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Synthetic microbial consortia-based platform for flavonoids production using synthetic biology

Deliverables

Press Release 1

A press release will announce the project kick-off and it will be translated into the languages of all consortium members to be distributed to the national press agencies and general media.

Website

A website will be established and regular updates on project milestones, project related news and events will show the progress of the project. The website will also be equipped with a data repository of the most important files and data.

Project flyer

The project flyer will give a short overview of the project's aims and will introduce the consortium. It will be handed out on conferences and can be used to promote the project.

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Publications

A SsrA/NIa-based Strategy for Post-Translational Regulation of Protein Levels in Gram-negative Bacteria

Author(s): Gonzalo Durante-Rodríguez, Belén Calles, Víctor Lorenzo, Pablo Nikel
Published in: BIO-PROTOCOL, 10/14, 2020, ISSN 2331-8325
Publisher: Bio-Protocol
DOI: 10.21769/bioprotoc.3688

Quantitative assessment of morphological traits of planktonic bacterial aggregates

Author(s): Espeso, D.R., Martínez-García, E., de Lorenzo, V.
Published in: Water Research, 2020, ISSN 0043-1354
Publisher: Elsevier BV
DOI: 10.1016/j.watres.2020.116468

Terpenoids and Polyphenols as Natural Antioxidant Agents in Food Preservation

Author(s): Ignacio Gutiérrez-del-Río, Sara López-Ibáñez, Patricia Magadán-Corpas, Luis Fernández-Calleja, Álvaro Pérez-Valero, Mateo Tuñón-Granda, Elisa M. Miguélez, Claudio J. Villar, Felipe Lombó
Published in: Antioxidants, 10/8, 2021, Page(s) 1264, ISSN 2076-3921
Publisher: MDPI
DOI: 10.3390/antiox10081264

Entdeckung neuer bakterieller Chalconisomerasen durch eine Sequenz‐Struktur‐Funktions‐Evolutions‐Strategie für die enzymatische Synthese von ( S )‐Flavanonen

Author(s): Hannes Meinert, Dong Yi, Bastian Zirpel, Eva Schuiten, Torsten Geißler, Egon Gross, Stephan I. Brückner, Beate Hartmann, Carsten Röttger, Jakob P. Ley, Uwe T. Bornscheuer
Published in: Angewandte Chemie, 133/31, 2021, Page(s) 17011-17016, ISSN 0044-8249
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/ange.202107182

Recent advances in model-assisted metabolic engineering

Author(s): Steinn Gudmundsson, Juan Nogales
Published in: Current Opinion in Systems Biology, 2021, Page(s) 100392, ISSN 2452-3100
Publisher: Elsevier
DOI: 10.1016/j.coisb.2021.100392

A portable library of phosphate‐depletion based synthetic promoters for customable and automata control of gene expression in bacteria

Author(s): Jesús Torres‐Bacete, José Luís García, Juan Nogales
Published in: Microbial Biotechnology, 2021, ISSN 1751-7915
Publisher: John Wiley & Sons
DOI: 10.1111/1751-7915.13808

Discovery of Novel Bacterial Chalcone Isomerases by a Sequence‐Structure‐Function‐Evolution Strategy for Enzymatic Synthesis of ( S )‐Flavanones

Author(s): Hannes Meinert, Dong Yi, Bastian Zirpel, Eva Schuiten, Torsten Geißler, Egon Gross, Stephan I. Brückner, Beate Hartmann, Carsten Röttger, Jakob P. Ley, Uwe T. Bornscheuer
Published in: Angewandte Chemie International Edition, 60/31, 2021, Page(s) 16874-16879, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202107182

Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies

Author(s): Espeso D. R., Algar, E., Martínez-García, E., de Lorenzo, V.
Published in: BMC Bioinformatics, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-3490-1

Contextual dependencies expand the re-usability of genetic inverters

Author(s): Huseyin Tas, Lewis Grozinger, Ruud Stoof, Victor de Lorenzo, Ángel Goñi-Moreno
Published in: Nature Communications, 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-20656-5

Environmental Performance of Pseudomonas putida with a Uracylated Genome

Author(s): Elena Algar, Yamal Al‐Ramahi, Víctor Lorenzo, Esteban Martínez‐García
Published in: ChemBioChem, 21/22, 2020, Page(s) 3255-3265, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000330

A Standardized Inverter Package Borne by Broad Host Range Plasmids for Genetic Circuit Design in Gram-Negative Bacteria

Author(s): Huseyin Tas, Ángel Goñi-Moreno, Víctor de Lorenzo
Published in: ACS Synthetic Biology, 10/1, 2021, Page(s) 213-217, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00529

Naked Bacterium: Emerging Properties of a Surfome-Streamlined Pseudomonas putida Strain

