Modular cell factories for the production of 100 compounds from the shikimate pathway

Informacje na temat projektu

SHIKIFACTORY100

Identyfikator umowy o grant: 814408

DOI

10.3030/814408

Projekt został zamknięty

Data podpisania przez KE 12 Grudnia 2018

Data rozpoczęcia 1 Stycznia 2019

Data zakończenia 30 Czerwca 2023

Finansowanie w ramach

• INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies – Biotechnology

Koszt całkowity

€ 7 997 537,51

Wkład UE

€ 7 995 343,75

Koordynowany przez

SILICOLIFE LDA
Portugal

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

Other (2)

Public final version of the updated models

Updated models publicly available on the DDDeCaF platform and as SBML exchangeable files

Pathway database with all ranking and analysis metrics

Database containing the pathways and ranking metrics used

Documents, reports (3)

Communication Channels (Website, Twitter, LinkedIn)

Report detailing the communication channels, such as the website and social media accounts

Project visuals and messaging

Report detailing project visuals and messaging plaforms

Sustainability appraisal and risk assessment of 10 target molecules

Publikacje

Book chapters (4)

Combinatorial Optimization of Succinate Production in Escherichia coli

Autorzy: Vítor Pereira, Miguel Rocha
Opublikowane w: Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021), 2021, ISBN 978-3-030-86257-2
Wydawca: Springer
DOI: 10.1007/978-3-030-86258-9_16

Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression

Autorzy: Fernando Cruz, Diogo Lima, José P. Faria, Miguel Rocha, Oscar Dias
Opublikowane w: Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, Numer 1005, 2020, Strona(/y) 173-181, ISBN 978-3-030-23872-8
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-030-23873-5_21

Artificial Intelligence in Biological Activity Prediction

Autorzy: João Correia, Tiago Resende, Delora Baptista, Miguel Rocha
Opublikowane w: Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, Numer 1005, 2020, Strona(/y) 164-172, ISBN 978-3-030-23872-8
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-030-23873-5_20

Chapter 14 - A retrobiosynthetic approach for production, conversion, sensing, dynamic regulation and degradation of molecules

Autorzy: Pablo Carbonell
Opublikowane w: New Frontiers and Applications of Synthetic Biology, 2022, Strona(/y) 205-214, ISBN 978-0-12-824469-2
Wydawca: Academic Press
DOI: 10.1016/b978-0-12-824469-2.00024-5

Peer reviewed articles (35)

Modulation of the cell wall protein Ecm33p in yeast <i>Saccharomyces cerevisiae</i> improves the production of small metabolites

Autorzy: Verónica Ramos-Viana; Iben Møller-Hansen; Paul Kempen; Irina Borodina
Opublikowane w: FEMS Yeast Research, Numer 1, 2022, ISSN 1567-1356
Wydawca: Blackwell
DOI: 10.1093/femsyr/foac037

Biotechnological application of Streptomyces for the production of clinical drugs and other bioactive molecules

Autorzy: Francesco Del Carratore, Erik KR Hanko, Rainer Breitling, Eriko Takano
Opublikowane w: Current Opinion in Biotechnology, 2022, ISSN 1879-0429
Wydawca: Elsevier
DOI: 10.1016/j.copbio.2022.102762

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Autorzy: Omid Oftadeh, Pierre Salvy, Maria Masid, Maxime Curvat, Ljubisa Miskovic & Vassily Hatzimanikatis
Opublikowane w: Nature Communications, Numer 12, 2021, Strona(/y) 4790, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-021-25158-6

TFBMiner: A User-Friendly Command Line Tool for the Rapid Mining of Transcription Factor-Based Biosensors

Autorzy: Erik K. R. Hanko, Tariq A. Joosab Noor Mahomed, Ruth A. Stoney, and Rainer Breitlin
Opublikowane w: ACS Synthetic Biology, 2023, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.2c00679

Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

Autorzy: Subham Choudhury; Michael Moret; Pierre Salvy; Daniel Weilandt; Vassily Hatzimanikatis; Ljubisa Miskovic
Opublikowane w: Nature Machine Intelligence, Numer 1, 2022, ISSN 2522-5839
Wydawca: Nature Group
DOI: 10.1101/2022.01.06.475020

New targets for drug design: importance of nsp14/nsp10 complex formation for the 3'-5' exoribonucleolytic activity on SARS-CoV-2.

