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

Deliverables

Documents, reports (3)

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.

Publications

Peer reviewed articles (49)

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

Other (3)

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

Book chapters (1)

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