Author(s): Esteban Martínez-García, Sofía Fraile, David Rodríguez Espeso, Davide Vecchietti, Giovanni Bertoni, Víctor de Lorenzo
Published in: ACS Synthetic Biology, 9/9, 2020, Page(s) 2477-2492, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00272

Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies

Author(s): Sofía Fraile, María Briones, Mónica Revenga-Parra, Víctor de Lorenzo, Encarnación Lorenzo, Esteban Martínez-García
Published in: ACS Synthetic Biology, 10/8, 2021, Page(s) 2049-2059, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00227

Transcriptional control of 2,4‐dinitrotoluene degradation in Burkholderia sp . R34 bears a regulatory patch that eases pathway evolution

Author(s): Danilo P´érez-Pantoja; Victor De Lorenzo; Pablo Ivan Nikel; Max Chavarría
Published in: Environmental Microbiology, 23, 2021, ISSN 1462-2920
Publisher: John Wiley & Sons
DOI: 10.1111/1462-2920.15472

An updated structural model of the A domain of the Pseudomonas putida   XylR  regulator poses an atypical interplay with aromatic effectors

Author(s): Pavel Dvořák, Carlos Alvarez‐Carreño, Sergio Ciordia, Alberto Paradela, Víctor Lorenzo
Published in: Environmental Microbiology, 23/8, 2021, Page(s) 4418-4433, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15628

Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress

Author(s): Pablo I. Nikel, Tobias Fuhrer, Max Chavarría, Alberto Sánchez-Pascuala, Uwe Sauer, Víctor de Lorenzo
Published in: The ISME Journal, 2021, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/s41396-020-00884-9

Automated design and implementation of a NOR gate in Pseudomonas putida.

Author(s): Huseyin Tas; Lewis Grozinger; Angel Goñi-Moreno; Angel Goñi-Moreno; Víctor de Lorenzo
Published in: Synthetic Biology, 1, 2021, ISSN 2397-7000
Publisher: Oxford University Press
DOI: 10.1093/synbio/ysab024

Biotransformation of d ‐xylose to d ‐xylonate coupled to medium‐chain‐length polyhydroxyalkanoate production in cellobiose‐grown Pseudomonas putida EM42

Author(s): Pavel Dvořák, Jozef Kováč, Víctor Lorenzo
Published in: Microbial Biotechnology, 13/4, 2020, Page(s) 1273-1283, ISSN 1751-7915
Publisher: Society for Applied Microbiology
DOI: 10.1111/1751-7915.13574

In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9

Author(s): Beatriz Álvarez, Mario Mencía, Víctor de Lorenzo, Luis Ángel Fernández
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-20230-z

Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells.

Author(s): Ting, S.Y., Martinez-Garcia, E., Huang, S., Bertolli, S.K., Kelly, K.A., Cutler, K.J., Su, E.D., Zhi, H., Tang, Q., Radey, M.C., Raffatellu, M., Peterson, S.B., de Lorenzo, V. and Mougous, J.D.
Published in: Cell Host & Microbe, 2020, ISSN 1934-6069
Publisher: Elsevier
DOI: 10.1016/j.chom.2020.05.006

Rewiring carbon metabolism in yeast for high level production of aromatic chemicals

Author(s): Quanli Liu, Tao Yu, Xiaowei Li, Yu Chen, Kate Campbell, Jens Nielsen, Yun Chen
Published in: Nature Communications, 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-12961-5

De novo biosynthesis of garbanzol and fustin in Streptomyces albus based on a potential flavanone 3‐hydroxylase with 2‐hydroxylase side activity

Author(s): Laura Marín, Ignacio Gutiérrez‐del‐Río, Claudio Jesús Villar, Felipe Lombó
Published in: Microbial Biotechnology, 2021, ISSN 1751-7915
Publisher: John Wiley & Sons
DOI: 10.1111/1751-7915.13874

An automated DIY framework for experimental evolution of Pseudomonas putida

Author(s): David R. Espeso, Pavel Dvořák, Tomás Aparicio, Víctor Lorenzo
Published in: Microbial Biotechnology, 2020, ISSN 1751-7915
Publisher: John Wiley and Sons Ltd
DOI: 10.1111/1751-7915.13678

Recent trends in biocatalysis

Author(s): Dong Yi, Thomas Bayer, Christoffel P. S. Badenhorst, Shuke Wu, Mark Doerr, Matthias Höhne, Uwe T. Bornscheuer
Published in: Chemical Society Reviews, 50/14, 2021, Page(s) 8003-8049, ISSN 0306-0012
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cs01575j

Surface Display of Designer Protein Scaffolds on Genome-Reduced Strains of Pseudomonas putida

Author(s): Pavel Dvořák, Edward A. Bayer, Víctor de Lorenzo
Published in: ACS Synthetic Biology, 9/10, 2020, Page(s) 2749-2764, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00276