Autorzy: Margarida Saramago; Cátia Bárria; Vanessa G. Costa; Caio S. Souza; Sandra C. Viegas; Susana Domingues; Diana Lousa; Cláudio M. Soares; Cecília M. Arraiano; Rute G. Matos
Opublikowane w: The Febs Journal, Numer 1, 2021, ISSN 1742-464X
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/febs.15815

NICEgame: A workflow for annotating the knowledge gaps in metabolic reconstructions, using known and hypothetical reactions

Autorzy: Evangelia Vayena; Anush Chiappino-Pepe; Homa MohammadiPeyhani; Yannick Francioli; Noushin Hadadi; Meriç Ataman; Jasmin Hafner; Stavros Pavlou; Vassily Hatzimanikatis
Opublikowane w: PNAS, Numer 1, 2022, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1101/2022.02.10.479881

Engineering <i>Saccharomyces cerevisiae</i> for the <i>de novo</i> Production of Halogenated Tryptophan and Tryptamine Derivatives

Autorzy: Nicholas Milne; Javier Sáez‐Sáez; Annette Munch Nielsen; Jane Dannow Dyekjær; Daniela Rago; Mette Kristensen; Tune Wulff; Irina Borodina
Opublikowane w: ChemistryOpen, Numer 1, 2023, ISSN 2191-1363
Wydawca: Weinheim: Wiley-VCH-Verl.
DOI: 10.1002/open.202200266

Rational strain design with minimal phenotype perturbation

Autorzy: Bharath Narayanan; Daniel Weilandt; Maria Masid; Ljubisa Miskovic; Vassily Hatzimanikatis
Opublikowane w: Nature Communications, Numer 1, 2024, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1101/2022.11.14.516382

Metabolic Engineering of Saccharomyces cerevisiae for Rosmarinic Acid Production.

Autorzy: Mahsa Babaei; Gheorghe Manuel Borja Zamfir; Xiao Chen; Hanne Bjerre Christensen; Mette Kristensen; Jens Nielsen; Jens Nielsen; Irina Borodina
Opublikowane w: ACS Synthetic Biology, Numer 6, 2020, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.0c00048

Generative deep learning for targeted compound design

Autorzy: Tiago J. C. Sousa; João Correia; Vitor Pereira; Miguel Rocha
Opublikowane w: Journal of Chemical Information and Modeling, Numer 61 (11), 2021, Strona(/y) 5343–5361, ISSN 1549-9596
Wydawca: American Chemical Society
DOI: 10.1021/acs.jcim.0c01496

Microbial production of the plant flavanone hesperetin from caffeic acid

Autorzy: Erik K. R. Hanko; João Correia; Caio S. Souza; Alison Green; Jakub Chromy; Ruth Stoney; Cunyu Yan; Eriko Takano; Diana Lousa; Cláudio M. Soares; Rainer Breitling
Opublikowane w: BMC Research Notes, Numer 1, 2023, ISSN 1756-0500
Wydawca: BioMed Central
DOI: 10.21203/rs.3.rs-2742541/v1

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

Autorzy: Asli Sahin; Daniel R. Weilandt; Vassily Hatzimanikatis
Opublikowane w: Nature Communications, Numer 1, 2023, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-023-38159-4

Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol

Autorzy: Mark S Dunstan, Christopher J Robinson, Adrian J Jervis, Cunyu Yan, Pablo Carbonell, Katherine A Hollywood, Andrew Currin, Neil Swainston, Rosalind Le Feuvre, Jason Micklefield, Jean-Loup Faulon, Rainer Breitling, Nicholas Turner, Eriko Takano, Nigel S Scrutton
Opublikowane w: Synthetic Biology, Numer 5 (1), 2020, ISSN 2397-7000
Wydawca: Oxford University Press
DOI: 10.1093/synbio/ysaa012

An integrated yeast-based process for cis,cis-muconic acid production

Autorzy: Guokun Wang; Guokun Wang; Aline Tavares; Simone Schmitz; Simone Schmitz; Lucas Gabriel Souza França; Hugo Almeida; João Cavalheiro; Ana Carolas; Süleyman Øzmerih; Lars M. Blank; Bruno Sommer Ferreira; Irina Borodina
Opublikowane w: Biotechnology and Bioengineering, Numer 7, 2021, ISSN 0006-3592
Wydawca: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/bit.27992

