1002/biot.201900013

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

Author(s): 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
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-020-17910-1

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Author(s): Gang Li; Yating Hu; Hao Wang; Aleksej Zelezniak; Boyang Ji; Jan Zrimec; Jens Nielsen
Published in: Crossref, Issue 2, 2020, ISSN 2041-1723
DOI: 10.1101/2020.04.01.019620

Engineering microbial fatty acid metabolism for biofuels and biochemicals

Author(s): Eko Roy Marella, Carina Holkenbrink, Verena Siewers, Irina Borodina
Published in: Current Opinion in Biotechnology, Issue 50, 2018, Page(s) 39-46, ISSN 0958-1669
DOI: 10.1016/j.copbio.2017.10.002

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

Author(s): Pierre Salvy, Georgios Fengos, Meric Ataman, Thomas Pathier, Keng C Soh, Vassily Hatzimanikatis
Published in: Bioinformatics, 2018, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty499

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

Author(s): Farshad Darvishi, Mehdi Ariana, Eko Roy Marella, Irina Borodina
Published in: Applied Microbiology and Biotechnology, Issue 102/14, 2018, Page(s) 5925-5938, ISSN 0175-7598
DOI: 10.1007/s00253-018-9099-x

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

Author(s): Søren D Petersen, Jie Zhang, Jae S Lee, Tadas Jakočiūnas, Lise M Grav, Helene F Kildegaard, Jay D Keasling, Michael K Jensen
Published in: Nucleic Acids Research, 2018, ISSN 0305-1048
DOI: 10.1093/nar/gky734

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

Lighting up yeast cell factories by transcription factor-based biosensors

Author(s): Vasil D'Ambrosio, Michael K. Jensen
Published in: FEMS Yeast Research, Issue 17/7, 2017, ISSN 1567-1364
DOI: 10.1093/femsyr/fox076

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

Author(s): Eko Roy Marella, Jonathan Dahlin, Marie Inger Dam, Jolanda ter Horst, Hanne Bjerre Christensen, Suresh Sudarsan, Guokun Wang, Carina Holkenbrink, Irina Borodina
Published in: Metabolic Engineering, 2019, ISSN 1096-7176
DOI: 10.1016/j.ymben.2019.08.009

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

Author(s): 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
Published in: Frontiers in Genetics, Issue 10, 2019, ISSN 1664-8021
DOI: 10.3389/fgene.2019.00747

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

Author(s): Christoph S Börlin, Nevena Cvetesic, Petter Holland, David Bergenholm, Verena Siewers, Boris Lenhard, Jens Nielsen
Published in: FEMS Yeast Research, Issue 19/2, 2018, ISSN 1567-1364
DOI: 10.1093/femsyr/foy128

A bioinformatic pipeline to analyze ChIP-exo datasets

Author(s): Christoph S Börlin, David Bergenholm, Petter Holland, Jens Nielsen
Published in: Biology Methods and Protocols, Issue 4/1, 2019, ISSN 2396-8923
DOI: 10.1093/biomethods/bpz011

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

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

Author(s): Petter Holland, David Bergenholm, Christoph S Börlin, Guodong Liu, Jens Nielsen
Published in: Nucleic Acids Research, Issue 47/10, 2019, Page(s) 4986-5000, ISSN 0305-1048
DOI: 10.1093/nar/gkz253

The pan-genome of Saccharomyces cerevisiae

Author(s): Gang Li, Boyang Ji, Jens Nielsen
Published in: FEMS Yeast Research, Issue 19/7, 2019, ISSN 1567-1356
DOI: 10.1093/femsyr/foz064

Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima

Author(s): Gang Li, Kersten S. Rabe, Jens Nielsen, Martin K. M. Engqvist
Published in: ACS Synthetic Biology, Issue 8/6, 2019, Page(s) 1411-1420, ISSN 2161-5063
DOI: 10.1021/acssynbio.9b00099

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

Author(s): Noushin Hadadi, Homa MohammadiPeyhani, Ljubisa Miskovic, Marianne Seijo, Vassily Hatzimanikatis
Published in: Proceedings of the National Academy of Sciences, Issue 116/15, 2019, Page(s) 7298-7307, ISSN 0027-8424
DOI: 10.1073/pnas.1818877116

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

Author(s): Pierre Salvy, Vassily Hatzimanikatis
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-019-13818-7

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

Author(s): Mu‐En Chung, Kati Goroncy, Alisa Kolesnikova, David Schönauer, Ulrich Schwaneberg
Published in: Biotechnology and Bioengineering, 2020, ISSN 0006-3592
DOI: 10.1002/bit.27542

Vitamin requirements and biosynthesis in Saccharomyces cerevisiae

Author(s): Thomas Perli, Anna K. Wronska, Raúl A. Ortiz‐Merino, Jack T. Pronk, Jean‐Marc Daran
Published in: Yeast, 2020, ISSN 0749-503X
DOI: 10.1002/yea.3461

Directed evolution of VanR biosensor specificity in yeast

Author(s): Vasil D'Ambrosio, Subrata Pramanik, Kati Goroncy, Tadas Jakočiūnas, David Schönauer, Mehdi D. Davari, Ulrich Schwaneberg, Jay D. Keasling, Michael K. Jensen
Published in: Biotechnology Notes, Issue 1, 2020, Page(s) 9-15, ISSN 2665-9069
DOI: 10.1016/j.biotno.2020.01.002

Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges

Author(s): Yu Chen, Gang Li, Jens Nielsen
Published in: Yeast Systems Biology - Methods and Protocols, Issue 2049, 2019, Page(s) 329-345
DOI: 10.1007/978-1-4939-9736-7_19