Picking the right metaphors for addressing microbial systems: economic theory helps understanding biological complexity

Author(s): Juhyun Kim; Rafael Silva-Rocha; Víctor de Lorenzo
Published in: International Microbiology, 24, 2021, ISSN 1618-1905
Publisher: Springer-Nature
DOI: 10.1007/s10123-021-00194-w

Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis

Author(s): Cheewin Kittikunapong, Suhui Ye, Patricia Magadán-Corpas, Álvaro Pérez-Valero, Claudio J. Villar, Felipe Lombó, Eduard J. Kerkhoven
Published in: Metabolites, 11/5, 2021, Page(s) 304, ISSN 2218-1989
Publisher: MDPI
DOI: 10.3390/metabo11050304

The faulty SOS response of Pseudomonas putida KT2440 stems from an inefficient RecA‐LexA interplay

Author(s): Özlem Akkaya, Tomás Aparicio, Danilo Pérez‐Pantoja, Víctor Lorenzo
Published in: Environmental Microbiology, 2021, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15384

Antiproliferative and palliative activity of flavonoids in colorectal cancer

Author(s): Javier Fernández, Blanca Silván, Rodrigo Entrialgo-Cadierno, Claudio J. Villar, Raffaele Capasso, José Antonio Uranga, Felipe Lombó, Raquel Abalo
Published in: Biomedicine & Pharmacotherapy, 143, 2021, Page(s) 112241, ISSN 0753-3322
Publisher: Elsevier Masson
DOI: 10.1016/j.biopha.2021.112241

High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Author(s): Juan Nogales, Joshua Mueller, Steinn Gudmundsson, Francisco J. Canalejo, Estrella Duque, Jonathan Monk, Adam M. Feist, Juan Luis Ramos, Wei Niu, Bernhard O. Palsson
Published in: Environmental Microbiology, 22/1, 2019, Page(s) 255-269, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14843

Digitalizing heterologous gene expression in Gram‐negative bacteria with a portable ON/OFF module

Author(s): Belén Calles, Ángel Goñi‐Moreno, Víctor Lorenzo
Published in: Molecular Systems Biology, 15/12, 2019, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20188777

High-Efficiency Multi-site Genomic Editing of Pseudomonas putida through Thermoinducible ssDNA Recombineering

Author(s): Tomas Aparicio, Akos Nyerges, Esteban Martínez-García, Víctor de Lorenzo
Published in: iScience, 23/3, 2020, Page(s) 100946, ISSN 2589-0042
Publisher: Elsevier
DOI: 10.1016/j.isci.2020.100946

Multiple-Site Diversification of Regulatory Sequences Enables Interspecies Operability of Genetic Devices

Author(s): Angeles Hueso-Gil, Ákos Nyerges, Csaba Pál, Belén Calles, Víctor de Lorenzo
Published in: ACS Synthetic Biology, 9/1, 2019, Page(s) 104-114, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.9b00375

Recombination-Independent Genome Editing through CRISPR/Cas9-Enhanced TargeTron Delivery

Author(s): Elena Velázquez, Víctor de Lorenzo, Yamal Al-Ramahi
Published in: ACS Synthetic Biology, 8/9, 2019, Page(s) 2186-2193, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.9b00293

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

Author(s): Esteban Martínez-García, Angel Goñi-Moreno, Bryan Bartley, James McLaughlin, Lucas Sánchez-Sampedro, Héctor Pascual del Pozo, Clara Prieto Hernández, Ada Serena Marletta, Davide De Lucrezia, Guzmán Sánchez-Fernández, Sofía Fraile, Víctor de Lorenzo
Published in: Nucleic Acids Research, 48/D1, 2019, Page(s) D1164-D1170, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1024

Assembly of a Custom-made Device to Study Spreading Patterns of Pseudomonas putida Biofilms

Author(s): David Espeso, Esteban Martínez-García, Víctor Lorenzo
Published in: BIO-PROTOCOL, 9/10, 2019, ISSN 2331-8325
Publisher: Bio-protocol
DOI: 10.21769/bioprotoc.3238

Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene

Author(s): Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, Víctor Lorenzo
Published in: Environmental Microbiology, 22/1, 2019, Page(s) 45-58, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14814

Pseudomonas putida in the quest of programmable chemistry

Author(s): Esteban Martínez-García, Víctor de Lorenzo
Published in: Current Opinion in Biotechnology, 59, 2019, Page(s) 111-121, ISSN 0958-1669
Publisher: Elsevier BV
DOI: 10.1016/j.copbio.2019.03.012

Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida

Author(s): Alberto Sánchez-Pascuala, Lorena Fernández-Cabezón, Víctor de Lorenzo, Pablo I. Nikel
Published in: Metabolic Engineering, 54, 2019, Page(s) 200-211, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1016/j.ymben.2019.04.005