Engineering the oleaginous yeast Yarrowia lipolytica for high-level resveratrol production

Autorzy: Javier Sáez-Sáez; Guokun Wang; Eko Roy Marella; Suresh Sudarsan; Marc Cernuda Pastor; Irina Borodina
Opublikowane w: Metabolic Engineering, 2020, ISSN 1096-7176
Wydawca: Academic Press
DOI: 10.1016/j.ymben.2020.08.009

Coupling High-Throughput and Targeted Screening for Identification of Nonobvious Metabolic Engineering Targets

Autorzy: Mahsa Babaei, Philip Tinggaard Thomsen, Marc Cernuda Pastor, Michael Krogh Jensen, and Irina Borodina
Opublikowane w: ACS Synthetic Biology, 2024, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.3c00396

Automated engineering of synthetic metabolic pathways for efficient biomanufacturing

Autorzy: Irene Otero-Muras, Pablo Carbonell
Opublikowane w: Metabolic Engineering, Numer 63, 2020, Strona(/y) 61-80, ISSN 1096-7176
Wydawca: Academic Press
DOI: 10.1016/j.ymben.2020.11.012

Resveratrol Production from Hydrothermally Pretreated Eucalyptus Wood Using Recombinant Industrial Saccharomyces cerevisiae Strains.

Autorzy: Carlos Costa; Iben Møller-Hansen; Aloia Romaní; José A. Teixeira; Irina Borodina; Lucília Domingues
Opublikowane w: ACS Synthetic Biology, Numer 6, 2021, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.1c00120

Valorisation of wine wastes by <i>de novo</i> biosynthesis of resveratrol using a recombinant xylose-consuming industrial <i>Saccharomyces cerevisiae</i> strain

Autorzy: Carlos E. Costa; Aloia Romaní; Iben Møller-Hansen; José A. Teixeira; Irina Borodina; Lucília Domingues
Opublikowane w: Green Chemistry, Numer 1, 2022, ISSN 1463-9270
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d2gc02429b

Comparison of pathway analysis and constraint-based methods for cell factory design

Autorzy: Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
Opublikowane w: BMC Bioinformatics, Numer 20/1, 2019, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-019-2934-y

Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers

Autorzy: Christopher J. Robinson, Pablo Carbonell, Adrian J. Jervis, Cunyu Yan, Katherine A. Hollywood, Mark S. Dunstan, Andrew Currin, Neil Swainston, Reynard Spiess, Sandra Taylor, Paul Mulherin, Steven Parker, William Rowe, Nicholas E. Matthews, Kirk J. Malone, Rosalind Le Feuvre, Philip Shapira, Perdita Barran, Nicholas J. Turner, Jason Micklefield, Rainer Breitling, Eriko Takano, Nigel S. Scrutton
Opublikowane w: Metabolic Engineering, Numer 60, 2020, Strona(/y) 168-182, ISSN 1096-7176
Wydawca: Academic Press
DOI: 10.1016/j.ymben.2020.04.008

Metabolic engineering of Saccharomyces cerevisiae for the de novo production of psilocybin and related tryptamine derivatives

Autorzy: N. Milne, P. Thomsen, N. Mølgaard Knudsen, P. Rubaszka, M. Kristensen, I. Borodina
Opublikowane w: Metabolic Engineering, Numer 60, 2020, Strona(/y) 25-36, ISSN 1096-7176
Wydawca: Academic Press
DOI: 10.1016/j.ymben.2019.12.007

Metabolic engineering and transcriptomic analysis of Saccharomyces cerevisiae producing p-coumaric acid from xylose

Autorzy: Gheorghe M. Borja, Angelica Rodriguez, Kate Campbell, Irina Borodina, Yun Chen, Jens Nielsen
Opublikowane w: Microbial Cell Factories, Numer 18/1, 2019, ISSN 1475-2859
Wydawca: BioMed Central
DOI: 10.1186/s12934-019-1244-4

CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models

Autorzy: Vítor Vieira, Miguel Rocha
Opublikowane w: Bioinformatics, Numer 35/24, 2019, Strona(/y) 5361-5362, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btz598

Pathways to cellular supremacy in biocomputing

Autorzy: Lewis Grozinger, Martyn Amos, Thomas E. Gorochowski, Pablo Carbonell, Diego A. Oyarzún, Ruud Stoof, Harold Fellermann, Paolo Zuliani, Huseyin Tas, Angel Goñi-Moreno
Opublikowane w: Nature Communications, Numer 10/1, 2019, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-019-13232-z

Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships

Autorzy: Francesco Del Carratore, Kamila Schmidt, Maria Vinaixa, Katherine A. Hollywood, Caitlin Greenland-Bews, Eriko Takano, Simon Rogers, Rainer Breitling
Opublikowane w: Analytical Chemistry, Numer 91/20, 2019, Strona(/y) 12799-12807, ISSN 0003-2700
Wydawca: American Chemical Society
DOI: 10.1021/acs.analchem.9b02354

Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries

Autorzy: Andrew Currin, Neil Swainston, Mark S Dunstan, Adrian J Jervis, Paul Mulherin, Christopher J Robinson, Sandra Taylor, Pablo Carbonell, Katherine A Hollywood, Cunyu Yan, Eriko Takano, Nigel S Scrutton, Rainer Breitling
Opublikowane w: Synthetic Biology, 2019, ISSN 2397-7000
Wydawca: Oxford University Press
DOI: 10.1093/synbio/ysz025

Efficient learning in metabolic pathway designs through optimal assembling

Autorzy: Pablo Carbonell, Jean-Loup Faulon, Rainer Breitling
Opublikowane w: IFAC-PapersOnLine, Numer 52/26, 2019, Strona(/y) 7-12, ISSN 2405-8963
Wydawca: Elsevier
DOI: 10.1016/j.ifacol.2019.12.228

The nsp15 Nuclease as a Good Target to Combat SARS-CoV-2: Mechanism of Action and Its Inactivation with FDA-Approved Drugs

Autorzy: Margarida Saramago; Vanessa Costa; Caio Souza; Cátia Bárria; Susana Domingues; Sandra Viegas; Diana Lousa; Cláudio Soares; Cecília Arraiano; Rute Matos
Opublikowane w: Microorganisms, Numer 1, 2022, ISSN 2076-2607
Wydawca: MDPI
DOI: 10.3390/microorganisms10020342

In silico design and automated learning to boost next-generation smart biomanufacturing.

Autorzy: Pablo Carbonell; Pablo Carbonell; Rosalind Le Feuvre; Eriko Takano; Nigel S. Scrutton
Opublikowane w: Synthetic Biology, Numer 5 (1), 2020, Strona(/y) ysaa020, ISSN 2397-7000
Wydawca: Oxford University Press
DOI: 10.1093/synbio/ysaa020

Harnessing the yeast Saccharomyces cerevisiae for the production of fungal secondary metabolites

Autorzy: Guokun Wang; Douglas B. Kell; Irina Borodina
Opublikowane w: Essays in Biochemistry, 2021, ISSN 0071-1365
Wydawca: Portland Press, Ltd.
DOI: 10.1042/ebc20200137

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

Autorzy: Jasmin Hafner, Homa MohammadiPeyhani, Anastasia Sveshnikova, Alan Scheidegger, and Vassily Hatzimanikatis
Opublikowane w: ACS Synthetic Biology, Numer 9 (6), 2020, Strona(/y) 1479-1482, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.0c00052

MEWpy: a computational strain optimization workbench in Python

Autorzy: Vítor Pereira, Fernando Cruz, Miguel Rocha
Opublikowane w: Bioinformatics, Numer 37 (16), 2021, Strona(/y) 2494-2496, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btab013

Expansion of EasyClone-MarkerFree toolkit for Saccharomyces cerevisiae genome with new integration sites

Autorzy: Mahsa Babaei; Luisa Sartori; Alexey Karpukhin; Dmitrii Abashkin; Elena Matrosova; Irina Borodina
Opublikowane w: FEMS Yeast Research, Numer 3, 2021, ISSN 1567-1356
Wydawca: Blackwell
DOI: 10.1093/femsyr/foab027

Conference proceedings (4)

Combining multi-objective evolutionary algorithms with deep generative models towards focused molecular design