Concomitant prediction of environmental fate and toxicity of chemical compounds

Author(s): Juan Antonio Garcia-Martin, Max Chavarría, Victor de Lorenzo, Florencio Pazos
Published in: Biology Methods and Protocols, 5/1, 2020, ISSN 2396-8923
Publisher: Oxford University Press
DOI: 10.1093/biomethods/bpaa025

The Wsp intermembrane complex mediates metabolic control of the swim‐attach decision of Pseudomonas putida

Author(s): Ángeles Hueso‐Gil, Belén Calles, Víctor Lorenzo
Published in: Environmental Microbiology, 22/8, 2020, Page(s) 3535-3547, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15126

Metabolic modelling approaches for describing and engineering microbial communities

Author(s): Beatriz García-Jiménez, Jesús Torres-Bacete, Juan Nogales
Published in: Computational and Structural Biotechnology Journal, 19, 2021, Page(s) 226-246, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2020.12.003

For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!

Author(s): Víctor de Lorenzo, Natalio Krasnogor, Markus Schmidt
Published in: New Biotechnology, 60, 2021, Page(s) 44-51, ISSN 1871-6784
Publisher: Elsevier BV
DOI: 10.1016/j.nbt.2020.08.004

Subcellular Architecture of the xyl Gene Expression Flow of the TOL Catabolic Plasmid of Pseudomonas putida mt-2

Author(s): Juhyun Kim, Angel Goñi-Moreno, Víctor de Lorenzo
Published in: mBio, 12/1, 2021, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.03685-20

Multifunctional SEVA shuttle vectors for actinomycetes and Gram‐negative bacteria

Author(s): Coral García‐Gutiérrez, Tomás Aparicio, Lucía Torres‐Sánchez, Esteban Martínez‐García, Víctor Lorenzo, Claudio J. Villar, Felipe Lombó
Published in: MicrobiologyOpen, 9/6, 2020, Page(s) 1135-1149, ISSN 2045-8827
Publisher: John Wiley and Sons Inc.
DOI: 10.1002/mbo3.1024

Low CyaA expression and anti‐cooperative binding of cAMP to CRP frames the scope of the cognate regulon of Pseudomonas putida

Author(s): Alejandro Arce‐Rodríguez, Pablo I. Nikel, Belén Calles, Max Chavarría, Raúl Platero, Tino Krell, Victor Lorenzo
Published in: Environmental Microbiology, 2021, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15422

Standardization of inducer-activated broad host range expression modules: debugging and refactoring an alkane-responsive AlkS/PalkB device

Author(s): Alejandro Arce-Rodríguez; Alejandro Arce-Rodríguez; Ilaria Benedetti; José Manuel Borrero-de Acuña; Rafael Silva-Rocha; Rafael Silva-Rocha; Víctor de Lorenzo
Published in: Synthetic Biology, 4, 2021, ISSN 2397-7000
Publisher: Oxfor University Press
DOI: 10.1093/synbio/ysab030

ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic

Author(s): Páez-Espino, A.D., Nikel, P., Chavarría, M., de Lorenzo, V.
Published in: Environmental Microbiology, 2020, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.14991

Repositioning microbial biotechnology against COVID‐19: the case of microbial production of flavonoids

Author(s): Tobias Goris, Álvaro Pérez‐Valero, Igor Martínez, Dong Yi, Luis Fernández‐Calleja, David San León, Uwe T. Bornscheuer, Patricia Magadán‐Corpas, Felipe Lombó, Juan Nogales
Published in: Microbial Biotechnology, 2020, ISSN 1751-7915
Publisher: Society for applied Microbiology
DOI: 10.1111/1751-7915.13675

Multiple-site diversification of regulatory sequences enables inter-species operability of genetic devices

Author(s): Angeles Hueso-Gil; Victor de Lorenzo; Akos Nyerges
Published in: bioRxiv, 2019
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/771782

Surface display of designer protein scaffolds on genome-reduced strains of Pseudomonas putida

Author(s): Pavel Dvořák; Edward A. Bayer; Víctor de Lorenzo
Published in: bioRxiv, 2020
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.05.13.093500

Metabolic Modelling Approaches for Describing and Engineering Microbial Communities

Author(s): Beatriz García-Jiménez , Jesús Torres, Juan Nogales
Published in: 2020
Publisher: Preprints
DOI: 10.20944/preprints202009.0548.v1

A Broad Host Range Plasmid-Based Roadmap for ssDNA-Based Recombineering in Gram-Negative Bacteria.

Author(s): Aparicio T., de Lorenzo V., Martínez-García E.
Published in: Horizontal Gene Transfer, 2019, ISBN 978-1-4939-9877-7
Publisher: Humana, New York
DOI: 10.1007/978-1-4939-9877-7_27