Autorzy: Tiago J. C. Sousa; João Correia; Vitor Pereira; Miguel Rocha
Opublikowane w: Applications of Evolutionary Computation, Numer 24th International Conference, EvoApplications 2021, Held as Part of EvoStar 2021, Virtual Event, April 7–9, 2021, Proceedings, 2021, Strona(/y) 81-96, ISBN 978-3-030-72699-7
Wydawca: Springer
DOI: 10.1007/978-3-030-72699-7_6

Variational Autoencoders and Evolutionary Algorithms for Targeted Novel Enzyme Design

Autorzy: Miguel Martins; Miguel Rocha; Vitor Pereira
Opublikowane w: 2022 IEEE Congress on Evolutionary Computation (CEC), Numer 1, 2022, ISBN 9788070439876
Wydawca: IEEE
DOI: 10.1109/cec55065.2022.9870421

Gene variant space for biosensor-based dynamic regulation

Autorzy: Maria Guadalupe Camarena; Yadira Boada; Jesús Picó; Pablo Carbonell
Opublikowane w: Actas de las Jornadas de Automática, Numer yearly, 2021, ISBN 978-84-9749-804-3
Wydawca: CEA-IFAC
DOI: 10.17979/spudc.9788497498043.485

Combining Evolutionary Algorithms with Reaction Rules Towards Focused Molecular Design

Autorzy: João Correia; Vítor Pereira; Miguel Rocha
Opublikowane w: GECCO '23: Proceedings of the Genetic and Evolutionary Computation Conference, Numer 1, 2023
Wydawca: Association for Computing Machinery
DOI: 10.1145/3583131.3590413

Thesis and dissertations (2)

Engineering microbial hosts for the production of aromatic compounds

Autorzy: Saez Saez, Javier (PhD Student)Borodina, Irina (Main Supervisor)Babaei, Mahsa (Supervisor)Ingemann Jensen, Sheila (Supervisor)Morrissey, John (Examiner)Siewers, Verena (Examiner)
Opublikowane w: 2023
Wydawca: DTU

Modeling biochemical reaction networks in complex intracellular environments

Autorzy: Weilandt, Daniel Robert
Opublikowane w: 2020
Wydawca: EPFL
DOI: 10.5075/epfl-thesis-7900

Non-peer reviewed articles (4)

Symbolic Kinetic Models in Python (SKiMpy): Intuitive modeling of large-scale biological kinetic models

Autorzy: Daniel R. Weilandt, Pierre Salvy, Maria Masid, Georgios Fengos, Robin Denhardt-Erikson, Zhaleh Hosseini, Vassily Hatzimanikatis
Opublikowane w: bioRxiv, 2022, ISSN 2692-8205
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.01.17.476618

Developing an enzyme selection tool supporting multiple hosts contexts

Autorzy: María Camarena, Pablo Carbonell
Opublikowane w: bioRxiv, 2021, ISSN 2692-8205
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.09.09.459461

ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds

Autorzy: Anastasia Sveshnikova, Homa MohammadiPeyhani, Vassily Hatzimanikatis
Opublikowane w: bioRxiv, 2021, ISSN 2692-8205
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.12.06.471405

ATLASx: a computational map for the exploration of biochemical space

Autorzy: Homa Mohammadi-Peyhani, Jasmin Hafner, Anastasia Sveshnikova, Victor Viterbo, Vassily Hatzimanikatis
Opublikowane w: bioRxiv, 2021, ISSN 2692-8205
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.02.17.431583

Other (1)

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Autorzy: Subham Choudhury; Bharath Narayanan; Michael Moret; Vassily Hatzimanikatis; Ljubisa Miskovic
Opublikowane w: bioRxiv, Numer 1, 2023
Wydawca: bioRxiv
DOI: 10.1101/2023.02.21.529387

Prawa własności intelektualnej

Patent (2)

YEAST CELLS AND METHODS FOR PRODUCTION OF TRYPTOPHAN DERIVATIVES

Numer wniosku/publikacji: 20 20075823
Data: 2020-09-16
Wnioskodawca/wnioskodawcy: DANMARKS TEKNISKE UNIVERSITET

MICROBIAL PRODUCTION OF TYROSOL AND SALIDROSIDE

Numer wniosku/publikacji: 20 22053036
Data: 2022-02-08
Wnioskodawca/wnioskodawcy: SILICOLIFE LDA